Starting phenix.real_space_refine on Fri Feb 6 16:28:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arw_43796/02_2026/9arw_43796.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arw_43796/02_2026/9arw_43796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9arw_43796/02_2026/9arw_43796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arw_43796/02_2026/9arw_43796.map" model { file = "/net/cci-nas-00/data/ceres_data/9arw_43796/02_2026/9arw_43796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arw_43796/02_2026/9arw_43796.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 44 5.16 5 C 9156 2.51 5 N 2466 2.21 5 O 2504 1.98 5 H 11857 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26028 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1370 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 152} Chain breaks: 7 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 532 Unresolved non-hydrogen dihedrals: 344 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'ASN:plan1': 5, 'TYR:plan': 6, 'PHE:plan': 6, 'ASP:plan': 6, 'GLU:plan': 9, 'GLN:plan1': 5, 'ARG:plan': 2, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 200 Chain: "A" Number of atoms: 7658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 7658 Classifications: {'peptide': 592} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 576} Unresolved non-hydrogen bonds: 694 Unresolved non-hydrogen angles: 843 Unresolved non-hydrogen dihedrals: 560 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 38, 'GLN:plan1': 8, 'ASP:plan': 35, 'ASN:plan1': 17, 'ARG:plan': 11, 'PHE:plan': 2, 'TYR:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 433 Chain: "C" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 3309 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 262} Chain breaks: 5 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 3, 'ASN:plan1': 11, 'ASP:plan': 14, 'GLU:plan': 17, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 208 Chain: "D" Number of atoms: 4015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 4015 Classifications: {'peptide': 296} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 283} Chain breaks: 2 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 8, 'ASP:plan': 14, 'GLU:plan': 19, 'ARG:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 159 Chain: "E" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 3821 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain breaks: 2 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 385 Unresolved non-hydrogen dihedrals: 245 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 20, 'ASN:plan1': 9, 'ASP:plan': 12, 'HIS:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 191 Chain: "F" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2041 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1385 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 4, 'ASP:plan': 5, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2428 Classifications: {'peptide': 251} Modifications used: {'NH1NOTPRO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 236} Chain breaks: 7 Unresolved non-hydrogen bonds: 534 Unresolved non-hydrogen angles: 664 Unresolved non-hydrogen dihedrals: 427 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'ARG:plan': 9, 'ASN:plan1': 8, 'TYR:plan': 5, 'PHE:plan': 2, 'HIS:plan': 2, 'ASP:plan': 15, 'GLU:plan': 16, 'GLN:plan1': 8} Unresolved non-hydrogen planarities: 267 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3514 SG CYS A 166 61.489 48.682 39.992 1.00 64.39 S ATOM 3538 SG CYS A 169 59.144 51.472 38.888 1.00 64.80 S ATOM 4051 SG CYS A 222 61.750 49.070 36.872 1.00 61.29 S ATOM 4084 SG CYS A 225 62.717 52.342 38.683 1.00 60.09 S Time building chain proxies: 5.19, per 1000 atoms: 0.20 Number of scatterers: 26028 At special positions: 0 Unit cell: (100.57, 108.48, 162.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 44 16.00 O 2504 8.00 N 2466 7.00 C 9156 6.00 H 11857 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 762.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 166 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 222 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 169 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 225 " Number of angles added : 6 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4006 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 21 sheets defined 43.0% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'H' and resid 141 through 160 removed outlier: 4.060A pdb=" N ILE H 145 " --> pdb=" O ASN H 141 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER H 149 " --> pdb=" O ILE H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 218 Processing helix chain 'H' and resid 224 through 229 removed outlier: 3.556A pdb=" N LYS H 228 " --> pdb=" O LYS H 225 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASP H 229 " --> pdb=" O ALA H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 235 Processing helix chain 'H' and resid 349 through 359 Processing helix chain 'A' and resid 14 through 20 removed outlier: 3.634A pdb=" N ILE A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 49 Processing helix chain 'A' and resid 74 through 104 removed outlier: 4.357A pdb=" N GLN A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ALA A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 149 removed outlier: 3.687A pdb=" N LYS A 149 " --> pdb=" O MET A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.797A pdb=" N LYS A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 222 through 228 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.616A pdb=" N ALA A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.521A pdb=" N GLU A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.563A pdb=" N ALA A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 removed outlier: 4.191A pdb=" N ASP A 290 " --> pdb=" O ASN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 313 Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 343 through 366 removed outlier: 3.675A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 434 through 450 removed outlier: 3.733A pdb=" N VAL A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 497 removed outlier: 3.523A pdb=" N LEU A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 514 removed outlier: 3.999A pdb=" N LYS A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 540 removed outlier: 3.764A pdb=" N ILE A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 563 removed outlier: 4.085A pdb=" N ALA A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 570 Processing helix chain 'A' and resid 574 through 591 Processing helix chain 'C' and resid 43 through 58 removed outlier: 3.804A pdb=" N GLY C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 81 removed outlier: 3.768A pdb=" N PHE C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 131 removed outlier: 4.037A pdb=" N LEU C 130 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 189 removed outlier: 3.815A pdb=" N PHE C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 203 removed outlier: 3.608A pdb=" N LYS C 203 " --> pdb=" O LYS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.537A pdb=" N ARG C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP C 216 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 293 Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'D' and resid 43 through 58 removed outlier: 3.547A pdb=" N ALA D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 82 Processing helix chain 'D' and resid 117 through 131 removed outlier: 3.711A pdb=" N LEU D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N CYS D 131 " --> pdb=" O ASP D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 188 Processing helix chain 'D' and resid 196 through 203 removed outlier: 3.719A pdb=" N LYS D 203 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 220 removed outlier: 4.205A pdb=" N VAL D 218 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 220 " --> pdb=" O ASP D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 275 removed outlier: 4.352A pdb=" N GLY D 272 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D 274 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS D 275 " --> pdb=" O GLY D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 291 Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.629A pdb=" N ILE D 305 " --> pdb=" O ASN D 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 57 Processing helix chain 'E' and resid 73 through 81 removed outlier: 3.678A pdb=" N ILE E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER E 78 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU E 79 " --> pdb=" O SER E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 131 removed outlier: 3.887A pdb=" N LEU E 130 " --> pdb=" O SER E 126 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N CYS E 131 " --> pdb=" O ASP E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 189 removed outlier: 3.610A pdb=" N GLU E 186 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE E 189 " --> pdb=" O SER E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 199 removed outlier: 3.922A pdb=" N TRP E 198 " --> pdb=" O ILE E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 221 removed outlier: 3.558A pdb=" N ASP E 216 " --> pdb=" O ASP E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 275 removed outlier: 3.736A pdb=" N PHE E 274 " --> pdb=" O LYS E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 292 removed outlier: 3.662A pdb=" N MET E 284 " --> pdb=" O ASN E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'F' and resid 7 through 12 removed outlier: 3.854A pdb=" N ILE F 12 " --> pdb=" O ILE F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 30 removed outlier: 3.805A pdb=" N ALA F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 41 removed outlier: 3.793A pdb=" N LYS F 41 " --> pdb=" O LYS F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 51 through 62 Processing helix chain 'F' and resid 71 through 88 removed outlier: 3.580A pdb=" N LYS F 75 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU F 85 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 98 removed outlier: 3.541A pdb=" N LEU F 97 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN F 98 " --> pdb=" O TYR F 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 93 through 98' Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 110 through 136 removed outlier: 3.890A pdb=" N TRP F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG F 130 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 134 " --> pdb=" O ARG F 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 28 removed outlier: 3.622A pdb=" N ALA G 17 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA G 18 " --> pdb=" O ARG G 14 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE G 19 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY G 27 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 49 removed outlier: 3.579A pdb=" N LYS G 37 " --> pdb=" O SER G 33 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 3.507A pdb=" N THR G 49 " --> pdb=" O MET G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 62 Processing helix chain 'G' and resid 71 through 87 removed outlier: 4.221A pdb=" N GLU G 79 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU G 85 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN G 87 " --> pdb=" O GLU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 107 removed outlier: 3.527A pdb=" N VAL G 107 " --> pdb=" O VAL G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 136 removed outlier: 3.666A pdb=" N PHE G 125 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.745A pdb=" N ILE B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 145 through 152 removed outlier: 3.641A pdb=" N TYR B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 335 removed outlier: 3.721A pdb=" N LEU B 335 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 350 removed outlier: 3.518A pdb=" N GLN B 349 " --> pdb=" O GLN B 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 53 removed outlier: 3.801A pdb=" N GLU A 52 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 69 " --> pdb=" O PHE A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 179 removed outlier: 3.614A pdb=" N TYR A 177 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 202 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 371 through 375 removed outlier: 7.092A pdb=" N LEU A 382 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 423 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ALA A 458 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N HIS A 430 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 463 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 471 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 206 through 207 removed outlier: 8.506A pdb=" N VAL C 207 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TRP C 114 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL C 253 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 63 removed outlier: 3.524A pdb=" N ILE C 69 " --> pdb=" O ILE C 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AA7, first strand: chain 'C' and resid 157 through 158 Processing sheet with id=AA8, first strand: chain 'D' and resid 41 through 42 removed outlier: 6.780A pdb=" N VAL D 253 " --> pdb=" O LEU D 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 253 through 260 current: chain 'D' and resid 206 through 208 Processing sheet with id=AA9, first strand: chain 'D' and resid 93 through 95 removed outlier: 6.780A pdb=" N VAL D 253 " --> pdb=" O LEU D 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 98 through 106 current: chain 'D' and resid 309 through 314 Processing sheet with id=AB1, first strand: chain 'D' and resid 61 through 64 removed outlier: 3.738A pdb=" N LEU D 67 " --> pdb=" O VAL D 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 157 through 158 Processing sheet with id=AB3, first strand: chain 'D' and resid 223 through 226 Processing sheet with id=AB4, first strand: chain 'E' and resid 41 through 42 removed outlier: 6.985A pdb=" N VAL E 253 " --> pdb=" O LEU E 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 253 through 260 current: chain 'E' and resid 206 through 208 Processing sheet with id=AB5, first strand: chain 'E' and resid 93 through 95 removed outlier: 6.985A pdb=" N VAL E 253 " --> pdb=" O LEU E 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 98 through 106 current: chain 'E' and resid 310 through 314 Processing sheet with id=AB6, first strand: chain 'E' and resid 61 through 64 Processing sheet with id=AB7, first strand: chain 'E' and resid 157 through 158 Processing sheet with id=AB8, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AB9, first strand: chain 'B' and resid 106 through 107 Processing sheet with id=AC1, first strand: chain 'B' and resid 109 through 111 removed outlier: 3.653A pdb=" N MET B 109 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 111 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 124 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 275 through 277 removed outlier: 3.567A pdb=" N GLY B 276 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR B 287 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 319 " --> pdb=" O THR B 287 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 294 through 296 634 hydrogen bonds defined for protein. 1794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.83 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11841 1.03 - 1.23: 30 1.23 - 1.42: 5959 1.42 - 1.62: 8390 1.62 - 1.81: 68 Bond restraints: 26288 Sorted by residual: bond pdb=" N MET D 1 " pdb=" H1 MET D 1 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" N MET B 1 " pdb=" H1 MET B 1 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" CA PRO H 202 " pdb=" C PRO H 202 " ideal model delta sigma weight residual 1.518 1.487 0.031 1.37e-02 5.33e+03 5.25e+00 bond pdb=" N ILE H 201 " pdb=" CA ILE H 201 " ideal model delta sigma weight residual 1.461 1.487 -0.026 1.23e-02 6.61e+03 4.37e+00 bond pdb=" CA TYR H 200 " pdb=" C TYR H 200 " ideal model delta sigma weight residual 1.526 1.497 0.029 1.42e-02 4.96e+03 4.22e+00 ... (remaining 26283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.41: 46949 7.41 - 14.82: 1 14.82 - 22.23: 0 22.23 - 29.63: 1 29.63 - 37.04: 20 Bond angle restraints: 46971 Sorted by residual: angle pdb=" CB GLU D 161 " pdb=" CA GLU D 161 " pdb=" HA GLU D 161 " ideal model delta sigma weight residual 109.00 71.96 37.04 3.00e+00 1.11e-01 1.52e+02 angle pdb=" N CYS A 166 " pdb=" CA CYS A 166 " pdb=" HA CYS A 166 " ideal model delta sigma weight residual 110.00 73.84 36.16 3.00e+00 1.11e-01 1.45e+02 angle pdb=" CB GLU F 88 " pdb=" CA GLU F 88 " pdb=" HA GLU F 88 " ideal model delta sigma weight residual 109.00 73.05 35.95 3.00e+00 1.11e-01 1.44e+02 angle pdb=" C CYS A 166 " pdb=" CA CYS A 166 " pdb=" HA CYS A 166 " ideal model delta sigma weight residual 109.00 73.83 35.17 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C ALA C 279 " pdb=" CA ALA C 279 " pdb=" HA ALA C 279 " ideal model delta sigma weight residual 109.00 73.84 35.16 3.00e+00 1.11e-01 1.37e+02 ... (remaining 46966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 11806 17.81 - 35.61: 804 35.61 - 53.41: 267 53.41 - 71.22: 86 71.22 - 89.02: 14 Dihedral angle restraints: 12977 sinusoidal: 5897 harmonic: 7080 Sorted by residual: dihedral pdb=" C ILE H 201 " pdb=" N ILE H 201 " pdb=" CA ILE H 201 " pdb=" CB ILE H 201 " ideal model delta harmonic sigma weight residual -122.00 -139.80 17.80 0 2.50e+00 1.60e-01 5.07e+01 dihedral pdb=" N ILE H 201 " pdb=" C ILE H 201 " pdb=" CA ILE H 201 " pdb=" CB ILE H 201 " ideal model delta harmonic sigma weight residual 123.40 138.61 -15.21 0 2.50e+00 1.60e-01 3.70e+01 dihedral pdb=" C GLU F 88 " pdb=" N GLU F 88 " pdb=" CA GLU F 88 " pdb=" CB GLU F 88 " ideal model delta harmonic sigma weight residual -122.60 -133.27 10.67 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 12974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2313 0.107 - 0.213: 78 0.213 - 0.320: 0 0.320 - 0.427: 5 0.427 - 0.533: 2 Chirality restraints: 2398 Sorted by residual: chirality pdb=" CA ILE H 201 " pdb=" N ILE H 201 " pdb=" C ILE H 201 " pdb=" CB ILE H 201 " both_signs ideal model delta sigma weight residual False 2.43 1.90 0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" CA GLU F 88 " pdb=" N GLU F 88 " pdb=" C GLU F 88 " pdb=" CB GLU F 88 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CA GLU A 131 " pdb=" N GLU A 131 " pdb=" C GLU A 131 " pdb=" CB GLU A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 2395 not shown) Planarity restraints: 4568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE H 111 " 0.067 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO H 112 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO H 112 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO H 112 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 43 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO G 44 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO G 44 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 44 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 6 " -0.156 9.50e-02 1.11e+02 5.21e-02 3.22e+00 pdb=" NE ARG E 6 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG E 6 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG E 6 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 6 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG E 6 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG E 6 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG E 6 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 6 " -0.000 2.00e-02 2.50e+03 ... (remaining 4565 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 989 2.18 - 2.78: 46315 2.78 - 3.39: 62547 3.39 - 3.99: 78323 3.99 - 4.60: 122444 Nonbonded interactions: 310618 Sorted by model distance: nonbonded pdb=" H THR H 260 " pdb=" HA THR H 260 " model vdw 1.569 1.816 nonbonded pdb=" H CYS A 166 " pdb=" HA CYS A 166 " model vdw 1.582 1.816 nonbonded pdb=" O GLU D 287 " pdb=" HG1 THR D 291 " model vdw 1.620 2.450 nonbonded pdb=" O PRO B 89 " pdb=" HH TYR B 253 " model vdw 1.625 2.450 nonbonded pdb=" OD1 ASP A 547 " pdb=" H ALA A 550 " model vdw 1.630 2.450 ... (remaining 310613 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 5 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 15 through 17 \ or (resid 18 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 19 or (resid 20 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 21 through 53 or (resid 54 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 55 \ through 77 or (resid 78 through 79 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 80 through 83 or resid 91 through 107 \ or (resid 108 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 109 through 110 or (resid 111 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 112 through 121 or (re \ sid 122 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 123 through 150 or (resid 151 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 152 through 155 or (resid 15 \ 6 through 157 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 158 through 159 or (resid 160 through 162 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 163 throug \ h 165 or (resid 166 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 167 through 168 or (resid 169 through 174 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 175 \ through 177 or (resid 178 through 179 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 180 through 184 or (resid 185 throu \ gh 188 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 189 through 196 or (resid 197 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 198 or (resid 199 through 200 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 201 through 204 or (resid 205 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 206 through 210 or (resid 211 throu \ gh 213 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 214 through 245 or (resid 246 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 247 through 297 or (resid 298 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 299 through 306 or (resid 307 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 308 through 310 or (resid 311 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 312 or (resid 313 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 314 through 315)) selection = (chain 'D' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 7 through 8 or (resid 9 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 10 thr \ ough 12 or (resid 13 through 14 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 15 through 33 or (resid 34 through 35 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 36 through 40 or (resid 41 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 42 or (resid 43 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 44 or (resid 45 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 46 through 47 or (resid 48 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 49 through 51 or (resid 52 through 54 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 55 through 61 or (resid 62 through 63 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or (resid 64 and (name N or name CA or na \ me C or name O or name CB or name CG1 or name CG2 or name H or name HA )) or res \ id 65 or (resid 66 through 79 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 80 or (resid 81 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 82 through 83 or res \ id 91 through 92 or (resid 93 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or (resid 96 through 97 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 98 or (resid 99 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 100 through 121 or (resid 122 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 123 through 125 or (resid 126 through 127 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 128 through 130 or (resid 131 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 132 through 133 or (resid 134 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 135 through 140 or (resid 141 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 142 or (resid 143 through 144 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 145 \ through 147 or (resid 148 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 149 through 150 or (resid 151 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 152 throug \ h 155 or (resid 156 through 157 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 158 through 159 or (resid 160 through 162 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 163 through 168 or (resid 169 through 174 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 175 through 176 or (res \ id 177 through 179 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 180 through 181 or (resid 182 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 183 through 184 o \ r (resid 185 through 188 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 189 through 190 or (resid 196 through 197 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 198 or (resid 199 through 200 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 201 through 202 or (resid 203 through 205 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 206 through 208 or (resid 209 through 213 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 214 or (resid 215 throug \ h 216 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 217 through 220 or (resid 221 through 227 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 242 through 243 or \ (resid 244 through 246 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 247 through 250 or (resid 251 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 252 through \ 258 or (resid 259 through 261 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 272 or (resid 273 through 278 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 279 or \ (resid 280 through 283 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or (resid 284 and (name N or name CA or name C or name O o \ r name CB or name CG or name SD or name CE or name H or name HA )) or (resid 285 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 286 through 289 or (resid 290 through 291 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 292 through 295 or (res \ id 296 through 298 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 299 through 305 or (resid 306 and (name N or name CA o \ r name C or name O or name H )) or (resid 307 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 308 through 310 or (resid 3 \ 11 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 312 through 315)) selection = (chain 'E' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 7 through 8 or (resid 9 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 10 thr \ ough 27 or (resid 28 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 29 through 33 or (resid 34 through 35 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 36 thro \ ugh 40 or (resid 41 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 42 through 44 or (resid 45 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 46 through 47 or (r \ esid 48 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 49 through 51 or (resid 52 through 54 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 55 or (resid 56 thro \ ugh 57 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 58 or (resid 59 through 63 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or (resid 64 and (name N or name CA or na \ me C or name O or name CB or name CG1 or name CG2 or name H or name HA )) or res \ id 65 through 67 or (resid 68 through 79 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 80 or (resid 81 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 82 throug \ h 83 or resid 91 through 92 or (resid 93 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or (resid 96 through 97 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 98 or (res \ id 99 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 100 through 107 or (resid 108 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 109 through 125 or (resid 126 \ through 127 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 128 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 132 through 133 or (resi \ d 134 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 135 through 137 or (resid 138 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 139 through 153 or (resid 154 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 155 through 175 or (resid 176 through 179 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 180 through 190 or resid \ 196 through 208 or (resid 209 through 213 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 214 or (resid 215 through 216 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 217 through 220 or (resid 221 through 227 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 242 through 258 or (resi \ d 259 through 261 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 272 through 273 or (resid 274 through 278 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 279 th \ rough 283 or (resid 284 and (name N or name CA or name C or name O or name CB or \ name CG or name SD or name CE or name H or name HA )) or (resid 285 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 286 \ through 289 or (resid 290 through 291 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 292 through 295 or (resid 296 throu \ gh 298 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 299 through 303 or (resid 304 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 305 or (resid 306 and (name N \ or name CA or name C or name O or name H )) or resid 307 through 312 or (resid \ 313 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 314 or (resid 315 and (name N or name CA or name C or name O or name \ CB or name OXT or name H or name HA )))) } ncs_group { reference = (chain 'F' and (resid 9 or (resid 10 through 11 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 12 or (resid 13 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 14 \ through 21 or (resid 22 through 23 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 24 through 29 or (resid 30 through 35 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 36 through 39 or (resid 40 through 43 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 44 through 45 or (resid 46 \ through 49 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 54 or (resid 55 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 56 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 61 or \ (resid 62 through 64 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 65 through 69 or (resid 70 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 71 through 74 or \ (resid 75 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 76 through 78 or (resid 79 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 80 or (resid 81 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 82 or \ (resid 83 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 84 through 85 or (resid 86 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 87 through 91 or (resid 92 th \ rough 95 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 96 or (resid 97 through 104 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 105 or (resid 106 through 113 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 114 through 117 or (resid 118 through 119 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 120 through 121 or (res \ id 122 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 123 through 128 or (resid 129 through 130 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 131 through 132 o \ r (resid 133 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 134 or (resid 135 through 136 and (name N or name CA or name \ C or name O or name CB or name H or name HA )))) selection = (chain 'G' and (resid 9 through 32 or (resid 33 through 35 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 36 through 136 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.190 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14435 Z= 0.122 Angle : 0.562 23.806 19738 Z= 0.286 Chirality : 0.046 0.533 2398 Planarity : 0.005 0.103 2552 Dihedral : 14.045 87.920 4415 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 19.59 % Favored : 80.41 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.19), residues: 2066 helix: 0.91 (0.19), residues: 773 sheet: -1.31 (0.33), residues: 249 loop : -1.59 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 35 TYR 0.013 0.001 TYR E 163 PHE 0.018 0.001 PHE A 37 TRP 0.004 0.001 TRP E 198 HIS 0.003 0.001 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00266 (14431) covalent geometry : angle 0.51832 (19732) hydrogen bonds : bond 0.22522 ( 628) hydrogen bonds : angle 7.24811 ( 1794) metal coordination : bond 0.00675 ( 4) metal coordination : angle 12.51883 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue TYR 93 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue ILE 101 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue TYR 113 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue TYR 140 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue ILE 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue ILE 198 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue MET 315 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue ILE 350 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue MET 47 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue ILE 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue MET 179 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LEU 194 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 267 is missing expected H atoms. Skipping. Residue ILE 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue SER 271 is missing expected H atoms. Skipping. Residue TYR 274 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue TYR 312 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue SER 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue LYS 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue LYS 544 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue THR 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue ILE 297 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue VAL 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue VAL 103 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue SER 226 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue ILE 332 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 340 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 332 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7871 (ttmm) REVERT: C 37 THR cc_start: 0.6935 (m) cc_final: 0.6504 (m) REVERT: C 135 LEU cc_start: 0.7225 (mp) cc_final: 0.6994 (mp) REVERT: C 137 PHE cc_start: 0.6696 (p90) cc_final: 0.5962 (p90) REVERT: C 211 ASP cc_start: 0.5767 (t0) cc_final: 0.5564 (t0) REVERT: E 6 ARG cc_start: 0.6711 (mtp85) cc_final: 0.6481 (mtp85) REVERT: E 42 ILE cc_start: 0.7181 (mt) cc_final: 0.6899 (mm) REVERT: E 202 ILE cc_start: 0.6132 (tp) cc_final: 0.5338 (tt) REVERT: B 318 TYR cc_start: 0.6526 (m-80) cc_final: 0.6037 (m-80) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2854 time to fit residues: 130.8702 Evaluate side-chains 255 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 497 ASN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089723 restraints weight = 75120.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.092219 restraints weight = 34291.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.093799 restraints weight = 19177.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.094671 restraints weight = 12477.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.095421 restraints weight = 9404.128| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 14435 Z= 0.308 Angle : 0.821 15.963 19738 Z= 0.443 Chirality : 0.054 0.417 2398 Planarity : 0.006 0.079 2552 Dihedral : 5.500 21.552 2202 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.24 % Favored : 90.66 % Rotamer: Outliers : 4.11 % Allowed : 19.78 % Favored : 76.10 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.17), residues: 2066 helix: -0.12 (0.17), residues: 801 sheet: -1.44 (0.33), residues: 222 loop : -2.20 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 499 TYR 0.035 0.003 TYR G 39 PHE 0.048 0.003 PHE H 232 TRP 0.029 0.003 TRP G 84 HIS 0.010 0.002 HIS D 36 Details of bonding type rmsd covalent geometry : bond 0.00683 (14431) covalent geometry : angle 0.79937 (19732) hydrogen bonds : bond 0.06034 ( 628) hydrogen bonds : angle 5.47084 ( 1794) metal coordination : bond 0.01861 ( 4) metal coordination : angle 10.71425 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue TYR 93 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue ILE 101 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue TYR 113 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue TYR 140 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue ILE 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue ILE 198 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue MET 315 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue ILE 350 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue MET 47 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue ILE 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue MET 179 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LEU 194 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 267 is missing expected H atoms. Skipping. Residue ILE 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue SER 271 is missing expected H atoms. Skipping. Residue TYR 274 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue TYR 312 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue SER 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue LYS 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue LYS 544 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue THR 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue ILE 297 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue VAL 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue VAL 103 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue SER 226 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue ILE 332 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 340 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 321 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 279 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.8295 (ttmt) cc_final: 0.8084 (ttmm) REVERT: A 323 MET cc_start: 0.8321 (tmm) cc_final: 0.7852 (tmt) REVERT: A 446 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8139 (tm-30) REVERT: A 532 ILE cc_start: 0.8276 (mm) cc_final: 0.7877 (mt) REVERT: A 563 GLN cc_start: 0.8165 (mt0) cc_final: 0.7908 (mt0) REVERT: C 137 PHE cc_start: 0.7157 (p90) cc_final: 0.6785 (p90) REVERT: D 93 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6963 (tp) REVERT: E 34 GLU cc_start: 0.7378 (tt0) cc_final: 0.7163 (tt0) REVERT: E 97 ASP cc_start: 0.7872 (p0) cc_final: 0.7643 (p0) REVERT: E 227 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7346 (ptp-170) REVERT: F 108 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7363 (mm-30) outliers start: 42 outliers final: 21 residues processed: 307 average time/residue: 0.2604 time to fit residues: 113.1697 Evaluate side-chains 262 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain G residue 58 PHE Chi-restraints excluded: chain G residue 77 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 150 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 133 optimal weight: 0.0470 chunk 3 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN C 119 GLN D 32 GLN E 17 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.100436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.089811 restraints weight = 74207.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.092396 restraints weight = 33285.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.093944 restraints weight = 18264.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.094959 restraints weight = 11882.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095628 restraints weight = 8694.981| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14435 Z= 0.127 Angle : 0.565 21.919 19738 Z= 0.283 Chirality : 0.046 0.411 2398 Planarity : 0.004 0.054 2552 Dihedral : 4.378 18.435 2202 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.06 % Allowed : 21.06 % Favored : 76.89 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.18), residues: 2066 helix: 0.88 (0.19), residues: 821 sheet: -1.26 (0.32), residues: 235 loop : -1.91 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 227 TYR 0.018 0.001 TYR G 39 PHE 0.023 0.001 PHE H 232 TRP 0.013 0.001 TRP G 84 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00286 (14431) covalent geometry : angle 0.52672 (19732) hydrogen bonds : bond 0.04591 ( 628) hydrogen bonds : angle 4.63473 ( 1794) metal coordination : bond 0.00994 ( 4) metal coordination : angle 11.79763 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue TYR 93 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue ILE 101 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue TYR 113 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue TYR 140 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue ILE 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue ILE 198 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue MET 315 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue ILE 350 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue MET 47 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue ILE 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue MET 179 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LEU 194 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 267 is missing expected H atoms. Skipping. Residue ILE 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue SER 271 is missing expected H atoms. Skipping. Residue TYR 274 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue TYR 312 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue SER 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue LYS 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue LYS 544 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue THR 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue ILE 297 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue VAL 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue VAL 103 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue SER 226 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue ILE 332 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 340 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 PHE cc_start: 0.7859 (t80) cc_final: 0.7626 (t80) REVERT: A 149 LYS cc_start: 0.8307 (ttmt) cc_final: 0.8087 (ttmm) REVERT: A 172 ARG cc_start: 0.7641 (mtt90) cc_final: 0.7340 (mtt90) REVERT: D 31 ILE cc_start: 0.8489 (pt) cc_final: 0.8261 (pt) REVERT: D 35 ARG cc_start: 0.8078 (tpp-160) cc_final: 0.7723 (tpt90) REVERT: D 93 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6935 (tp) REVERT: F 108 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7335 (mm-30) outliers start: 21 outliers final: 16 residues processed: 261 average time/residue: 0.2646 time to fit residues: 97.4353 Evaluate side-chains 255 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 238 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 1 optimal weight: 0.0670 chunk 181 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.099169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.088355 restraints weight = 74850.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.090948 restraints weight = 34002.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.092539 restraints weight = 18967.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.093544 restraints weight = 12410.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.094195 restraints weight = 9130.600| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.7199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14435 Z= 0.162 Angle : 0.561 20.808 19738 Z= 0.286 Chirality : 0.046 0.412 2398 Planarity : 0.004 0.044 2552 Dihedral : 3.995 17.986 2202 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.25 % Allowed : 19.69 % Favored : 78.06 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.19), residues: 2066 helix: 1.37 (0.19), residues: 824 sheet: -1.23 (0.33), residues: 242 loop : -1.81 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 95 TYR 0.029 0.002 TYR G 39 PHE 0.034 0.002 PHE H 232 TRP 0.007 0.001 TRP A 441 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00370 (14431) covalent geometry : angle 0.52900 (19732) hydrogen bonds : bond 0.04044 ( 628) hydrogen bonds : angle 4.29658 ( 1794) metal coordination : bond 0.01042 ( 4) metal coordination : angle 10.72054 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue TYR 93 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue ILE 101 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue TYR 113 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue TYR 140 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue ILE 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue ILE 198 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue MET 315 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue ILE 350 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue MET 47 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue ILE 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue MET 179 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LEU 194 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 267 is missing expected H atoms. Skipping. Residue ILE 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue SER 271 is missing expected H atoms. Skipping. Residue TYR 274 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue TYR 312 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue SER 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue LYS 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue LYS 544 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue THR 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue ILE 297 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue VAL 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue VAL 103 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue SER 226 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue ILE 332 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 340 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8434 (t80) cc_final: 0.8216 (t80) REVERT: A 446 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8011 (tm-30) REVERT: D 35 ARG cc_start: 0.8276 (tpp-160) cc_final: 0.7959 (tpt90) REVERT: D 69 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7655 (pt) REVERT: D 93 LEU cc_start: 0.7461 (tp) cc_final: 0.7218 (tp) REVERT: E 52 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7460 (ttt-90) REVERT: E 57 GLU cc_start: 0.6518 (mt-10) cc_final: 0.6255 (mt-10) REVERT: F 77 ILE cc_start: 0.8645 (mm) cc_final: 0.8411 (mt) REVERT: F 79 GLU cc_start: 0.7322 (tm-30) cc_final: 0.7086 (tm-30) outliers start: 23 outliers final: 18 residues processed: 254 average time/residue: 0.2569 time to fit residues: 92.6375 Evaluate side-chains 247 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 158 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 152 optimal weight: 0.1980 chunk 193 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.088706 restraints weight = 74741.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.091320 restraints weight = 33732.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.092930 restraints weight = 18757.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.093942 restraints weight = 12243.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.094499 restraints weight = 8996.122| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.7450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14435 Z= 0.112 Angle : 0.512 18.582 19738 Z= 0.258 Chirality : 0.045 0.413 2398 Planarity : 0.004 0.042 2552 Dihedral : 3.862 17.992 2202 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.96 % Allowed : 20.37 % Favored : 77.67 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.19), residues: 2066 helix: 1.57 (0.19), residues: 823 sheet: -1.11 (0.33), residues: 246 loop : -1.73 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 95 TYR 0.020 0.001 TYR G 39 PHE 0.015 0.001 PHE E 288 TRP 0.005 0.001 TRP C 114 HIS 0.002 0.001 HIS E 17 Details of bonding type rmsd covalent geometry : bond 0.00259 (14431) covalent geometry : angle 0.48196 (19732) hydrogen bonds : bond 0.03785 ( 628) hydrogen bonds : angle 4.14801 ( 1794) metal coordination : bond 0.00923 ( 4) metal coordination : angle 9.91128 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue TYR 93 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue ILE 101 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue TYR 113 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue TYR 140 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue ILE 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue ILE 198 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue MET 315 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue ILE 350 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue MET 47 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue ILE 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue MET 179 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LEU 194 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 267 is missing expected H atoms. Skipping. Residue ILE 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue SER 271 is missing expected H atoms. Skipping. Residue TYR 274 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue TYR 312 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue SER 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue LYS 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue LYS 544 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue THR 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue ILE 297 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue VAL 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue VAL 103 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue SER 226 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue ILE 332 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 340 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8407 (t80) cc_final: 0.8192 (t80) REVERT: A 499 ARG cc_start: 0.8438 (ptm-80) cc_final: 0.8096 (mtm180) REVERT: D 93 LEU cc_start: 0.7463 (tp) cc_final: 0.7246 (tp) REVERT: E 52 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7550 (ttt-90) REVERT: E 57 GLU cc_start: 0.6344 (mt-10) cc_final: 0.5965 (mt-10) REVERT: F 77 ILE cc_start: 0.8670 (mm) cc_final: 0.8463 (mt) outliers start: 20 outliers final: 19 residues processed: 247 average time/residue: 0.2672 time to fit residues: 93.8310 Evaluate side-chains 248 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 176 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 56 optimal weight: 0.0030 chunk 7 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.097116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.085967 restraints weight = 76804.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.088727 restraints weight = 34015.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090424 restraints weight = 18573.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.091489 restraints weight = 11907.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.092188 restraints weight = 8650.443| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.7871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14435 Z= 0.124 Angle : 0.531 24.494 19738 Z= 0.261 Chirality : 0.045 0.414 2398 Planarity : 0.004 0.040 2552 Dihedral : 3.763 17.894 2202 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.25 % Allowed : 20.57 % Favored : 77.18 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.19), residues: 2066 helix: 1.64 (0.19), residues: 825 sheet: -1.01 (0.33), residues: 246 loop : -1.69 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 35 TYR 0.026 0.001 TYR G 39 PHE 0.017 0.001 PHE A 226 TRP 0.005 0.001 TRP C 114 HIS 0.004 0.001 HIS E 17 Details of bonding type rmsd covalent geometry : bond 0.00282 (14431) covalent geometry : angle 0.48402 (19732) hydrogen bonds : bond 0.03655 ( 628) hydrogen bonds : angle 4.05512 ( 1794) metal coordination : bond 0.00926 ( 4) metal coordination : angle 12.50519 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue TYR 93 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue ILE 101 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue TYR 113 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue TYR 140 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue ILE 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue ILE 198 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue MET 315 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue ILE 350 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue MET 47 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue ILE 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue MET 179 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LEU 194 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 267 is missing expected H atoms. Skipping. Residue ILE 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue SER 271 is missing expected H atoms. Skipping. Residue TYR 274 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue TYR 312 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue SER 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue LYS 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue LYS 544 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue THR 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue ILE 297 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue VAL 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue VAL 103 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue SER 226 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue ILE 332 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 340 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 232 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8483 (t80) cc_final: 0.8222 (t80) REVERT: A 374 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8419 (t) REVERT: A 499 ARG cc_start: 0.8499 (ptm-80) cc_final: 0.8182 (mtm180) REVERT: D 69 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7842 (pt) REVERT: D 93 LEU cc_start: 0.7548 (tp) cc_final: 0.7345 (tp) REVERT: E 218 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8539 (p) REVERT: G 15 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7768 (tt0) outliers start: 23 outliers final: 16 residues processed: 245 average time/residue: 0.2553 time to fit residues: 88.8235 Evaluate side-chains 245 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 158 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.094051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.083496 restraints weight = 76096.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.085990 restraints weight = 34338.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.087494 restraints weight = 19090.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.088539 restraints weight = 12514.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.089066 restraints weight = 9103.091| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.8707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14435 Z= 0.242 Angle : 0.624 25.848 19738 Z= 0.319 Chirality : 0.048 0.426 2398 Planarity : 0.005 0.099 2552 Dihedral : 4.438 22.526 2202 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.47 % Favored : 91.48 % Rotamer: Outliers : 2.64 % Allowed : 21.06 % Favored : 76.30 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.19), residues: 2066 helix: 1.06 (0.19), residues: 822 sheet: -1.12 (0.35), residues: 234 loop : -1.96 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 6 TYR 0.027 0.002 TYR G 39 PHE 0.019 0.002 PHE D 288 TRP 0.009 0.002 TRP E 198 HIS 0.004 0.001 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00556 (14431) covalent geometry : angle 0.57303 (19732) hydrogen bonds : bond 0.04991 ( 628) hydrogen bonds : angle 4.58243 ( 1794) metal coordination : bond 0.01461 ( 4) metal coordination : angle 14.12816 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue TYR 93 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue ILE 101 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue TYR 113 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue TYR 140 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue ILE 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue ILE 198 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue MET 315 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue ILE 350 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue MET 47 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue ILE 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue MET 179 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LEU 194 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 267 is missing expected H atoms. Skipping. Residue ILE 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue SER 271 is missing expected H atoms. Skipping. Residue TYR 274 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue TYR 312 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue SER 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue LYS 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue LYS 544 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue THR 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue ILE 297 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue VAL 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue VAL 103 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue SER 226 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue ILE 332 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 340 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.8576 (mm-40) cc_final: 0.7686 (tm-30) REVERT: A 374 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8586 (t) REVERT: A 405 VAL cc_start: 0.8366 (t) cc_final: 0.8056 (p) REVERT: D 69 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8141 (pt) REVERT: F 85 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8467 (mp) outliers start: 27 outliers final: 19 residues processed: 252 average time/residue: 0.2602 time to fit residues: 93.6742 Evaluate side-chains 251 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain E residue 55 PHE Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 86 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 168 optimal weight: 0.0060 chunk 120 optimal weight: 0.0770 chunk 182 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.096576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.085822 restraints weight = 76539.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.088378 restraints weight = 35295.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.089926 restraints weight = 19769.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.090948 restraints weight = 12990.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.091472 restraints weight = 9623.036| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.8782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14435 Z= 0.105 Angle : 0.534 22.325 19738 Z= 0.263 Chirality : 0.045 0.414 2398 Planarity : 0.004 0.042 2552 Dihedral : 3.942 19.573 2202 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.68 % Rotamer: Outliers : 2.06 % Allowed : 22.14 % Favored : 75.81 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.19), residues: 2066 helix: 1.54 (0.19), residues: 822 sheet: -0.90 (0.35), residues: 234 loop : -1.76 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 147 TYR 0.024 0.001 TYR G 39 PHE 0.014 0.001 PHE E 288 TRP 0.018 0.001 TRP E 114 HIS 0.004 0.001 HIS E 17 Details of bonding type rmsd covalent geometry : bond 0.00239 (14431) covalent geometry : angle 0.49134 (19732) hydrogen bonds : bond 0.03798 ( 628) hydrogen bonds : angle 4.14435 ( 1794) metal coordination : bond 0.01070 ( 4) metal coordination : angle 12.04112 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue TYR 93 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue ILE 101 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue TYR 113 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue TYR 140 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue ILE 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue ILE 198 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue MET 315 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue ILE 350 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue MET 47 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue ILE 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue MET 179 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LEU 194 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 267 is missing expected H atoms. Skipping. Residue ILE 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue SER 271 is missing expected H atoms. Skipping. Residue TYR 274 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue TYR 312 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue SER 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue LYS 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue LYS 544 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue THR 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue ILE 297 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue VAL 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue VAL 103 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue SER 226 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue ILE 332 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 340 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7567 (tm-30) REVERT: A 374 VAL cc_start: 0.8863 (OUTLIER) cc_final: 0.8520 (t) REVERT: F 85 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8472 (mp) REVERT: G 15 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7811 (tt0) outliers start: 21 outliers final: 18 residues processed: 237 average time/residue: 0.2652 time to fit residues: 89.5832 Evaluate side-chains 243 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain E residue 55 PHE Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 206 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 192 optimal weight: 0.0170 chunk 43 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.084464 restraints weight = 76818.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.086962 restraints weight = 35480.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.088472 restraints weight = 19981.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.089500 restraints weight = 13285.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.090124 restraints weight = 9862.736| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.9048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14435 Z= 0.163 Angle : 0.556 22.157 19738 Z= 0.279 Chirality : 0.046 0.414 2398 Planarity : 0.004 0.053 2552 Dihedral : 4.013 18.932 2202 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.08 % Favored : 91.87 % Rotamer: Outliers : 2.15 % Allowed : 22.04 % Favored : 75.81 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.19), residues: 2066 helix: 1.44 (0.19), residues: 823 sheet: -0.96 (0.35), residues: 237 loop : -1.82 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 147 TYR 0.028 0.002 TYR G 39 PHE 0.014 0.001 PHE E 288 TRP 0.011 0.001 TRP E 114 HIS 0.003 0.001 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00380 (14431) covalent geometry : angle 0.51362 (19732) hydrogen bonds : bond 0.04170 ( 628) hydrogen bonds : angle 4.23036 ( 1794) metal coordination : bond 0.01230 ( 4) metal coordination : angle 12.18264 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue TYR 93 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue ILE 101 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue TYR 113 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue TYR 140 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue ILE 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue ILE 198 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue MET 315 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue ILE 350 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue MET 47 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue ILE 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue MET 179 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LEU 194 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 267 is missing expected H atoms. Skipping. Residue ILE 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue SER 271 is missing expected H atoms. Skipping. Residue TYR 274 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue TYR 312 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue SER 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue LYS 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue LYS 544 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue THR 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue ILE 297 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue VAL 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue VAL 103 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue SER 226 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue ILE 332 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 340 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8545 (t) REVERT: D 69 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8224 (pt) REVERT: F 85 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8377 (mp) REVERT: G 15 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8015 (tt0) outliers start: 22 outliers final: 17 residues processed: 238 average time/residue: 0.2846 time to fit residues: 95.2083 Evaluate side-chains 244 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain E residue 55 PHE Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 15 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 196 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.084358 restraints weight = 76373.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.086843 restraints weight = 35192.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.088417 restraints weight = 19821.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.089422 restraints weight = 13002.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.089928 restraints weight = 9589.235| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.9318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14435 Z= 0.164 Angle : 0.558 22.200 19738 Z= 0.279 Chirality : 0.046 0.418 2398 Planarity : 0.004 0.042 2552 Dihedral : 4.072 20.075 2202 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.85 % Rotamer: Outliers : 2.06 % Allowed : 21.65 % Favored : 76.30 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.19), residues: 2066 helix: 1.41 (0.19), residues: 822 sheet: -1.10 (0.34), residues: 240 loop : -1.84 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 147 TYR 0.024 0.001 TYR G 39 PHE 0.016 0.001 PHE E 288 TRP 0.010 0.001 TRP E 198 HIS 0.003 0.001 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00380 (14431) covalent geometry : angle 0.51539 (19732) hydrogen bonds : bond 0.04116 ( 628) hydrogen bonds : angle 4.23682 ( 1794) metal coordination : bond 0.01194 ( 4) metal coordination : angle 12.24971 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue TYR 93 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue ILE 101 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue TYR 113 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue TYR 140 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue ILE 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue ILE 198 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue MET 315 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue ILE 350 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue MET 47 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue ILE 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue MET 179 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LEU 194 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 267 is missing expected H atoms. Skipping. Residue ILE 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue SER 271 is missing expected H atoms. Skipping. Residue TYR 274 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue TYR 312 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue SER 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue LYS 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue LYS 544 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue THR 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue ILE 297 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue ILE 24 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue VAL 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue VAL 103 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue SER 226 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue ILE 332 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 340 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 247 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8576 (t) REVERT: A 560 LYS cc_start: 0.8892 (ttpp) cc_final: 0.8626 (ttpp) REVERT: D 299 LEU cc_start: 0.8538 (tt) cc_final: 0.8318 (mt) REVERT: F 85 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8431 (mp) REVERT: G 15 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7944 (tt0) outliers start: 21 outliers final: 16 residues processed: 239 average time/residue: 0.2852 time to fit residues: 96.5071 Evaluate side-chains 237 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 218 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain E residue 55 PHE Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 15 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.083006 restraints weight = 76986.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.085619 restraints weight = 34654.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.087266 restraints weight = 19210.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.088308 restraints weight = 12443.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.088973 restraints weight = 9080.310| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.9483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14435 Z= 0.194 Angle : 0.576 22.968 19738 Z= 0.290 Chirality : 0.046 0.415 2398 Planarity : 0.004 0.040 2552 Dihedral : 4.173 21.010 2202 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.99 % Favored : 91.97 % Rotamer: Outliers : 1.96 % Allowed : 21.94 % Favored : 76.10 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.19), residues: 2066 helix: 1.26 (0.19), residues: 823 sheet: -1.21 (0.34), residues: 242 loop : -1.90 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 147 TYR 0.027 0.002 TYR G 39 PHE 0.015 0.002 PHE C 8 TRP 0.007 0.001 TRP A 441 HIS 0.003 0.001 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00454 (14431) covalent geometry : angle 0.53020 (19732) hydrogen bonds : bond 0.04381 ( 628) hydrogen bonds : angle 4.34166 ( 1794) metal coordination : bond 0.01413 ( 4) metal coordination : angle 12.93120 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3730.32 seconds wall clock time: 64 minutes 11.21 seconds (3851.21 seconds total)