Starting phenix.real_space_refine on Sat Aug 8 21:52:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vtq_65339/08_2026/9vtq_65339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vtq_65339/08_2026/9vtq_65339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vtq_65339/08_2026/9vtq_65339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vtq_65339/08_2026/9vtq_65339.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vtq_65339/08_2026/9vtq_65339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vtq_65339/08_2026/9vtq_65339.map" } resolution = 2.84 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= 0.000 sd= 0.021 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 P 98 5.49 5 Mg 1 5.21 5 S 142 5.16 5 C 18727 2.51 5 N 5169 2.21 5 O 5791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29928 Number of models: 1 Model: "" Number of chains: 14 Chain: "1" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1221 Classifications: {'RNA': 57} Modifications used: {'5*END': 1, 'rna2p_pur': 18, 'rna2p_pyr': 6, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 23, 'rna3p': 33} Chain breaks: 1 Chain: "2" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 737 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "3" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 123 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2725 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2745 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2752 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2756 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 326} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2727 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 19, 'TRANS': 320} Chain breaks: 1 Chain: "F" Number of atoms: 2387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2387 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 277} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 4790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4790 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 29, 'TRANS': 566} Chain breaks: 2 Chain: "H" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1452 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 175} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2876 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 5, 'GLU:plan': 5, 'ASN:plan1': 5, 'HIS:plan': 3, 'TRP:plan': 1, 'PHE:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 148 Chain: "J" Number of atoms: 2636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2636 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 4, 'ASN:plan1': 6, 'GLU:plan': 5, 'ASP:plan': 6, 'TRP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 110 Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.70, per 1000 atoms: 0.22 Number of scatterers: 29928 At special positions: 0 Unit cell: (121.824, 181.232, 192.512, 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) S 142 16.00 P 98 15.00 Mg 1 11.99 O 5791 8.00 N 5169 7.00 C 18727 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS I 132 " - pdb=" SG CYS I 135 " distance=2.03 Simple disulfide: pdb=" SG CYS I 165 " - pdb=" SG CYS I 185 " distance=2.03 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: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6654 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 48 sheets defined 38.5% alpha, 15.9% beta 35 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.063A pdb=" N ALA A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 179 through 185 Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 255 through 264 Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 322 through 339 Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.650A pdb=" N ALA B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 123 Processing helix chain 'B' and resid 125 through 138 Processing helix chain 'B' and resid 139 through 147 removed outlier: 6.404A pdb=" N ARG B 144 " --> pdb=" O TRP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.550A pdb=" N PHE B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 255 through 264 Processing helix chain 'B' and resid 300 through 307 removed outlier: 3.863A pdb=" N LYS B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 322 through 339 Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 63 through 67 removed outlier: 3.534A pdb=" N GLN C 67 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 179 through 185 removed outlier: 3.535A pdb=" N PHE C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 300 through 307 removed outlier: 3.548A pdb=" N LEU C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 317 Processing helix chain 'C' and resid 322 through 339 Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 105 through 123 Processing helix chain 'D' and resid 125 through 138 Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.967A pdb=" N CYS D 148 " --> pdb=" O ASN D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 removed outlier: 3.545A pdb=" N TYR D 177 " --> pdb=" O ILE D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 185 removed outlier: 3.572A pdb=" N PHE D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 255 through 264 Processing helix chain 'D' and resid 300 through 307 removed outlier: 3.590A pdb=" N LEU D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 317 Processing helix chain 'D' and resid 322 through 339 Processing helix chain 'E' and resid 51 through 55 removed outlier: 3.925A pdb=" N GLN E 55 " --> pdb=" O TYR E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 66 removed outlier: 3.600A pdb=" N ALA E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 123 Processing helix chain 'E' and resid 125 through 138 Processing helix chain 'E' and resid 144 through 148 removed outlier: 3.749A pdb=" N CYS E 148 " --> pdb=" O ASN E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 185 Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 255 through 264 Processing helix chain 'E' and resid 300 through 307 removed outlier: 3.527A pdb=" N LEU E 304 " --> pdb=" O ASP E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 318 Processing helix chain 'E' and resid 322 through 339 Processing helix chain 'F' and resid 105 through 123 Processing helix chain 'F' and resid 125 through 138 Processing helix chain 'F' and resid 139 through 147 removed outlier: 6.642A pdb=" N ARG F 144 " --> pdb=" O TRP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 255 through 264 Processing helix chain 'F' and resid 294 through 298 Processing helix chain 'F' and resid 300 through 306 removed outlier: 3.561A pdb=" N LEU F 304 " --> pdb=" O ASP F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.534A pdb=" N GLN F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 339 Processing helix chain 'G' and resid 18 through 24 Processing helix chain 'G' and resid 35 through 46 removed outlier: 4.172A pdb=" N ALA G 39 " --> pdb=" O THR G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 67 Processing helix chain 'G' and resid 69 through 77 Processing helix chain 'G' and resid 78 through 82 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 129 through 134 removed outlier: 3.525A pdb=" N CYS G 134 " --> pdb=" O MET G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 158 through 167 removed outlier: 3.755A pdb=" N ASN G 162 " --> pdb=" O HIS G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 184 removed outlier: 3.533A pdb=" N ILE G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 230 Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 243 through 248 removed outlier: 3.689A pdb=" N MET G 247 " --> pdb=" O ARG G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 254 removed outlier: 3.871A pdb=" N CYS G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 270 removed outlier: 3.546A pdb=" N LYS G 269 " --> pdb=" O PRO G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 296 removed outlier: 4.609A pdb=" N SER G 296 " --> pdb=" O TYR G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 325 Processing helix chain 'G' and resid 337 through 349 Processing helix chain 'G' and resid 353 through 357 removed outlier: 3.749A pdb=" N ALA G 357 " --> pdb=" O ASN G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 375 removed outlier: 3.517A pdb=" N HIS G 375 " --> pdb=" O GLY G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 432 removed outlier: 3.504A pdb=" N THR G 432 " --> pdb=" O ARG G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 502 Processing helix chain 'G' and resid 516 through 520 Processing helix chain 'G' and resid 528 through 535 Processing helix chain 'G' and resid 554 through 563 removed outlier: 3.511A pdb=" N VAL G 558 " --> pdb=" O SER G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 587 through 591 Processing helix chain 'G' and resid 613 through 617 removed outlier: 3.517A pdb=" N TYR G 617 " --> pdb=" O PRO G 614 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 35 removed outlier: 3.926A pdb=" N ILE H 20 " --> pdb=" O ASN H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 71 removed outlier: 3.510A pdb=" N LEU H 66 " --> pdb=" O ASN H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 81 Processing helix chain 'H' and resid 104 through 111 removed outlier: 3.794A pdb=" N ASP H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR H 111 " --> pdb=" O ILE H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'H' and resid 134 through 139 removed outlier: 3.909A pdb=" N ALA H 137 " --> pdb=" O ASP H 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 30 Processing helix chain 'I' and resid 33 through 47 removed outlier: 3.949A pdb=" N ASP I 47 " --> pdb=" O ARG I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 53 removed outlier: 6.711A pdb=" N ARG I 51 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 85 removed outlier: 3.764A pdb=" N ARG I 75 " --> pdb=" O HIS I 71 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU I 85 " --> pdb=" O HIS I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 138 Processing helix chain 'I' and resid 143 through 148 removed outlier: 3.770A pdb=" N PHE I 148 " --> pdb=" O ARG I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 177 Processing helix chain 'I' and resid 201 through 208 Processing helix chain 'I' and resid 219 through 234 removed outlier: 3.517A pdb=" N ARG I 223 " --> pdb=" O PRO I 219 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP I 224 " --> pdb=" O LEU I 220 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY I 225 " --> pdb=" O SER I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 251 removed outlier: 3.737A pdb=" N PHE I 245 " --> pdb=" O ASN I 241 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS I 251 " --> pdb=" O ALA I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 270 Processing helix chain 'I' and resid 284 through 289 Processing helix chain 'I' and resid 302 through 315 Processing helix chain 'I' and resid 321 through 325 removed outlier: 3.997A pdb=" N ASN I 325 " --> pdb=" O LYS I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 337 Processing helix chain 'I' and resid 340 through 351 removed outlier: 3.766A pdb=" N GLY I 351 " --> pdb=" O MET I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 384 Processing helix chain 'J' and resid 22 through 29 Processing helix chain 'J' and resid 33 through 49 removed outlier: 3.536A pdb=" N PHE J 37 " --> pdb=" O ASP J 33 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE J 48 " --> pdb=" O TYR J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 63 removed outlier: 3.548A pdb=" N ILE J 63 " --> pdb=" O ILE J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 83 removed outlier: 3.536A pdb=" N ARG J 75 " --> pdb=" O HIS J 71 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER J 83 " --> pdb=" O LEU J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 139 removed outlier: 3.655A pdb=" N GLU J 138 " --> pdb=" O CYS J 134 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS J 139 " --> pdb=" O CYS J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 148 Processing helix chain 'J' and resid 172 through 177 Processing helix chain 'J' and resid 197 through 207 Processing helix chain 'J' and resid 219 through 233 removed outlier: 3.858A pdb=" N MET J 227 " --> pdb=" O ARG J 223 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS J 228 " --> pdb=" O TRP J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 243 No H-bonds generated for 'chain 'J' and resid 241 through 243' Processing helix chain 'J' and resid 244 through 249 Processing helix chain 'J' and resid 251 through 271 removed outlier: 3.900A pdb=" N PHE J 256 " --> pdb=" O TRP J 252 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N HIS J 257 " --> pdb=" O PRO J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 289 removed outlier: 3.747A pdb=" N PHE J 289 " --> pdb=" O GLY J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 310 Processing helix chain 'J' and resid 342 through 350 Processing helix chain 'J' and resid 376 through 385 removed outlier: 3.942A pdb=" N LEU J 380 " --> pdb=" O ASP J 376 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 395 removed outlier: 3.718A pdb=" N PHE J 394 " --> pdb=" O ASN J 391 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 18 through 23 current: chain 'A' and resid 151 through 158 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 94 current: chain 'A' and resid 243 through 246 Processing sheet with id=AA4, first strand: chain 'A' and resid 35 through 41 Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.666A pdb=" N TYR A 290 " --> pdb=" O HIS A 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AA8, first strand: chain 'B' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 18 through 24 current: chain 'B' and resid 151 through 158 Processing sheet with id=AA9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.863A pdb=" N ARG B 28 " --> pdb=" O TRP B 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 94 current: chain 'B' and resid 243 through 246 Processing sheet with id=AB1, first strand: chain 'B' and resid 34 through 42 Processing sheet with id=AB2, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.653A pdb=" N TYR B 290 " --> pdb=" O HIS B 285 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 23 current: chain 'C' and resid 151 through 158 Processing sheet with id=AB5, first strand: chain 'C' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 94 current: chain 'C' and resid 243 through 246 Processing sheet with id=AB6, first strand: chain 'C' and resid 35 through 41 Processing sheet with id=AB7, first strand: chain 'C' and resid 283 through 285 removed outlier: 3.661A pdb=" N TYR C 290 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 102 through 103 removed outlier: 3.578A pdb=" N LYS D 102 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 23 current: chain 'D' and resid 151 through 158 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 84 through 94 current: chain 'D' and resid 243 through 246 Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 42 Processing sheet with id=AC3, first strand: chain 'D' and resid 265 through 267 Processing sheet with id=AC4, first strand: chain 'D' and resid 283 through 285 Processing sheet with id=AC5, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AC6, first strand: chain 'E' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 23 current: chain 'E' and resid 151 through 158 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 84 through 94 current: chain 'E' and resid 243 through 246 Processing sheet with id=AC8, first strand: chain 'E' and resid 35 through 42 Processing sheet with id=AC9, first strand: chain 'E' and resid 265 through 267 Processing sheet with id=AD1, first strand: chain 'E' and resid 284 through 285 removed outlier: 3.738A pdb=" N TYR E 290 " --> pdb=" O HIS E 285 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 8 through 9 Processing sheet with id=AD3, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.552A pdb=" N GLU F 14 " --> pdb=" O SER F 92 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.552A pdb=" N GLU F 14 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER F 151 " --> pdb=" O ARG F 216 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AD6, first strand: chain 'F' and resid 74 through 75 Processing sheet with id=AD7, first strand: chain 'F' and resid 283 through 285 Processing sheet with id=AD8, first strand: chain 'G' and resid 85 through 86 removed outlier: 4.071A pdb=" N VAL G 217 " --> pdb=" O ASN G 86 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 97 through 99 Processing sheet with id=AE1, first strand: chain 'G' and resid 139 through 142 Processing sheet with id=AE2, first strand: chain 'G' and resid 201 through 204 removed outlier: 9.036A pdb=" N ALA G 594 " --> pdb=" O TYR G 210 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER G 212 " --> pdb=" O ALA G 594 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL G 596 " --> pdb=" O SER G 212 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N SER G 214 " --> pdb=" O VAL G 596 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR G 598 " --> pdb=" O SER G 214 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL G 444 " --> pdb=" O LEU G 544 " (cutoff:3.500A) removed outlier: 10.077A pdb=" N LEU G 546 " --> pdb=" O PHE G 442 " (cutoff:3.500A) removed outlier: 14.557A pdb=" N PHE G 442 " --> pdb=" O LEU G 546 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER G 441 " --> pdb=" O ARG G 488 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA G 482 " --> pdb=" O HIS G 447 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE G 449 " --> pdb=" O ASP G 480 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP G 480 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL G 451 " --> pdb=" O GLN G 478 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLN G 478 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N CYS G 479 " --> pdb=" O GLY G 401 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY G 401 " --> pdb=" O CYS G 479 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU G 485 " --> pdb=" O PRO G 395 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU G 487 " --> pdb=" O LEU G 393 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU G 393 " --> pdb=" O LEU G 487 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 201 through 204 removed outlier: 9.036A pdb=" N ALA G 594 " --> pdb=" O TYR G 210 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER G 212 " --> pdb=" O ALA G 594 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL G 596 " --> pdb=" O SER G 212 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N SER G 214 " --> pdb=" O VAL G 596 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR G 598 " --> pdb=" O SER G 214 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE G 595 " --> pdb=" O ARG G 577 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ARG G 577 " --> pdb=" O PHE G 595 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU G 597 " --> pdb=" O TYR G 575 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR G 575 " --> pdb=" O GLU G 597 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE G 599 " --> pdb=" O ILE G 573 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 236 through 239 Processing sheet with id=AE5, first strand: chain 'G' and resid 461 through 462 Processing sheet with id=AE6, first strand: chain 'G' and resid 619 through 624 Processing sheet with id=AE7, first strand: chain 'H' and resid 55 through 58 removed outlier: 3.685A pdb=" N THR H 9 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AE9, first strand: chain 'H' and resid 150 through 155 Processing sheet with id=AF1, first strand: chain 'I' and resid 99 through 105 removed outlier: 5.892A pdb=" N ASN I 101 " --> pdb=" O ILE I 113 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE I 113 " --> pdb=" O ASN I 101 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N MET I 103 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA I 111 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR I 109 " --> pdb=" O PHE I 105 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 98 through 101 removed outlier: 4.430A pdb=" N ALA J 111 " --> pdb=" O ASN J 101 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 181 through 182 1071 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 5.86 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5442 1.32 - 1.45: 8586 1.45 - 1.57: 16470 1.57 - 1.69: 193 1.69 - 1.81: 187 Bond restraints: 30878 Sorted by residual: bond pdb=" C3' DC 2 21 " pdb=" C2' DC 2 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DC 2 56 " pdb=" C2' DC 2 56 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.99e+00 bond pdb=" N9 A 1 36 " pdb=" C4 A 1 36 " ideal model delta sigma weight residual 1.374 1.358 0.016 6.00e-03 2.78e+04 7.56e+00 bond pdb=" C3' DC 2 50 " pdb=" O3' DC 2 50 " ideal model delta sigma weight residual 1.435 1.402 0.033 1.30e-02 5.92e+03 6.59e+00 bond pdb=" C3' DA 2 38 " pdb=" O3' DA 2 38 " ideal model delta sigma weight residual 1.435 1.402 0.033 1.30e-02 5.92e+03 6.50e+00 ... (remaining 30873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 41839 2.52 - 5.05: 458 5.05 - 7.57: 32 7.57 - 10.10: 14 10.10 - 12.62: 3 Bond angle restraints: 42346 Sorted by residual: angle pdb=" N3 DT 2 32 " pdb=" C4 DT 2 32 " pdb=" O4 DT 2 32 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT 2 44 " pdb=" C4 DT 2 44 " pdb=" O4 DT 2 44 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT 3 3 " pdb=" C4 DT 3 3 " pdb=" O4 DT 3 3 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT 2 24 " pdb=" C4 DT 2 24 " pdb=" O4 DT 2 24 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT 2 51 " pdb=" C4 DT 2 51 " pdb=" O4 DT 2 51 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 ... (remaining 42341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 15261 17.76 - 35.52: 2082 35.52 - 53.27: 680 53.27 - 71.03: 211 71.03 - 88.79: 57 Dihedral angle restraints: 18291 sinusoidal: 7980 harmonic: 10311 Sorted by residual: dihedral pdb=" O4' C 1 15 " pdb=" C1' C 1 15 " pdb=" N1 C 1 15 " pdb=" C2 C 1 15 " ideal model delta sinusoidal sigma weight residual -128.00 -55.32 -72.68 1 1.70e+01 3.46e-03 2.33e+01 dihedral pdb=" CA LEU G 394 " pdb=" C LEU G 394 " pdb=" N PRO G 395 " pdb=" CA PRO G 395 " ideal model delta harmonic sigma weight residual -180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" O4' C 1 18 " pdb=" C1' C 1 18 " pdb=" N1 C 1 18 " pdb=" C2 C 1 18 " ideal model delta sinusoidal sigma weight residual -160.00 -106.03 -53.97 1 1.50e+01 4.44e-03 1.76e+01 ... (remaining 18288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4089 0.074 - 0.147: 531 0.147 - 0.221: 14 0.221 - 0.295: 1 0.295 - 0.368: 1 Chirality restraints: 4636 Sorted by residual: chirality pdb=" CG LEU J 79 " pdb=" CB LEU J 79 " pdb=" CD1 LEU J 79 " pdb=" CD2 LEU J 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CG LEU J 38 " pdb=" CB LEU J 38 " pdb=" CD1 LEU J 38 " pdb=" CD2 LEU J 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C3' DT 2 44 " pdb=" C4' DT 2 44 " pdb=" O3' DT 2 44 " pdb=" C2' DT 2 44 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 4633 not shown) Planarity restraints: 5083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP J 49 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO J 50 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO J 50 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO J 50 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 6 " -0.031 2.00e-02 2.50e+03 1.42e-02 5.56e+00 pdb=" N9 A 1 6 " 0.033 2.00e-02 2.50e+03 pdb=" C8 A 1 6 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 1 6 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 1 6 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A 1 6 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A 1 6 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A 1 6 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 1 6 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 1 6 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A 1 6 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 30 " 0.169 9.50e-02 1.11e+02 7.66e-02 4.87e+00 pdb=" NE ARG H 30 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG H 30 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG H 30 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG H 30 " -0.000 2.00e-02 2.50e+03 ... (remaining 5080 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4744 2.76 - 3.29: 28797 3.29 - 3.83: 51309 3.83 - 4.36: 61510 4.36 - 4.90: 102031 Nonbonded interactions: 248391 Sorted by model distance: nonbonded pdb=" OP2 A 1 6 " pdb="MG MG 1 101 " model vdw 2.219 2.170 nonbonded pdb=" O ASP D 247 " pdb=" OD1 ASP D 247 " model vdw 2.416 3.040 nonbonded pdb=" O ASN G 564 " pdb=" OD1 ASN G 565 " model vdw 2.458 3.040 nonbonded pdb=" N GLU I 342 " pdb=" OE1 GLU I 342 " model vdw 2.470 3.120 nonbonded pdb=" O2 U 1 2 " pdb=" O ILE G 508 " model vdw 2.484 3.040 ... (remaining 248386 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 'A' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 177 or res \ id 183 through 231 or (resid 236 through 238 and (name N or name CA or name C or \ name O or name CB )) or resid 239 through 317 or (resid 318 through 320 and (na \ me N or name CA or name C or name O or name CB )) or resid 321 through 345)) selection = (chain 'B' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 177 or res \ id 183 through 231 or (resid 236 through 238 and (name N or name CA or name C or \ name O or name CB )) or resid 239 through 345)) selection = (chain 'C' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 177 or res \ id 183 through 231 or (resid 236 through 238 and (name N or name CA or name C or \ name O or name CB )) or resid 239 through 317 or (resid 318 through 320 and (na \ me N or name CA or name C or name O or name CB )) or resid 321 through 345)) selection = (chain 'D' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 177 or res \ id 183 through 231 or (resid 236 through 238 and (name N or name CA or name C or \ name O or name CB )) or resid 239 through 317 or (resid 318 through 320 and (na \ me N or name CA or name C or name O or name CB )) or resid 321 through 345)) selection = (chain 'E' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 177 or res \ id 183 through 231 or (resid 236 through 238 and (name N or name CA or name C or \ name O or name CB )) or resid 239 through 317 or (resid 318 through 320 and (na \ me N or name CA or name C or name O or name CB )) or resid 321 through 345)) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 14 through 88 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 209 or (resid 210 through 219 and \ (name N or name CA or name C or name O or name CB )) or resid 220 through 233 or \ resid 241 through 251 or (resid 252 through 260 and (name N or name CA or name \ C or name O or name CB )) or resid 261 or (resid 262 through 279 and (name N or \ name CA or name C or name O or name CB )) or resid 280 through 319 or (resid 331 \ through 333 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 34 through 346 or (resid 347 through 350 and (name N or name CA or name C or nam \ e O or name CB )) or resid 351 or (resid 352 through 355 and (name N or name CA \ or name C or name O or name CB )) or resid 375 through 395)) selection = (chain 'J' and ((resid 14 through 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 31 or (resid 32 through 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 through 66 or (resid 67 throug \ h 74 and (name N or name CA or name C or name O or name CB )) or resid 75 throug \ h 88 or resid 92 through 188 or (resid 189 through 201 and (name N or name CA or \ name C or name O or name CB )) or resid 202 through 230 or (resid 231 through 2 \ 42 and (name N or name CA or name C or name O or name CB )) or resid 243 or (res \ id 244 and (name N or name CA or name C or name O or name CB )) or resid 245 thr \ ough 395)) } 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 individual isotropic 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: 7.840 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: 0.030 Extract box with map and model: 0.750 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 30.050 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 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 : 0.006 0.053 30880 Z= 0.339 Angle : 0.655 12.619 42350 Z= 0.396 Chirality : 0.047 0.368 4636 Planarity : 0.004 0.077 5083 Dihedral : 18.908 88.790 11631 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.95 % Allowed : 31.02 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.14), residues: 3476 helix: 1.15 (0.15), residues: 1184 sheet: 0.18 (0.22), residues: 543 loop : -0.91 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG H 30 TYR 0.020 0.001 TYR C 52 PHE 0.020 0.002 PHE C 302 TRP 0.032 0.001 TRP G 280 HIS 0.005 0.001 HIS J 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.34 (30878) covalent geometry : angle 0.65474 / 0.40 (42346) SS BOND : bond 0.00178 / 0.25 ( 2) SS BOND : angle 0.38489 / 0.42 ( 4) hydrogen bonds : bond 0.13948 / 14.81 ( 1126) hydrogen bonds : angle 5.80092 / 7.61 ( 3082) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 168 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 306 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: C 180 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8652 (m) REVERT: E 10 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8807 (tpp) REVERT: F 220 ASN cc_start: 0.8615 (m-40) cc_final: 0.8063 (p0) REVERT: F 230 LYS cc_start: 0.7597 (pptt) cc_final: 0.7115 (pmtt) REVERT: F 239 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7119 (ttt180) REVERT: F 311 TYR cc_start: 0.8448 (m-10) cc_final: 0.8247 (m-80) REVERT: G 147 HIS cc_start: 0.9020 (OUTLIER) cc_final: 0.8460 (m90) REVERT: G 252 MET cc_start: 0.9218 (tmm) cc_final: 0.8920 (tmm) REVERT: G 271 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7861 (tp40) REVERT: G 498 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7958 (tmm-80) REVERT: H 35 TYR cc_start: 0.7962 (m-80) cc_final: 0.7473 (m-80) REVERT: H 70 ILE cc_start: 0.8539 (mm) cc_final: 0.8052 (mt) REVERT: H 77 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8364 (mp10) REVERT: I 83 SER cc_start: 0.6631 (OUTLIER) cc_final: 0.6277 (p) REVERT: I 146 TRP cc_start: 0.8490 (m-10) cc_final: 0.7773 (m-10) REVERT: J 184 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.5949 (pm20) outliers start: 87 outliers final: 64 residues processed: 245 average time/residue: 0.4632 time to fit residues: 141.1452 Evaluate side-chains 224 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 150 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 498 ARG Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 83 SER Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 199 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS I 77 HIS ** I 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 HIS J 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.082612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.052152 restraints weight = 78455.697| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.61 r_work: 0.2664 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.0529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30880 Z= 0.147 Angle : 0.549 9.486 42350 Z= 0.294 Chirality : 0.042 0.308 4636 Planarity : 0.004 0.053 5083 Dihedral : 15.065 129.539 5243 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.11 % Allowed : 28.95 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.13 (0.15), residues: 3476 helix: 1.31 (0.15), residues: 1213 sheet: 0.33 (0.22), residues: 524 loop : -0.87 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 30 TYR 0.013 0.001 TYR I 395 PHE 0.016 0.001 PHE A 302 TRP 0.015 0.001 TRP J 249 HIS 0.003 0.001 HIS J 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (30878) covalent geometry : angle 0.54935 / 0.29 (42346) SS BOND : bond 0.00212 / 0.25 ( 2) SS BOND : angle 0.43618 / 0.43 ( 4) hydrogen bonds : bond 0.04522 / 4.84 ( 1126) hydrogen bonds : angle 4.90879 / 6.44 ( 3082) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 160 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 306 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: C 187 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8900 (ptmm) REVERT: F 1 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.6504 (pmt) REVERT: F 14 GLU cc_start: 0.8475 (pm20) cc_final: 0.8262 (pm20) REVERT: F 121 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8937 (mp0) REVERT: F 220 ASN cc_start: 0.8359 (m-40) cc_final: 0.7974 (p0) REVERT: F 230 LYS cc_start: 0.7476 (pptt) cc_final: 0.6931 (pmtt) REVERT: F 321 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7916 (mt) REVERT: G 147 HIS cc_start: 0.8968 (OUTLIER) cc_final: 0.8427 (m90) REVERT: G 218 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8708 (p) REVERT: G 252 MET cc_start: 0.9060 (tmm) cc_final: 0.8735 (tmm) REVERT: G 293 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8485 (p) REVERT: H 32 ASN cc_start: 0.8045 (m110) cc_final: 0.7807 (t0) REVERT: H 35 TYR cc_start: 0.8107 (m-80) cc_final: 0.7326 (m-80) REVERT: H 77 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8460 (mp10) REVERT: I 146 TRP cc_start: 0.8501 (m-10) cc_final: 0.7736 (m-10) REVERT: I 308 MET cc_start: 0.9602 (OUTLIER) cc_final: 0.9354 (tpp) REVERT: J 184 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6357 (pm20) REVERT: J 293 GLN cc_start: 0.8050 (pp30) cc_final: 0.7794 (pp30) REVERT: J 386 GLN cc_start: 0.8073 (tp40) cc_final: 0.7722 (tp40) outliers start: 151 outliers final: 63 residues processed: 294 average time/residue: 0.4766 time to fit residues: 176.5441 Evaluate side-chains 224 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 150 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 469 THR Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 308 MET Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 228 HIS Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 40 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 chunk 334 optimal weight: 0.0050 chunk 330 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 331 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 309 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS I 386 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.083251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.053003 restraints weight = 78789.915| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.61 r_work: 0.2690 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30880 Z= 0.127 Angle : 0.528 9.506 42350 Z= 0.282 Chirality : 0.041 0.334 4636 Planarity : 0.004 0.060 5083 Dihedral : 14.772 87.540 5184 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.54 % Allowed : 29.50 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.15), residues: 3476 helix: 1.42 (0.15), residues: 1207 sheet: 0.43 (0.22), residues: 536 loop : -0.85 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 357 TYR 0.015 0.001 TYR H 74 PHE 0.014 0.001 PHE A 302 TRP 0.019 0.001 TRP J 249 HIS 0.005 0.001 HIS I 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (30878) covalent geometry : angle 0.52763 / 0.28 (42346) SS BOND : bond 0.00160 / 0.15 ( 2) SS BOND : angle 0.43261 / 0.41 ( 4) hydrogen bonds : bond 0.03898 / 4.17 ( 1126) hydrogen bonds : angle 4.66319 / 6.09 ( 3082) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 160 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8503 (mttm) REVERT: B 306 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: B 323 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8314 (t70) REVERT: C 187 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8800 (ptmm) REVERT: D 247 ASP cc_start: 0.8439 (t0) cc_final: 0.8227 (t0) REVERT: F 1 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.6457 (pmt) REVERT: F 121 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8913 (mp0) REVERT: F 220 ASN cc_start: 0.8345 (m-40) cc_final: 0.7965 (p0) REVERT: F 230 LYS cc_start: 0.7485 (pptt) cc_final: 0.6941 (pmtt) REVERT: F 239 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.6761 (ttt180) REVERT: F 286 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7052 (mtp85) REVERT: F 321 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7886 (mt) REVERT: G 147 HIS cc_start: 0.8969 (OUTLIER) cc_final: 0.8449 (m90) REVERT: G 218 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8693 (p) REVERT: G 223 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8476 (tp30) REVERT: G 252 MET cc_start: 0.9054 (tmm) cc_final: 0.8779 (tmm) REVERT: G 293 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8545 (p) REVERT: H 32 ASN cc_start: 0.8108 (m110) cc_final: 0.7903 (t0) REVERT: H 35 TYR cc_start: 0.8143 (m-80) cc_final: 0.7323 (m-80) REVERT: H 77 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8423 (mp10) REVERT: H 155 ASP cc_start: 0.8778 (p0) cc_final: 0.8401 (t0) REVERT: I 104 GLN cc_start: 0.7702 (tp-100) cc_final: 0.7410 (tp40) REVERT: I 146 TRP cc_start: 0.8479 (m-10) cc_final: 0.7698 (m-10) REVERT: J 36 TRP cc_start: 0.8663 (m100) cc_final: 0.8445 (m100) REVERT: J 184 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6214 (pm20) REVERT: J 293 GLN cc_start: 0.8064 (pp30) cc_final: 0.7765 (pp30) REVERT: J 308 MET cc_start: 0.9436 (tpp) cc_final: 0.9054 (tmm) REVERT: J 386 GLN cc_start: 0.8081 (tp40) cc_final: 0.7573 (tp40) outliers start: 134 outliers final: 62 residues processed: 279 average time/residue: 0.5116 time to fit residues: 177.5007 Evaluate side-chains 229 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 152 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 337 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 281 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 255 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 140 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 ASN I 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.082405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.052043 restraints weight = 78452.273| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.61 r_work: 0.2667 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 30880 Z= 0.191 Angle : 0.550 10.344 42350 Z= 0.290 Chirality : 0.042 0.362 4636 Planarity : 0.004 0.060 5083 Dihedral : 14.716 86.602 5176 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.38 % Allowed : 28.21 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.14), residues: 3476 helix: 1.45 (0.15), residues: 1205 sheet: 0.35 (0.23), residues: 500 loop : -0.88 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 357 TYR 0.014 0.001 TYR H 74 PHE 0.015 0.001 PHE A 302 TRP 0.018 0.001 TRP J 249 HIS 0.004 0.001 HIS J 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (30878) covalent geometry : angle 0.55021 / 0.29 (42346) SS BOND : bond 0.00317 / 0.43 ( 2) SS BOND : angle 0.80337 / 1.05 ( 4) hydrogen bonds : bond 0.03911 / 4.21 ( 1126) hydrogen bonds : angle 4.62289 / 6.02 ( 3082) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 161 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8528 (mttm) REVERT: B 306 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: C 187 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8855 (ptmm) REVERT: F 1 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.6482 (pmt) REVERT: F 14 GLU cc_start: 0.8516 (pm20) cc_final: 0.8204 (pm20) REVERT: F 121 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8912 (mp0) REVERT: F 194 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8708 (tttp) REVERT: F 220 ASN cc_start: 0.8349 (m-40) cc_final: 0.7976 (p0) REVERT: F 230 LYS cc_start: 0.7468 (pptt) cc_final: 0.6955 (pmtt) REVERT: F 239 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.6723 (ttt180) REVERT: F 286 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7108 (mtp85) REVERT: F 321 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7889 (mt) REVERT: F 335 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8880 (m-40) REVERT: G 147 HIS cc_start: 0.8978 (OUTLIER) cc_final: 0.8451 (m90) REVERT: G 218 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8692 (p) REVERT: G 223 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8487 (tp30) REVERT: G 252 MET cc_start: 0.9066 (tmm) cc_final: 0.8769 (tmm) REVERT: G 271 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7599 (tp40) REVERT: G 293 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8495 (p) REVERT: H 35 TYR cc_start: 0.8141 (m-80) cc_final: 0.7340 (m-80) REVERT: H 77 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8425 (mp10) REVERT: H 155 ASP cc_start: 0.8757 (p0) cc_final: 0.8376 (t0) REVERT: H 158 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.9064 (p) REVERT: I 146 TRP cc_start: 0.8471 (m-10) cc_final: 0.7689 (m-10) REVERT: J 36 TRP cc_start: 0.8670 (m100) cc_final: 0.8455 (m100) REVERT: J 293 GLN cc_start: 0.7961 (pp30) cc_final: 0.7657 (pp30) REVERT: J 386 GLN cc_start: 0.8026 (tp40) cc_final: 0.7615 (tp40) outliers start: 159 outliers final: 81 residues processed: 308 average time/residue: 0.5097 time to fit residues: 195.4505 Evaluate side-chains 246 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 148 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 155 HIS Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 336 optimal weight: 10.0000 chunk 324 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 257 optimal weight: 6.9990 chunk 338 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 353 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 348 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 ASN D 114 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 522 HIS H 144 HIS ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS J 343 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.082572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.052261 restraints weight = 78698.523| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.62 r_work: 0.2671 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30880 Z= 0.170 Angle : 0.547 11.147 42350 Z= 0.287 Chirality : 0.042 0.366 4636 Planarity : 0.004 0.063 5083 Dihedral : 14.686 86.872 5170 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.55 % Allowed : 28.51 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.14), residues: 3476 helix: 1.45 (0.15), residues: 1205 sheet: 0.35 (0.23), residues: 500 loop : -0.89 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 341 TYR 0.015 0.001 TYR C 52 PHE 0.015 0.001 PHE A 302 TRP 0.024 0.001 TRP J 249 HIS 0.003 0.001 HIS J 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (30878) covalent geometry : angle 0.54708 / 0.29 (42346) SS BOND : bond 0.00410 / 0.56 ( 2) SS BOND : angle 0.58507 / 0.57 ( 4) hydrogen bonds : bond 0.03784 / 4.07 ( 1126) hydrogen bonds : angle 4.56655 / 5.94 ( 3082) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 159 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8526 (mttm) REVERT: A 323 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8428 (t0) REVERT: B 28 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7525 (mtp-110) REVERT: B 306 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: B 323 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8349 (t70) REVERT: C 187 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8837 (ptmm) REVERT: F 1 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.6489 (pmt) REVERT: F 121 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8919 (mp0) REVERT: F 194 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8705 (tttp) REVERT: F 220 ASN cc_start: 0.8355 (m-40) cc_final: 0.7982 (p0) REVERT: F 230 LYS cc_start: 0.7460 (pptt) cc_final: 0.6968 (pmtt) REVERT: F 239 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.6712 (ttt180) REVERT: F 286 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7118 (mtp85) REVERT: F 309 ASP cc_start: 0.9327 (OUTLIER) cc_final: 0.8855 (OUTLIER) REVERT: F 321 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7861 (mt) REVERT: F 335 ASN cc_start: 0.9139 (OUTLIER) cc_final: 0.8871 (m-40) REVERT: G 147 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8469 (m90) REVERT: G 218 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8693 (p) REVERT: G 223 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8489 (tp30) REVERT: G 252 MET cc_start: 0.9084 (tmm) cc_final: 0.8799 (tmm) REVERT: G 271 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7597 (tp40) REVERT: G 293 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8539 (p) REVERT: H 35 TYR cc_start: 0.8095 (m-80) cc_final: 0.7419 (m-10) REVERT: H 77 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8433 (mp10) REVERT: H 155 ASP cc_start: 0.8743 (p0) cc_final: 0.8368 (t0) REVERT: H 158 SER cc_start: 0.9280 (OUTLIER) cc_final: 0.9061 (p) REVERT: I 146 TRP cc_start: 0.8471 (m-10) cc_final: 0.7698 (m-10) REVERT: J 36 TRP cc_start: 0.8664 (m100) cc_final: 0.8402 (m100) REVERT: J 293 GLN cc_start: 0.8032 (pp30) cc_final: 0.7723 (pp30) REVERT: J 386 GLN cc_start: 0.7974 (tp40) cc_final: 0.7600 (tp40) outliers start: 164 outliers final: 91 residues processed: 308 average time/residue: 0.5062 time to fit residues: 194.9078 Evaluate side-chains 259 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 148 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 330 MET Chi-restraints excluded: chain I residue 340 SER Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 155 HIS Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 217 optimal weight: 0.8980 chunk 264 optimal weight: 3.9990 chunk 91 optimal weight: 0.0470 chunk 166 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 322 optimal weight: 5.9990 chunk 294 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 GLN F 242 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.084042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.053916 restraints weight = 78455.435| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.63 r_work: 0.2716 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30880 Z= 0.106 Angle : 0.532 12.028 42350 Z= 0.278 Chirality : 0.041 0.368 4636 Planarity : 0.004 0.067 5083 Dihedral : 14.682 88.348 5170 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.23 % Allowed : 30.21 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.27 (0.15), residues: 3476 helix: 1.48 (0.15), residues: 1205 sheet: 0.47 (0.23), residues: 493 loop : -0.82 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 357 TYR 0.018 0.001 TYR J 173 PHE 0.035 0.001 PHE J 248 TRP 0.026 0.001 TRP J 249 HIS 0.003 0.001 HIS C 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (30878) covalent geometry : angle 0.53244 / 0.28 (42346) SS BOND : bond 0.00267 / 0.34 ( 2) SS BOND : angle 0.44030 / 0.41 ( 4) hydrogen bonds : bond 0.03383 / 3.65 ( 1126) hydrogen bonds : angle 4.44358 / 5.75 ( 3082) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 162 time to evaluate : 0.936 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 67 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8502 (mt0) REVERT: A 144 ARG cc_start: 0.9468 (OUTLIER) cc_final: 0.8863 (ttt180) REVERT: B 306 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: C 187 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8777 (ptmm) REVERT: F 1 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.6319 (pmt) REVERT: F 74 ASP cc_start: 0.8226 (t70) cc_final: 0.7712 (m-30) REVERT: F 194 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8554 (ttpt) REVERT: F 220 ASN cc_start: 0.8331 (m-40) cc_final: 0.7982 (p0) REVERT: F 230 LYS cc_start: 0.7472 (pptt) cc_final: 0.6957 (pmtt) REVERT: F 239 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.6534 (ttt180) REVERT: F 242 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8677 (mt0) REVERT: F 286 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6952 (mtp85) REVERT: F 321 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7750 (mt) REVERT: G 147 HIS cc_start: 0.8964 (OUTLIER) cc_final: 0.8458 (m90) REVERT: G 218 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8668 (p) REVERT: G 252 MET cc_start: 0.9038 (tmm) cc_final: 0.8757 (tmm) REVERT: G 271 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7521 (tp40) REVERT: G 293 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8558 (p) REVERT: H 77 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8474 (mp10) REVERT: H 155 ASP cc_start: 0.8715 (p0) cc_final: 0.8348 (t0) REVERT: I 146 TRP cc_start: 0.8489 (m-10) cc_final: 0.7698 (m-10) REVERT: I 347 MET cc_start: 0.8841 (tpp) cc_final: 0.8589 (tpp) REVERT: J 36 TRP cc_start: 0.8665 (m100) cc_final: 0.8404 (m100) REVERT: J 184 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.6384 (pm20) REVERT: J 293 GLN cc_start: 0.8068 (pp30) cc_final: 0.7761 (pp30) REVERT: J 386 GLN cc_start: 0.7941 (tp40) cc_final: 0.7559 (tp40) outliers start: 125 outliers final: 70 residues processed: 274 average time/residue: 0.4973 time to fit residues: 167.8016 Evaluate side-chains 236 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 150 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 242 GLN Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 597 GLU Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 328 MET Chi-restraints excluded: chain I residue 330 MET Chi-restraints excluded: chain I residue 340 SER Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 39 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 169 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 134 optimal weight: 0.2980 chunk 148 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 5 optimal weight: 30.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.082989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.052802 restraints weight = 78389.629| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.61 r_work: 0.2681 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30880 Z= 0.170 Angle : 0.554 12.241 42350 Z= 0.288 Chirality : 0.042 0.374 4636 Planarity : 0.004 0.068 5083 Dihedral : 14.617 87.755 5166 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.50 % Allowed : 30.31 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.15), residues: 3476 helix: 1.51 (0.15), residues: 1208 sheet: 0.40 (0.23), residues: 499 loop : -0.85 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 300 TYR 0.016 0.001 TYR C 52 PHE 0.015 0.001 PHE C 302 TRP 0.028 0.001 TRP J 381 HIS 0.003 0.001 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (30878) covalent geometry : angle 0.55415 / 0.29 (42346) SS BOND : bond 0.00237 / 0.31 ( 2) SS BOND : angle 0.39518 / 0.36 ( 4) hydrogen bonds : bond 0.03585 / 3.87 ( 1126) hydrogen bonds : angle 4.46639 / 5.79 ( 3082) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 152 time to evaluate : 0.909 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 67 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: B 306 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: C 187 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8805 (ptmm) REVERT: F 1 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.6348 (pmt) REVERT: F 194 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8685 (tttp) REVERT: F 220 ASN cc_start: 0.8343 (m-40) cc_final: 0.7955 (p0) REVERT: F 230 LYS cc_start: 0.7521 (pptt) cc_final: 0.7026 (pmtt) REVERT: F 239 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.6691 (ttt180) REVERT: F 286 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6938 (mtp85) REVERT: F 309 ASP cc_start: 0.9332 (OUTLIER) cc_final: 0.8847 (p0) REVERT: F 321 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7827 (mt) REVERT: G 147 HIS cc_start: 0.8967 (OUTLIER) cc_final: 0.8480 (m90) REVERT: G 218 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8675 (p) REVERT: G 223 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8494 (tp30) REVERT: G 252 MET cc_start: 0.9072 (tmm) cc_final: 0.8797 (tmm) REVERT: G 271 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7598 (tp40) REVERT: G 293 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8557 (p) REVERT: H 77 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8472 (mp10) REVERT: H 155 ASP cc_start: 0.8726 (p0) cc_final: 0.8464 (t0) REVERT: H 158 SER cc_start: 0.9283 (OUTLIER) cc_final: 0.9064 (p) REVERT: I 146 TRP cc_start: 0.8468 (m-10) cc_final: 0.7680 (m-10) REVERT: J 36 TRP cc_start: 0.8671 (m100) cc_final: 0.8413 (m100) REVERT: J 184 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6324 (pm20) REVERT: J 293 GLN cc_start: 0.8104 (pp30) cc_final: 0.7799 (pp30) REVERT: J 386 GLN cc_start: 0.7962 (tp40) cc_final: 0.7541 (tp40) outliers start: 133 outliers final: 75 residues processed: 267 average time/residue: 0.4301 time to fit residues: 144.5783 Evaluate side-chains 239 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 147 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 597 GLU Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 330 MET Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 249 TRP Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 347 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 230 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.083108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.052924 restraints weight = 78586.591| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.61 r_work: 0.2684 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30880 Z= 0.155 Angle : 0.552 12.773 42350 Z= 0.286 Chirality : 0.042 0.371 4636 Planarity : 0.004 0.071 5083 Dihedral : 14.616 87.729 5166 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.44 % Allowed : 30.17 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.15), residues: 3476 helix: 1.52 (0.15), residues: 1206 sheet: 0.39 (0.23), residues: 499 loop : -0.85 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 300 TYR 0.014 0.001 TYR H 74 PHE 0.014 0.001 PHE J 22 TRP 0.036 0.001 TRP J 381 HIS 0.003 0.001 HIS C 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (30878) covalent geometry : angle 0.55186 / 0.29 (42346) SS BOND : bond 0.00241 / 0.29 ( 2) SS BOND : angle 0.40333 / 0.37 ( 4) hydrogen bonds : bond 0.03545 / 3.82 ( 1126) hydrogen bonds : angle 4.47201 / 5.78 ( 3082) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 154 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8502 (mt0) REVERT: A 343 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8528 (pt0) REVERT: B 28 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7514 (mtp-110) REVERT: B 44 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8504 (mt-10) REVERT: B 306 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: C 187 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8799 (ptmm) REVERT: E 123 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7274 (p) REVERT: F 1 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.6354 (pmt) REVERT: F 14 GLU cc_start: 0.8784 (pt0) cc_final: 0.8512 (pt0) REVERT: F 194 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8682 (tttp) REVERT: F 220 ASN cc_start: 0.8332 (m-40) cc_final: 0.7952 (p0) REVERT: F 230 LYS cc_start: 0.7498 (pptt) cc_final: 0.7007 (pmtt) REVERT: F 239 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.6695 (ttt180) REVERT: F 286 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7004 (mtp85) REVERT: F 309 ASP cc_start: 0.9330 (OUTLIER) cc_final: 0.8846 (p0) REVERT: F 321 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7789 (mt) REVERT: G 147 HIS cc_start: 0.8956 (OUTLIER) cc_final: 0.8464 (m90) REVERT: G 218 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8680 (p) REVERT: G 223 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8482 (tp30) REVERT: G 252 MET cc_start: 0.9054 (tmm) cc_final: 0.8773 (tmm) REVERT: G 271 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7566 (tp40) REVERT: G 293 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8558 (p) REVERT: H 77 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8497 (mp10) REVERT: H 155 ASP cc_start: 0.8750 (p0) cc_final: 0.8427 (t0) REVERT: H 158 SER cc_start: 0.9285 (OUTLIER) cc_final: 0.9062 (p) REVERT: I 146 TRP cc_start: 0.8486 (m-10) cc_final: 0.7731 (m-10) REVERT: I 347 MET cc_start: 0.8799 (tpp) cc_final: 0.8597 (tpp) REVERT: J 36 TRP cc_start: 0.8675 (m100) cc_final: 0.8408 (m100) REVERT: J 184 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6322 (pm20) REVERT: J 293 GLN cc_start: 0.8114 (pp30) cc_final: 0.7803 (pp30) REVERT: J 386 GLN cc_start: 0.7929 (tp40) cc_final: 0.7529 (tp40) outliers start: 131 outliers final: 80 residues processed: 270 average time/residue: 0.5129 time to fit residues: 172.4834 Evaluate side-chains 251 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 150 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 330 MET Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 155 HIS Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 339 CYS Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 122 optimal weight: 3.9990 chunk 318 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 311 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS I 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.082349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.052079 restraints weight = 78455.000| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.60 r_work: 0.2664 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30880 Z= 0.198 Angle : 0.581 12.914 42350 Z= 0.302 Chirality : 0.043 0.360 4636 Planarity : 0.004 0.072 5083 Dihedral : 14.599 87.385 5164 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.54 % Allowed : 30.00 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.14), residues: 3476 helix: 1.49 (0.15), residues: 1208 sheet: 0.37 (0.23), residues: 497 loop : -0.89 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 300 TYR 0.018 0.001 TYR C 52 PHE 0.017 0.001 PHE C 302 TRP 0.042 0.001 TRP J 381 HIS 0.020 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (30878) covalent geometry : angle 0.58092 / 0.30 (42346) SS BOND : bond 0.00230 / 0.30 ( 2) SS BOND : angle 0.39833 / 0.38 ( 4) hydrogen bonds : bond 0.03767 / 4.04 ( 1126) hydrogen bonds : angle 4.54638 / 5.88 ( 3082) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 156 time to evaluate : 1.248 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 43 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8510 (mttm) REVERT: A 67 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8388 (mt0) REVERT: B 28 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7546 (mtp-110) REVERT: B 44 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8554 (mt-10) REVERT: B 306 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: C 187 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8833 (ptmm) REVERT: D 247 ASP cc_start: 0.8481 (t0) cc_final: 0.8268 (t0) REVERT: F 1 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.6386 (pmt) REVERT: F 14 GLU cc_start: 0.8819 (pt0) cc_final: 0.8597 (pt0) REVERT: F 194 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8586 (ttpt) REVERT: F 220 ASN cc_start: 0.8343 (m-40) cc_final: 0.7962 (p0) REVERT: F 230 LYS cc_start: 0.7495 (pptt) cc_final: 0.7019 (pmtt) REVERT: F 239 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.6701 (ttt180) REVERT: F 242 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8536 (mt0) REVERT: F 286 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7025 (mtp85) REVERT: F 309 ASP cc_start: 0.9328 (OUTLIER) cc_final: 0.8856 (OUTLIER) REVERT: F 321 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7845 (mt) REVERT: G 147 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.8468 (m90) REVERT: G 218 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8715 (p) REVERT: G 223 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8491 (tp30) REVERT: G 252 MET cc_start: 0.9056 (tmm) cc_final: 0.8782 (tmm) REVERT: G 271 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7636 (tp40) REVERT: G 293 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8551 (p) REVERT: H 77 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8846 (mp10) REVERT: H 155 ASP cc_start: 0.8756 (p0) cc_final: 0.8449 (t0) REVERT: H 158 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.9058 (p) REVERT: I 146 TRP cc_start: 0.8468 (m-10) cc_final: 0.7709 (m-10) REVERT: J 36 TRP cc_start: 0.8684 (m100) cc_final: 0.8416 (m100) REVERT: J 184 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6358 (pm20) REVERT: J 293 GLN cc_start: 0.8171 (pp30) cc_final: 0.7850 (pp30) REVERT: J 386 GLN cc_start: 0.7924 (tp40) cc_final: 0.7495 (tp40) outliers start: 134 outliers final: 89 residues processed: 276 average time/residue: 0.5264 time to fit residues: 179.7939 Evaluate side-chains 258 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 149 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 242 GLN Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 330 MET Chi-restraints excluded: chain I residue 340 SER Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 155 HIS Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 339 CYS Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 151 optimal weight: 4.9990 chunk 329 optimal weight: 0.0370 chunk 105 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 312 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 275 optimal weight: 10.0000 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.082456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.052197 restraints weight = 78267.683| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.60 r_work: 0.2667 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30880 Z= 0.186 Angle : 0.583 12.978 42350 Z= 0.303 Chirality : 0.042 0.374 4636 Planarity : 0.004 0.119 5083 Dihedral : 14.607 87.322 5164 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.33 % Allowed : 30.21 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.15), residues: 3476 helix: 1.48 (0.15), residues: 1209 sheet: 0.36 (0.23), residues: 497 loop : -0.88 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG H 30 TYR 0.017 0.001 TYR C 52 PHE 0.016 0.001 PHE C 302 TRP 0.041 0.001 TRP J 381 HIS 0.007 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (30878) covalent geometry : angle 0.58278 / 0.30 (42346) SS BOND : bond 0.00229 / 0.30 ( 2) SS BOND : angle 0.42165 / 0.40 ( 4) hydrogen bonds : bond 0.03727 / 4.00 ( 1126) hydrogen bonds : angle 4.54166 / 5.87 ( 3082) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 152 time to evaluate : 1.167 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 43 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8519 (mttm) REVERT: A 67 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8389 (mt0) REVERT: A 343 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8523 (pt0) REVERT: B 28 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7546 (mtp-110) REVERT: B 306 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: C 187 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8831 (ptmm) REVERT: D 247 ASP cc_start: 0.8495 (t0) cc_final: 0.8288 (t0) REVERT: F 1 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.6389 (pmt) REVERT: F 14 GLU cc_start: 0.8800 (pt0) cc_final: 0.8586 (pt0) REVERT: F 121 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8925 (mp0) REVERT: F 194 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8583 (ttpt) REVERT: F 220 ASN cc_start: 0.8341 (m-40) cc_final: 0.7981 (p0) REVERT: F 230 LYS cc_start: 0.7491 (pptt) cc_final: 0.7015 (pmtt) REVERT: F 239 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.6699 (ttt180) REVERT: F 242 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8536 (mt0) REVERT: F 286 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7019 (mtp85) REVERT: F 309 ASP cc_start: 0.9325 (OUTLIER) cc_final: 0.8855 (OUTLIER) REVERT: F 321 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7854 (mt) REVERT: G 147 HIS cc_start: 0.8964 (OUTLIER) cc_final: 0.8439 (m90) REVERT: G 218 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8700 (p) REVERT: G 223 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8502 (tp30) REVERT: G 252 MET cc_start: 0.9044 (tmm) cc_final: 0.8746 (tmm) REVERT: G 271 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7606 (tp40) REVERT: G 293 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8544 (p) REVERT: H 33 TYR cc_start: 0.8187 (m-80) cc_final: 0.7636 (m-80) REVERT: H 77 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8874 (mp10) REVERT: H 155 ASP cc_start: 0.8758 (p0) cc_final: 0.8446 (t0) REVERT: H 158 SER cc_start: 0.9287 (OUTLIER) cc_final: 0.9052 (p) REVERT: I 146 TRP cc_start: 0.8462 (m-10) cc_final: 0.7724 (m-10) REVERT: J 36 TRP cc_start: 0.8686 (m100) cc_final: 0.8415 (m100) REVERT: J 145 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8419 (mpt-90) REVERT: J 184 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6324 (pm20) REVERT: J 293 GLN cc_start: 0.8168 (pp30) cc_final: 0.7856 (pp30) REVERT: J 386 GLN cc_start: 0.7873 (tp40) cc_final: 0.7452 (tp40) outliers start: 128 outliers final: 90 residues processed: 267 average time/residue: 0.5010 time to fit residues: 165.8356 Evaluate side-chains 261 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 149 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 242 GLN Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 330 MET Chi-restraints excluded: chain I residue 340 SER Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 145 ARG Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 155 HIS Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 339 CYS Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 329 optimal weight: 0.3980 chunk 334 optimal weight: 0.4980 chunk 107 optimal weight: 0.0770 chunk 336 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 208 optimal weight: 0.0770 chunk 41 optimal weight: 0.9990 chunk 319 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 5 optimal weight: 30.0000 chunk 93 optimal weight: 0.9980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 GLN F 242 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.084317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.054349 restraints weight = 78557.658| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.62 r_work: 0.2720 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 30880 Z= 0.108 Angle : 0.560 13.139 42350 Z= 0.290 Chirality : 0.041 0.380 4636 Planarity : 0.004 0.076 5083 Dihedral : 14.623 88.241 5164 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.25 % Allowed : 31.36 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.15), residues: 3476 helix: 1.56 (0.15), residues: 1207 sheet: 0.51 (0.23), residues: 487 loop : -0.81 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG H 30 TYR 0.016 0.001 TYR C 52 PHE 0.015 0.001 PHE J 22 TRP 0.039 0.001 TRP J 381 HIS 0.004 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (30878) covalent geometry : angle 0.55965 / 0.29 (42346) SS BOND : bond 0.00234 / 0.25 ( 2) SS BOND : angle 0.47604 / 0.46 ( 4) hydrogen bonds : bond 0.03335 / 3.58 ( 1126) hydrogen bonds : angle 4.41942 / 5.69 ( 3082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10935.45 seconds wall clock time: 187 minutes 6.91 seconds (11226.91 seconds total)