Starting phenix.real_space_refine on Sun Feb 8 10:30:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hve_52433/02_2026/9hve_52433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hve_52433/02_2026/9hve_52433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hve_52433/02_2026/9hve_52433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hve_52433/02_2026/9hve_52433.map" model { file = "/net/cci-nas-00/data/ceres_data/9hve_52433/02_2026/9hve_52433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hve_52433/02_2026/9hve_52433.cif" } resolution = 2.7 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= -0.001 sd= 0.016 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 242 5.16 5 C 27894 2.51 5 N 7646 2.21 5 O 8300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44088 Number of models: 1 Model: "" Number of chains: 18 Chain: "F" Number of atoms: 3212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3212 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain breaks: 2 Chain: "E" Number of atoms: 3212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3212 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain breaks: 2 Chain: "K" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2233 Classifications: {'peptide': 278} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 268} Chain: "I" Number of atoms: 4993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4993 Classifications: {'peptide': 630} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 603} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3508 Classifications: {'peptide': 460} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 434} Chain: "D" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2707 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 331} Chain: "A" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2338 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 291} Chain breaks: 1 Chain: "H" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2809 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 341} Chain: "M" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 212 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "N" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 212 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "L" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2233 Classifications: {'peptide': 278} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 268} Chain: "J" Number of atoms: 4993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4993 Classifications: {'peptide': 630} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 603} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3508 Classifications: {'peptide': 460} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 434} Chain: "C" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2707 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 331} Chain: "B" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2338 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 291} Chain breaks: 1 Chain: "G" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2809 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 341} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.53, per 1000 atoms: 0.22 Number of scatterers: 44088 At special positions: 0 Unit cell: (229.896, 220.832, 147.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 242 16.00 P 6 15.00 O 8300 8.00 N 7646 7.00 C 27894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.8 seconds 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10608 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 58 sheets defined 42.3% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'F' and resid 24 through 27 Processing helix chain 'F' and resid 36 through 47 removed outlier: 3.503A pdb=" N LEU F 40 " --> pdb=" O ILE F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 65 Processing helix chain 'F' and resid 85 through 94 Processing helix chain 'F' and resid 95 through 97 No H-bonds generated for 'chain 'F' and resid 95 through 97' Processing helix chain 'F' and resid 114 through 124 removed outlier: 4.138A pdb=" N LEU F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 176 No H-bonds generated for 'chain 'F' and resid 174 through 176' Processing helix chain 'F' and resid 184 through 190 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.770A pdb=" N VAL F 212 " --> pdb=" O LYS F 208 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 237 removed outlier: 4.237A pdb=" N PHE F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 267 removed outlier: 3.631A pdb=" N ILE F 267 " --> pdb=" O TYR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 334 Proline residue: F 327 - end of helix Processing helix chain 'E' and resid 13 through 17 removed outlier: 4.119A pdb=" N THR E 17 " --> pdb=" O SER E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 27 Processing helix chain 'E' and resid 36 through 47 Processing helix chain 'E' and resid 56 through 64 Processing helix chain 'E' and resid 85 through 94 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 114 through 124 removed outlier: 4.085A pdb=" N LEU E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 Processing helix chain 'E' and resid 208 through 218 removed outlier: 3.760A pdb=" N VAL E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 237 removed outlier: 4.216A pdb=" N PHE E 237 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 267 removed outlier: 3.939A pdb=" N PHE E 266 " --> pdb=" O ASP E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 334 Proline residue: E 327 - end of helix removed outlier: 3.839A pdb=" N ALA E 332 " --> pdb=" O LYS E 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 40 No H-bonds generated for 'chain 'K' and resid 38 through 40' Processing helix chain 'K' and resid 49 through 52 removed outlier: 4.318A pdb=" N SER K 52 " --> pdb=" O SER K 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 49 through 52' Processing helix chain 'K' and resid 58 through 62 Processing helix chain 'K' and resid 91 through 119 Processing helix chain 'K' and resid 123 through 134 removed outlier: 3.573A pdb=" N LEU K 127 " --> pdb=" O LYS K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 143 removed outlier: 3.691A pdb=" N PHE K 138 " --> pdb=" O THR K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 156 Processing helix chain 'K' and resid 159 through 163 removed outlier: 3.646A pdb=" N ILE K 162 " --> pdb=" O ASP K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 185 removed outlier: 3.526A pdb=" N THR K 185 " --> pdb=" O ASN K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 217 removed outlier: 3.502A pdb=" N VAL K 208 " --> pdb=" O GLY K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 265 Processing helix chain 'I' and resid 58 through 62 removed outlier: 3.754A pdb=" N ASP I 62 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 67 Processing helix chain 'I' and resid 75 through 87 Processing helix chain 'I' and resid 98 through 108 removed outlier: 3.663A pdb=" N LYS I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 113 removed outlier: 3.539A pdb=" N CYS I 112 " --> pdb=" O SER I 109 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG I 113 " --> pdb=" O LYS I 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 109 through 113' Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 161 through 175 Processing helix chain 'I' and resid 229 through 232 removed outlier: 3.673A pdb=" N GLN I 232 " --> pdb=" O SER I 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 229 through 232' Processing helix chain 'I' and resid 253 through 263 removed outlier: 4.190A pdb=" N ALA I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 279 Processing helix chain 'I' and resid 302 through 315 Processing helix chain 'I' and resid 455 through 461 Processing helix chain 'I' and resid 484 through 489 Processing helix chain 'I' and resid 498 through 503 removed outlier: 3.538A pdb=" N ASN I 503 " --> pdb=" O ALA I 499 " (cutoff:3.500A) Processing helix chain 'I' and resid 549 through 568 Processing helix chain 'I' and resid 570 through 586 Processing helix chain 'I' and resid 588 through 607 Proline residue: I 604 - end of helix removed outlier: 4.443A pdb=" N GLN I 607 " --> pdb=" O PHE I 603 " (cutoff:3.500A) Processing helix chain 'I' and resid 613 through 628 Proline residue: I 623 - end of helix Processing helix chain 'I' and resid 628 through 636 removed outlier: 3.793A pdb=" N PHE I 632 " --> pdb=" O TRP I 628 " (cutoff:3.500A) Processing helix chain 'I' and resid 640 through 656 Processing helix chain 'I' and resid 657 through 661 removed outlier: 4.764A pdb=" N ILE I 661 " --> pdb=" O ALA I 658 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 673 removed outlier: 4.006A pdb=" N ALA I 669 " --> pdb=" O LYS I 665 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU I 673 " --> pdb=" O ALA I 669 " (cutoff:3.500A) Processing helix chain 'I' and resid 677 through 685 removed outlier: 4.334A pdb=" N PHE I 685 " --> pdb=" O ILE I 681 " (cutoff:3.500A) Processing helix chain 'I' and resid 691 through 697 removed outlier: 3.539A pdb=" N GLN I 695 " --> pdb=" O THR I 691 " (cutoff:3.500A) Processing helix chain 'I' and resid 700 through 717 removed outlier: 4.507A pdb=" N ARG I 705 " --> pdb=" O GLN I 701 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS I 711 " --> pdb=" O ILE I 707 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU I 714 " --> pdb=" O LEU I 710 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 39 removed outlier: 3.940A pdb=" N ARG O 38 " --> pdb=" O GLU O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 63 removed outlier: 3.829A pdb=" N VAL O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 145 Processing helix chain 'O' and resid 170 through 180 Processing helix chain 'O' and resid 196 through 211 Processing helix chain 'O' and resid 231 through 241 removed outlier: 3.574A pdb=" N VAL O 235 " --> pdb=" O ASN O 231 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 274 Processing helix chain 'D' and resid 7 through 25 removed outlier: 3.836A pdb=" N GLU D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 49 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.523A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 97 removed outlier: 4.464A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 Processing helix chain 'D' and resid 128 through 153 removed outlier: 3.601A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 171 through 183 removed outlier: 3.599A pdb=" N ARG D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 210 removed outlier: 4.311A pdb=" N GLU D 202 " --> pdb=" O CYS D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 227 removed outlier: 4.207A pdb=" N SER D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.542A pdb=" N LYS D 273 " --> pdb=" O PRO D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.753A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 342 removed outlier: 3.515A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 Processing helix chain 'A' and resid 2 through 17 removed outlier: 3.609A pdb=" N ASP A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 37 Processing helix chain 'A' and resid 41 through 60 Processing helix chain 'A' and resid 62 through 83 removed outlier: 3.652A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 105 Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 131 through 144 Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.808A pdb=" N LYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 211 through 222 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.568A pdb=" N LYS A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 292 through 302 removed outlier: 3.853A pdb=" N VAL A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 181 removed outlier: 3.543A pdb=" N SER H 181 " --> pdb=" O SER H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 removed outlier: 3.919A pdb=" N GLN H 194 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE H 195 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET H 196 " --> pdb=" O THR H 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 191 through 196' Processing helix chain 'H' and resid 204 through 216 Processing helix chain 'H' and resid 221 through 239 Processing helix chain 'H' and resid 247 through 267 removed outlier: 4.320A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS H 257 " --> pdb=" O VAL H 253 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 270 through 286 Processing helix chain 'H' and resid 292 through 312 Processing helix chain 'H' and resid 312 through 327 removed outlier: 4.120A pdb=" N GLN H 325 " --> pdb=" O ARG H 321 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS H 326 " --> pdb=" O PHE H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 352 Processing helix chain 'H' and resid 368 through 379 removed outlier: 3.729A pdb=" N THR H 372 " --> pdb=" O GLU H 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 395 Processing helix chain 'H' and resid 419 through 430 Processing helix chain 'H' and resid 439 through 443 Processing helix chain 'H' and resid 459 through 464 Processing helix chain 'H' and resid 475 through 479 Processing helix chain 'H' and resid 493 through 497 Processing helix chain 'H' and resid 508 through 510 No H-bonds generated for 'chain 'H' and resid 508 through 510' Processing helix chain 'H' and resid 511 through 522 removed outlier: 4.088A pdb=" N ASP H 522 " --> pdb=" O VAL H 518 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 24 removed outlier: 3.736A pdb=" N LEU M 13 " --> pdb=" O THR M 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 24 removed outlier: 3.559A pdb=" N LYS N 24 " --> pdb=" O ILE N 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'L' and resid 49 through 52 removed outlier: 4.318A pdb=" N SER L 52 " --> pdb=" O SER L 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 49 through 52' Processing helix chain 'L' and resid 58 through 62 Processing helix chain 'L' and resid 91 through 119 Processing helix chain 'L' and resid 123 through 134 removed outlier: 3.575A pdb=" N LEU L 127 " --> pdb=" O LYS L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 143 removed outlier: 3.681A pdb=" N PHE L 138 " --> pdb=" O THR L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 159 removed outlier: 3.811A pdb=" N VAL L 157 " --> pdb=" O PHE L 153 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER L 158 " --> pdb=" O LYS L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 163 Processing helix chain 'L' and resid 169 through 185 removed outlier: 3.548A pdb=" N THR L 185 " --> pdb=" O ASN L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 217 Processing helix chain 'L' and resid 244 through 265 Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.760A pdb=" N ASP J 62 " --> pdb=" O ILE J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 67 Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 98 through 108 removed outlier: 3.662A pdb=" N LYS J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 113 removed outlier: 3.533A pdb=" N CYS J 112 " --> pdb=" O SER J 109 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG J 113 " --> pdb=" O LYS J 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 109 through 113' Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 161 through 175 Processing helix chain 'J' and resid 229 through 232 removed outlier: 3.696A pdb=" N GLN J 232 " --> pdb=" O SER J 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 229 through 232' Processing helix chain 'J' and resid 253 through 263 removed outlier: 4.182A pdb=" N ALA J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 279 Processing helix chain 'J' and resid 302 through 315 Processing helix chain 'J' and resid 455 through 461 Processing helix chain 'J' and resid 501 through 505 Processing helix chain 'J' and resid 548 through 568 Processing helix chain 'J' and resid 570 through 586 Processing helix chain 'J' and resid 588 through 607 Proline residue: J 604 - end of helix removed outlier: 4.312A pdb=" N GLN J 607 " --> pdb=" O PHE J 603 " (cutoff:3.500A) Processing helix chain 'J' and resid 613 through 628 Proline residue: J 623 - end of helix Processing helix chain 'J' and resid 628 through 636 removed outlier: 3.693A pdb=" N PHE J 632 " --> pdb=" O TRP J 628 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 656 Processing helix chain 'J' and resid 657 through 661 removed outlier: 4.533A pdb=" N ILE J 661 " --> pdb=" O ALA J 658 " (cutoff:3.500A) Processing helix chain 'J' and resid 662 through 673 removed outlier: 4.052A pdb=" N ALA J 669 " --> pdb=" O LYS J 665 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 673 " --> pdb=" O ALA J 669 " (cutoff:3.500A) Processing helix chain 'J' and resid 677 through 687 removed outlier: 3.501A pdb=" N ILE J 681 " --> pdb=" O ALA J 677 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN J 687 " --> pdb=" O SER J 683 " (cutoff:3.500A) Processing helix chain 'J' and resid 691 through 698 Processing helix chain 'J' and resid 700 through 717 removed outlier: 3.836A pdb=" N ARG J 705 " --> pdb=" O GLN J 701 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS J 711 " --> pdb=" O ILE J 707 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU J 714 " --> pdb=" O LEU J 710 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 39 removed outlier: 3.948A pdb=" N ARG P 38 " --> pdb=" O GLU P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 63 removed outlier: 3.822A pdb=" N VAL P 58 " --> pdb=" O LYS P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 145 Processing helix chain 'P' and resid 170 through 180 Processing helix chain 'P' and resid 196 through 211 Processing helix chain 'P' and resid 231 through 241 Processing helix chain 'P' and resid 270 through 274 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.837A pdb=" N GLU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 49 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.519A pdb=" N ARG C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 97 removed outlier: 4.472A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 128 through 153 removed outlier: 3.593A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 171 through 183 removed outlier: 3.600A pdb=" N ARG C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 210 removed outlier: 4.317A pdb=" N GLU C 202 " --> pdb=" O CYS C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 221 through 227 removed outlier: 4.213A pdb=" N SER C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.545A pdb=" N LYS C 273 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.754A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 342 removed outlier: 3.507A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.656A pdb=" N ASP B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 Processing helix chain 'B' and resid 41 through 60 Processing helix chain 'B' and resid 62 through 83 removed outlier: 3.660A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 105 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 131 through 144 Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.787A pdb=" N LYS B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.505A pdb=" N VAL B 246 " --> pdb=" O GLN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.574A pdb=" N LYS B 251 " --> pdb=" O PRO B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 removed outlier: 4.120A pdb=" N GLU B 269 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 292 through 304 removed outlier: 3.866A pdb=" N VAL B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 181 removed outlier: 3.541A pdb=" N SER G 181 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 3.941A pdb=" N GLN G 194 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET G 196 " --> pdb=" O THR G 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 191 through 196' Processing helix chain 'G' and resid 204 through 216 Processing helix chain 'G' and resid 221 through 239 Processing helix chain 'G' and resid 247 through 267 removed outlier: 4.325A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS G 257 " --> pdb=" O VAL G 253 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 270 through 286 Processing helix chain 'G' and resid 292 through 312 Processing helix chain 'G' and resid 312 through 327 removed outlier: 4.119A pdb=" N GLN G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS G 326 " --> pdb=" O PHE G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 352 Processing helix chain 'G' and resid 368 through 379 removed outlier: 3.728A pdb=" N THR G 372 " --> pdb=" O GLU G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 Processing helix chain 'G' and resid 419 through 430 Processing helix chain 'G' and resid 439 through 443 Processing helix chain 'G' and resid 459 through 464 Processing helix chain 'G' and resid 475 through 479 Processing helix chain 'G' and resid 493 through 497 Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 511 through 522 removed outlier: 4.150A pdb=" N ASP G 522 " --> pdb=" O VAL G 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 72 through 77 removed outlier: 6.283A pdb=" N VAL F 51 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL F 76 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL F 53 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N PHE F 3 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ILE F 52 " --> pdb=" O PHE F 3 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA F 5 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N VAL F 54 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL F 7 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN F 4 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU F 104 " --> pdb=" O GLN F 4 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL F 6 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 72 through 77 removed outlier: 6.283A pdb=" N VAL F 51 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL F 76 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL F 53 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N PHE F 3 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ILE F 52 " --> pdb=" O PHE F 3 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA F 5 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N VAL F 54 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL F 7 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN F 4 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU F 104 " --> pdb=" O GLN F 4 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL F 6 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU F 128 " --> pdb=" O TYR F 301 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N HIS F 303 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N MET F 130 " --> pdb=" O HIS F 303 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N MET F 305 " --> pdb=" O MET F 130 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET F 132 " --> pdb=" O MET F 305 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 29 through 30 Processing sheet with id=AA4, first strand: chain 'F' and resid 108 through 110 Processing sheet with id=AA5, first strand: chain 'F' and resid 167 through 172 removed outlier: 6.771A pdb=" N VAL I 202 " --> pdb=" O PHE I 215 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE I 215 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA I 204 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE I 287 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN I 286 " --> pdb=" O SER I 179 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET I 181 " --> pdb=" O GLN I 286 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL I 180 " --> pdb=" O ILE I 251 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE I 251 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR I 182 " --> pdb=" O ILE I 249 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE I 249 " --> pdb=" O THR I 182 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE I 184 " --> pdb=" O CYS I 247 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N HIS I 248 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR I 152 " --> pdb=" O HIS I 248 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA I 45 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N PHE I 94 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU I 47 " --> pdb=" O PHE I 94 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR I 91 " --> pdb=" O ARG I 121 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE I 123 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL I 93 " --> pdb=" O ILE I 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 179 through 182 Processing sheet with id=AA7, first strand: chain 'F' and resid 344 through 346 removed outlier: 6.707A pdb=" N GLN F 345 " --> pdb=" O ILE F 364 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ILE F 381 " --> pdb=" O GLU F 361 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN F 363 " --> pdb=" O ILE F 381 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU F 380 " --> pdb=" O VAL F 398 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 357 through 358 removed outlier: 6.060A pdb=" N LEU F 357 " --> pdb=" O ILE F 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 369 through 371 removed outlier: 6.313A pdb=" N ASN F 403 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS F 422 " --> pdb=" O ARG F 438 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 391 through 392 removed outlier: 6.780A pdb=" N LEU F 391 " --> pdb=" O ILE F 409 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL F 408 " --> pdb=" O ILE F 426 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU F 425 " --> pdb=" O ILE F 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 414 through 415 removed outlier: 7.660A pdb=" N VAL F 414 " --> pdb=" O ILE F 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 72 through 73 removed outlier: 4.139A pdb=" N VAL E 51 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N PHE E 3 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N ILE E 52 " --> pdb=" O PHE E 3 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA E 5 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL E 54 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL E 7 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN E 4 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU E 104 " --> pdb=" O GLN E 4 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL E 6 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 76 through 77 removed outlier: 8.168A pdb=" N PHE E 3 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N ILE E 52 " --> pdb=" O PHE E 3 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA E 5 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL E 54 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL E 7 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN E 4 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU E 104 " --> pdb=" O GLN E 4 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL E 6 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 30 Processing sheet with id=AB6, first strand: chain 'E' and resid 108 through 110 Processing sheet with id=AB7, first strand: chain 'E' and resid 167 through 172 removed outlier: 6.771A pdb=" N VAL J 202 " --> pdb=" O PHE J 215 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE J 215 " --> pdb=" O VAL J 202 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA J 204 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE J 287 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLN J 286 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET J 181 " --> pdb=" O GLN J 286 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL J 180 " --> pdb=" O ILE J 251 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE J 251 " --> pdb=" O VAL J 180 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR J 182 " --> pdb=" O ILE J 249 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE J 249 " --> pdb=" O THR J 182 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE J 184 " --> pdb=" O CYS J 247 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N HIS J 248 " --> pdb=" O TYR J 152 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR J 152 " --> pdb=" O HIS J 248 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA J 45 " --> pdb=" O PHE J 92 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N PHE J 94 " --> pdb=" O ALA J 45 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU J 47 " --> pdb=" O PHE J 94 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR J 91 " --> pdb=" O ARG J 121 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE J 123 " --> pdb=" O THR J 91 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL J 93 " --> pdb=" O ILE J 123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 179 through 182 Processing sheet with id=AB9, first strand: chain 'E' and resid 344 through 346 removed outlier: 6.689A pdb=" N GLN E 345 " --> pdb=" O ILE E 364 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ILE E 381 " --> pdb=" O GLU E 361 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLN E 363 " --> pdb=" O ILE E 381 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU E 380 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR E 397 " --> pdb=" O ILE E 415 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL E 414 " --> pdb=" O ILE E 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 357 through 358 removed outlier: 6.085A pdb=" N LEU E 357 " --> pdb=" O ILE E 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 368 through 371 removed outlier: 6.327A pdb=" N ASN E 403 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP E 420 " --> pdb=" O ARG E 438 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 391 through 392 removed outlier: 6.829A pdb=" N LEU E 391 " --> pdb=" O ILE E 409 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL E 408 " --> pdb=" O ILE E 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'K' and resid 19 through 27 removed outlier: 5.630A pdb=" N VAL K 24 " --> pdb=" O SER K 35 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER K 35 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLU K 43 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LEU K 85 " --> pdb=" O GLU K 43 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N MET K 45 " --> pdb=" O LEU K 85 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR K 82 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL K 76 " --> pdb=" O TYR K 82 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP K 84 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 225 through 231 removed outlier: 6.973A pdb=" N ARG K 234 " --> pdb=" O ILE K 230 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LYS K 190 " --> pdb=" O LYS K 276 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS K 276 " --> pdb=" O LYS K 190 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG K 192 " --> pdb=" O GLU K 274 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU K 274 " --> pdb=" O ARG K 192 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP K 194 " --> pdb=" O GLN K 272 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 69 through 70 Processing sheet with id=AC7, first strand: chain 'I' and resid 155 through 157 Processing sheet with id=AC8, first strand: chain 'I' and resid 336 through 338 removed outlier: 3.847A pdb=" N ILE I 342 " --> pdb=" O SER I 338 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU I 361 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL I 378 " --> pdb=" O LEU I 396 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TYR I 395 " --> pdb=" O LEU I 413 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU I 412 " --> pdb=" O LEU I 431 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL I 430 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 349 through 350 removed outlier: 6.395A pdb=" N SER I 349 " --> pdb=" O ILE I 368 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL I 367 " --> pdb=" O ILE I 385 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS I 384 " --> pdb=" O VAL I 402 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG I 401 " --> pdb=" O VAL I 419 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU I 418 " --> pdb=" O VAL I 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'I' and resid 355 through 356 removed outlier: 6.462A pdb=" N ILE I 355 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE I 373 " --> pdb=" O LEU I 391 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL I 390 " --> pdb=" O ILE I 408 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN I 407 " --> pdb=" O LEU I 425 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 102 through 105 removed outlier: 5.813A pdb=" N LYS O 90 " --> pdb=" O LEU O 126 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU O 126 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE O 113 " --> pdb=" O PHE O 124 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 102 through 105 removed outlier: 5.813A pdb=" N LYS O 90 " --> pdb=" O LEU O 126 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU O 126 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE O 42 " --> pdb=" O HIS O 129 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASN O 43 " --> pdb=" O ALA O 154 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LEU O 156 " --> pdb=" O ASN O 43 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLY O 45 " --> pdb=" O LEU O 156 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU O 158 " --> pdb=" O GLY O 45 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE O 47 " --> pdb=" O LEU O 158 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N ALA O 160 " --> pdb=" O ILE O 47 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA O 155 " --> pdb=" O LEU O 186 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU O 188 " --> pdb=" O ALA O 155 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU O 157 " --> pdb=" O LEU O 188 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN O 190 " --> pdb=" O LEU O 157 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE O 159 " --> pdb=" O ASN O 190 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 326 through 328 removed outlier: 4.033A pdb=" N LEU O 321 " --> pdb=" O LEU O 328 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS O 312 " --> pdb=" O PRO O 298 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE O 300 " --> pdb=" O MET O 310 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N MET O 310 " --> pdb=" O ILE O 300 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 288 through 289 Processing sheet with id=AD6, first strand: chain 'O' and resid 403 through 408 removed outlier: 9.645A pdb=" N SER O 412 " --> pdb=" O PRO O 432 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLY O 414 " --> pdb=" O THR O 430 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS O 426 " --> pdb=" O SER O 418 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL O 420 " --> pdb=" O LEU O 424 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU O 424 " --> pdb=" O VAL O 420 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N GLY O 425 " --> pdb=" O PHE O 376 " (cutoff:3.500A) removed outlier: 9.674A pdb=" N PHE O 376 " --> pdb=" O GLY O 425 " (cutoff:3.500A) removed outlier: 11.178A pdb=" N ILE O 427 " --> pdb=" O SER O 374 " (cutoff:3.500A) removed outlier: 10.572A pdb=" N SER O 374 " --> pdb=" O ILE O 427 " (cutoff:3.500A) removed outlier: 11.683A pdb=" N LEU O 429 " --> pdb=" O GLU O 372 " (cutoff:3.500A) removed outlier: 11.439A pdb=" N GLU O 372 " --> pdb=" O LEU O 429 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N ASN O 431 " --> pdb=" O GLU O 370 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLU O 370 " --> pdb=" O ASN O 431 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE O 368 " --> pdb=" O THR O 464 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR O 464 " --> pdb=" O PHE O 368 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU O 370 " --> pdb=" O GLY O 462 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY O 462 " --> pdb=" O GLU O 370 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU O 372 " --> pdb=" O ARG O 460 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN O 458 " --> pdb=" O SER O 374 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU O 453 " --> pdb=" O ARG O 445 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ARG O 445 " --> pdb=" O LEU O 453 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY O 455 " --> pdb=" O LEU O 443 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.587A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE D 168 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU D 163 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ILE D 190 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU D 213 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AD9, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.281A pdb=" N SER D 307 " --> pdb=" O TYR G 385 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N LEU G 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR G 336 " --> pdb=" O LEU G 402 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLY G 404 " --> pdb=" O TYR G 336 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL G 434 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE G 501 " --> pdb=" O VAL G 434 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL G 436 " --> pdb=" O ILE G 501 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 175 through 178 removed outlier: 8.754A pdb=" N THR A 176 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 150 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL A 178 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL A 152 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA A 123 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N TYR A 151 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE A 125 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR A 153 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR A 127 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 193 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL A 229 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE A 226 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N PHE A 285 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL A 228 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 206 through 209 Processing sheet with id=AE3, first strand: chain 'H' and resid 505 through 507 removed outlier: 6.901A pdb=" N VAL H 434 " --> pdb=" O LEU H 499 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ILE H 501 " --> pdb=" O VAL H 434 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL H 436 " --> pdb=" O ILE H 501 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL H 401 " --> pdb=" O LEU H 435 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N CYS H 437 " --> pdb=" O VAL H 401 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU H 403 " --> pdb=" O CYS H 437 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR H 336 " --> pdb=" O LEU H 402 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLY H 404 " --> pdb=" O TYR H 336 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 407 through 408 Processing sheet with id=AE5, first strand: chain 'H' and resid 482 through 484 removed outlier: 6.742A pdb=" N ARG H 483 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU C 213 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLU C 163 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE C 190 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE C 168 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 19 through 27 removed outlier: 5.624A pdb=" N VAL L 24 " --> pdb=" O SER L 35 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N SER L 35 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N GLU L 43 " --> pdb=" O ILE L 83 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N LEU L 85 " --> pdb=" O GLU L 43 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET L 45 " --> pdb=" O LEU L 85 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR L 82 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL L 76 " --> pdb=" O TYR L 82 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP L 84 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 225 through 231 removed outlier: 6.964A pdb=" N ARG L 234 " --> pdb=" O ILE L 230 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS L 190 " --> pdb=" O LYS L 276 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS L 276 " --> pdb=" O LYS L 190 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ARG L 192 " --> pdb=" O GLU L 274 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLU L 274 " --> pdb=" O ARG L 192 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP L 194 " --> pdb=" O GLN L 272 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 69 through 70 Processing sheet with id=AE9, first strand: chain 'J' and resid 155 through 157 Processing sheet with id=AF1, first strand: chain 'J' and resid 336 through 338 removed outlier: 3.847A pdb=" N ILE J 342 " --> pdb=" O SER J 338 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU J 361 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL J 378 " --> pdb=" O LEU J 396 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR J 395 " --> pdb=" O LEU J 413 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU J 412 " --> pdb=" O LEU J 431 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL J 430 " --> pdb=" O ILE J 449 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 349 through 350 removed outlier: 6.387A pdb=" N SER J 349 " --> pdb=" O ILE J 368 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL J 367 " --> pdb=" O ILE J 385 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N HIS J 384 " --> pdb=" O VAL J 402 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ARG J 401 " --> pdb=" O VAL J 419 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU J 418 " --> pdb=" O VAL J 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'J' and resid 355 through 356 removed outlier: 6.468A pdb=" N ILE J 355 " --> pdb=" O ILE J 374 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE J 373 " --> pdb=" O LEU J 391 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL J 390 " --> pdb=" O ILE J 408 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN J 407 " --> pdb=" O LEU J 425 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 102 through 105 removed outlier: 5.810A pdb=" N LYS P 90 " --> pdb=" O LEU P 126 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU P 126 " --> pdb=" O LYS P 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE P 113 " --> pdb=" O PHE P 124 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 102 through 105 removed outlier: 5.810A pdb=" N LYS P 90 " --> pdb=" O LEU P 126 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU P 126 " --> pdb=" O LYS P 90 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE P 42 " --> pdb=" O HIS P 129 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN P 43 " --> pdb=" O ALA P 154 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU P 156 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLY P 45 " --> pdb=" O LEU P 156 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU P 158 " --> pdb=" O GLY P 45 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA P 155 " --> pdb=" O LEU P 186 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU P 188 " --> pdb=" O ALA P 155 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU P 157 " --> pdb=" O LEU P 188 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASN P 190 " --> pdb=" O LEU P 157 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE P 159 " --> pdb=" O ASN P 190 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 262 through 263 removed outlier: 3.640A pdb=" N LYS P 312 " --> pdb=" O PRO P 298 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE P 300 " --> pdb=" O MET P 310 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N MET P 310 " --> pdb=" O ILE P 300 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU P 321 " --> pdb=" O LEU P 328 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 262 through 263 removed outlier: 3.838A pdb=" N GLY P 277 " --> pdb=" O THR P 341 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU P 321 " --> pdb=" O LEU P 328 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 288 through 289 Processing sheet with id=AF9, first strand: chain 'P' and resid 403 through 408 removed outlier: 9.701A pdb=" N SER P 412 " --> pdb=" O PRO P 432 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLY P 414 " --> pdb=" O THR P 430 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS P 426 " --> pdb=" O SER P 418 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL P 420 " --> pdb=" O LEU P 424 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU P 424 " --> pdb=" O VAL P 420 " (cutoff:3.500A) removed outlier: 10.650A pdb=" N GLY P 425 " --> pdb=" O PHE P 376 " (cutoff:3.500A) removed outlier: 9.608A pdb=" N PHE P 376 " --> pdb=" O GLY P 425 " (cutoff:3.500A) removed outlier: 11.104A pdb=" N ILE P 427 " --> pdb=" O SER P 374 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N SER P 374 " --> pdb=" O ILE P 427 " (cutoff:3.500A) removed outlier: 11.713A pdb=" N LEU P 429 " --> pdb=" O GLU P 372 " (cutoff:3.500A) removed outlier: 11.432A pdb=" N GLU P 372 " --> pdb=" O LEU P 429 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N ASN P 431 " --> pdb=" O GLU P 370 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU P 370 " --> pdb=" O ASN P 431 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE P 368 " --> pdb=" O THR P 464 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR P 464 " --> pdb=" O PHE P 368 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLU P 370 " --> pdb=" O GLY P 462 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY P 462 " --> pdb=" O GLU P 370 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU P 372 " --> pdb=" O ARG P 460 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN P 458 " --> pdb=" O SER P 374 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU P 453 " --> pdb=" O ARG P 445 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ARG P 445 " --> pdb=" O LEU P 453 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY P 455 " --> pdb=" O LEU P 443 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AG2, first strand: chain 'B' and resid 175 through 178 removed outlier: 8.751A pdb=" N THR B 176 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 150 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL B 178 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL B 152 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 123 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N TYR B 151 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE B 125 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR B 153 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR B 127 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL B 193 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL B 229 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 195 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE B 226 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N PHE B 285 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL B 228 " --> pdb=" O PHE B 285 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AG4, first strand: chain 'G' and resid 407 through 408 1880 hydrogen bonds defined for protein. 5229 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.11 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8781 1.33 - 1.45: 9818 1.45 - 1.57: 25871 1.57 - 1.70: 10 1.70 - 1.82: 370 Bond restraints: 44850 Sorted by residual: bond pdb=" C ASN C 331 " pdb=" N ALA C 332 " ideal model delta sigma weight residual 1.329 1.270 0.059 3.03e-02 1.09e+03 3.76e+00 bond pdb=" C ASN D 331 " pdb=" N ALA D 332 " ideal model delta sigma weight residual 1.329 1.271 0.058 3.03e-02 1.09e+03 3.65e+00 bond pdb=" CG MET M 21 " pdb=" SD MET M 21 " ideal model delta sigma weight residual 1.803 1.758 0.045 2.50e-02 1.60e+03 3.17e+00 bond pdb=" CB GLU I 655 " pdb=" CG GLU I 655 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.26e+00 bond pdb=" CD GLN L 253 " pdb=" OE1 GLN L 253 " ideal model delta sigma weight residual 1.231 1.204 0.027 1.90e-02 2.77e+03 2.05e+00 ... (remaining 44845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 60067 2.36 - 4.71: 505 4.71 - 7.07: 89 7.07 - 9.43: 37 9.43 - 11.79: 6 Bond angle restraints: 60704 Sorted by residual: angle pdb=" CA MET M 21 " pdb=" CB MET M 21 " pdb=" CG MET M 21 " ideal model delta sigma weight residual 114.10 124.92 -10.82 2.00e+00 2.50e-01 2.93e+01 angle pdb=" N MET M 21 " pdb=" CA MET M 21 " pdb=" CB MET M 21 " ideal model delta sigma weight residual 110.40 118.16 -7.76 1.63e+00 3.76e-01 2.27e+01 angle pdb=" C SER L 252 " pdb=" N GLN L 253 " pdb=" CA GLN L 253 " ideal model delta sigma weight residual 121.58 112.43 9.15 1.95e+00 2.63e-01 2.20e+01 angle pdb=" CA GLN L 253 " pdb=" CB GLN L 253 " pdb=" CG GLN L 253 " ideal model delta sigma weight residual 114.10 123.48 -9.38 2.00e+00 2.50e-01 2.20e+01 angle pdb=" CA GLN K 253 " pdb=" CB GLN K 253 " pdb=" CG GLN K 253 " ideal model delta sigma weight residual 114.10 123.46 -9.36 2.00e+00 2.50e-01 2.19e+01 ... (remaining 60699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 26415 33.37 - 66.74: 1002 66.74 - 100.11: 82 100.11 - 133.48: 0 133.48 - 166.85: 3 Dihedral angle restraints: 27502 sinusoidal: 11136 harmonic: 16366 Sorted by residual: dihedral pdb=" O5' GTP E 501 " pdb=" O3A GTP E 501 " pdb=" PA GTP E 501 " pdb=" PB GTP E 501 " ideal model delta sinusoidal sigma weight residual 274.12 107.27 166.85 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP E 501 " pdb=" C1' GTP E 501 " pdb=" N9 GTP E 501 " pdb=" O4' GTP E 501 " ideal model delta sinusoidal sigma weight residual 104.59 -59.48 164.07 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C8 GTP F 501 " pdb=" C1' GTP F 501 " pdb=" N9 GTP F 501 " pdb=" O4' GTP F 501 " ideal model delta sinusoidal sigma weight residual 104.59 -107.15 -148.26 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 27499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 5158 0.043 - 0.085: 1302 0.085 - 0.128: 564 0.128 - 0.171: 26 0.171 - 0.214: 4 Chirality restraints: 7054 Sorted by residual: chirality pdb=" CA MET M 21 " pdb=" N MET M 21 " pdb=" C MET M 21 " pdb=" CB MET M 21 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE O 140 " pdb=" CA ILE O 140 " pdb=" CG1 ILE O 140 " pdb=" CG2 ILE O 140 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CA MET J 593 " pdb=" N MET J 593 " pdb=" C MET J 593 " pdb=" CB MET J 593 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.22e-01 ... (remaining 7051 not shown) Planarity restraints: 7780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU O 448 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" CD GLU O 448 " -0.041 2.00e-02 2.50e+03 pdb=" OE1 GLU O 448 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU O 448 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 395 " -0.039 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO H 396 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO H 396 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 396 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 395 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO G 396 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " 0.033 5.00e-02 4.00e+02 ... (remaining 7777 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 19784 2.95 - 3.44: 44473 3.44 - 3.93: 74714 3.93 - 4.41: 86735 4.41 - 4.90: 140130 Nonbonded interactions: 365836 Sorted by model distance: nonbonded pdb=" O SER K 249 " pdb=" OE1 GLN K 253 " model vdw 2.463 3.040 nonbonded pdb=" N GLN C 128 " pdb=" OE1 GLN C 128 " model vdw 2.463 3.120 nonbonded pdb=" N GLN D 128 " pdb=" OE1 GLN D 128 " model vdw 2.464 3.120 nonbonded pdb=" O SER L 249 " pdb=" OE1 GLN L 253 " model vdw 2.465 3.040 nonbonded pdb=" N GLU L 243 " pdb=" OE1 GLU L 243 " model vdw 2.467 3.120 ... (remaining 365831 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } 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: 20.940 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: 0.060 Extract box with map and model: 0.930 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 40.940 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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:9.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 44850 Z= 0.145 Angle : 0.584 11.786 60704 Z= 0.299 Chirality : 0.044 0.214 7054 Planarity : 0.004 0.065 7780 Dihedral : 16.728 166.850 16894 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 2.10 % Allowed : 19.46 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.56 % 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: 0.55 (0.11), residues: 5574 helix: 1.32 (0.12), residues: 2010 sheet: -0.44 (0.19), residues: 760 loop : -0.01 (0.12), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 633 TYR 0.016 0.001 TYR I 671 PHE 0.013 0.001 PHE D 177 TRP 0.027 0.001 TRP I 628 HIS 0.011 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00334 (44850) covalent geometry : angle 0.58408 (60704) hydrogen bonds : bond 0.13494 ( 1849) hydrogen bonds : angle 5.86856 ( 5229) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 288 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 69 MET cc_start: 0.7592 (pmm) cc_final: 0.6397 (ptp) REVERT: F 71 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8829 (ptt) REVERT: F 306 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.9041 (mptt) REVERT: F 320 MET cc_start: 0.8948 (tmm) cc_final: 0.8716 (tpt) REVERT: K 18 ASP cc_start: 0.8007 (t0) cc_final: 0.7754 (t0) REVERT: K 64 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8827 (ttp-170) REVERT: K 114 HIS cc_start: 0.8673 (t70) cc_final: 0.8401 (t70) REVERT: K 276 LYS cc_start: 0.8831 (tmmt) cc_final: 0.8616 (ttpp) REVERT: I 236 ASP cc_start: 0.8133 (p0) cc_final: 0.7450 (p0) REVERT: I 508 GLU cc_start: 0.2094 (pt0) cc_final: 0.1837 (pt0) REVERT: I 547 MET cc_start: 0.6859 (tmm) cc_final: 0.6183 (tmt) REVERT: I 668 MET cc_start: 0.8360 (ppp) cc_final: 0.7850 (pmm) REVERT: O 89 TYR cc_start: 0.7072 (m-10) cc_final: 0.6163 (m-10) REVERT: D 84 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8720 (mmp-170) REVERT: D 107 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7158 (pm20) REVERT: D 166 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.9073 (ttt) REVERT: A 41 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8932 (t) REVERT: A 264 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.6055 (pm20) REVERT: M 19 ASN cc_start: 0.8973 (m-40) cc_final: 0.7935 (m-40) REVERT: N 18 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6814 (t80) REVERT: L 155 HIS cc_start: 0.7918 (t-90) cc_final: 0.7630 (t-170) REVERT: J 632 PHE cc_start: 0.8795 (m-80) cc_final: 0.8047 (m-80) REVERT: P 89 TYR cc_start: 0.7028 (m-10) cc_final: 0.6188 (m-10) REVERT: P 204 TYR cc_start: 0.8948 (t80) cc_final: 0.8601 (t80) REVERT: C 50 ARG cc_start: 0.8081 (tpp-160) cc_final: 0.7731 (tpm-80) REVERT: C 118 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7678 (pp) REVERT: B 14 MET cc_start: 0.8586 (mmm) cc_final: 0.8255 (mtp) REVERT: B 20 MET cc_start: 0.8928 (ttm) cc_final: 0.8697 (ttm) outliers start: 103 outliers final: 74 residues processed: 374 average time/residue: 0.7614 time to fit residues: 350.7944 Evaluate side-chains 357 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 273 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 306 LYS Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain K residue 64 ARG Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 292 THR Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain I residue 703 LEU Chi-restraints excluded: chain I residue 707 ILE Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 217 GLU Chi-restraints excluded: chain O residue 269 CYS Chi-restraints excluded: chain O residue 386 THR Chi-restraints excluded: chain O residue 389 ASP Chi-restraints excluded: chain O residue 413 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 470 HIS Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 234 VAL Chi-restraints excluded: chain P residue 269 CYS Chi-restraints excluded: chain P residue 413 THR Chi-restraints excluded: chain P residue 448 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 470 HIS Chi-restraints excluded: chain G residue 514 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 0.0030 chunk 497 optimal weight: 0.8980 chunk 414 optimal weight: 0.2980 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 169 GLN D 277 GLN ** L 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 169 GLN P 203 GLN C 277 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.096996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.060850 restraints weight = 99119.858| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.65 r_work: 0.2857 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.0407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 44850 Z= 0.129 Angle : 0.517 10.543 60704 Z= 0.264 Chirality : 0.043 0.180 7054 Planarity : 0.004 0.057 7780 Dihedral : 7.424 165.041 6249 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.46 % Favored : 96.43 % Rotamer: Outliers : 2.96 % Allowed : 18.05 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.56 % 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: 0.70 (0.11), residues: 5574 helix: 1.55 (0.12), residues: 2013 sheet: -0.47 (0.19), residues: 824 loop : 0.05 (0.12), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 633 TYR 0.016 0.001 TYR I 583 PHE 0.020 0.001 PHE J 685 TRP 0.015 0.001 TRP M 1 HIS 0.004 0.001 HIS B 270 Details of bonding type rmsd covalent geometry : bond 0.00295 (44850) covalent geometry : angle 0.51723 (60704) hydrogen bonds : bond 0.03954 ( 1849) hydrogen bonds : angle 4.55702 ( 5229) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 296 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 71 MET cc_start: 0.8934 (ptt) cc_final: 0.8696 (ptt) REVERT: F 320 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8714 (tpt) REVERT: F 393 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.6263 (mtp) REVERT: K 18 ASP cc_start: 0.8005 (t0) cc_final: 0.7549 (t0) REVERT: K 114 HIS cc_start: 0.8839 (t70) cc_final: 0.8566 (t70) REVERT: K 276 LYS cc_start: 0.8721 (tmmt) cc_final: 0.8465 (ttpp) REVERT: I 236 ASP cc_start: 0.7967 (p0) cc_final: 0.7251 (p0) REVERT: I 547 MET cc_start: 0.7010 (tmm) cc_final: 0.6275 (tmt) REVERT: I 668 MET cc_start: 0.8318 (ppp) cc_final: 0.7834 (pmm) REVERT: O 89 TYR cc_start: 0.6896 (m-10) cc_final: 0.5952 (m-10) REVERT: O 215 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8401 (p) REVERT: D 84 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8560 (mmp-170) REVERT: D 199 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: A 14 MET cc_start: 0.8583 (mmm) cc_final: 0.8268 (mtp) REVERT: A 41 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8698 (t) REVERT: N 18 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8027 (t80) REVERT: L 155 HIS cc_start: 0.7912 (t-90) cc_final: 0.7622 (t-170) REVERT: J 551 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8866 (pttp) REVERT: J 632 PHE cc_start: 0.8862 (m-80) cc_final: 0.8236 (m-80) REVERT: P 89 TYR cc_start: 0.6806 (m-10) cc_final: 0.5884 (m-10) REVERT: P 204 TYR cc_start: 0.9017 (t80) cc_final: 0.8577 (t80) REVERT: C 50 ARG cc_start: 0.8184 (tpp-160) cc_final: 0.7868 (tpm-80) REVERT: B 14 MET cc_start: 0.8620 (mmm) cc_final: 0.8302 (mtp) REVERT: B 117 THR cc_start: 0.9502 (OUTLIER) cc_final: 0.9300 (t) outliers start: 145 outliers final: 49 residues processed: 406 average time/residue: 0.7447 time to fit residues: 371.2815 Evaluate side-chains 327 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain I residue 703 LEU Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain O residue 353 MET Chi-restraints excluded: chain O residue 386 THR Chi-restraints excluded: chain O residue 389 ASP Chi-restraints excluded: chain O residue 413 THR Chi-restraints excluded: chain O residue 448 GLU Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain H residue 195 PHE Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 551 LYS Chi-restraints excluded: chain P residue 353 MET Chi-restraints excluded: chain P residue 413 THR Chi-restraints excluded: chain P residue 448 GLU Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain G residue 487 LEU Chi-restraints excluded: chain G residue 514 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 341 optimal weight: 5.9990 chunk 343 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 449 optimal weight: 10.0000 chunk 315 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 504 optimal weight: 4.9990 chunk 367 optimal weight: 0.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 272 GLN I 634 ASN O 169 GLN D 230 ASN H 470 HIS ** L 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 ASN J 634 ASN P 169 GLN P 203 GLN G 470 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.096453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.060249 restraints weight = 99065.185| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.64 r_work: 0.2843 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 44850 Z= 0.157 Angle : 0.528 10.914 60704 Z= 0.268 Chirality : 0.044 0.168 7054 Planarity : 0.004 0.059 7780 Dihedral : 6.840 165.596 6175 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.32 % Favored : 96.57 % Rotamer: Outliers : 3.41 % Allowed : 18.18 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.56 % 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: 0.71 (0.11), residues: 5574 helix: 1.56 (0.12), residues: 2014 sheet: -0.47 (0.19), residues: 798 loop : 0.04 (0.12), residues: 2762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 14 TYR 0.013 0.001 TYR O 102 PHE 0.016 0.001 PHE D 177 TRP 0.012 0.001 TRP I 628 HIS 0.008 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00369 (44850) covalent geometry : angle 0.52793 (60704) hydrogen bonds : bond 0.03799 ( 1849) hydrogen bonds : angle 4.36253 ( 5229) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 287 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 18 ASP cc_start: 0.8066 (t0) cc_final: 0.7647 (t0) REVERT: K 196 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7737 (tm-30) REVERT: K 276 LYS cc_start: 0.8746 (tmmt) cc_final: 0.8479 (ttpp) REVERT: I 236 ASP cc_start: 0.8005 (p0) cc_final: 0.7775 (p0) REVERT: I 324 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.8293 (pm20) REVERT: I 509 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6151 (mp0) REVERT: I 547 MET cc_start: 0.7073 (tmm) cc_final: 0.6373 (tmt) REVERT: I 668 MET cc_start: 0.8264 (ppp) cc_final: 0.7795 (pmm) REVERT: O 17 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6986 (mmm160) REVERT: O 89 TYR cc_start: 0.6784 (m-10) cc_final: 0.5913 (m-10) REVERT: O 215 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8399 (p) REVERT: D 50 ARG cc_start: 0.8240 (tpp-160) cc_final: 0.7871 (tpm-80) REVERT: D 84 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8611 (mmp-170) REVERT: D 107 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7363 (pm20) REVERT: A 14 MET cc_start: 0.8648 (mmm) cc_final: 0.8306 (mtp) REVERT: A 41 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8787 (t) REVERT: N 18 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8105 (t80) REVERT: L 155 HIS cc_start: 0.8049 (t-90) cc_final: 0.7745 (t-170) REVERT: J 324 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.8308 (pm20) REVERT: J 551 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8867 (pttp) REVERT: J 562 GLN cc_start: 0.9242 (mt0) cc_final: 0.8979 (mt0) REVERT: P 89 TYR cc_start: 0.6810 (m-10) cc_final: 0.5908 (m-10) REVERT: P 204 TYR cc_start: 0.9074 (t80) cc_final: 0.8577 (t80) REVERT: C 50 ARG cc_start: 0.8172 (tpp-160) cc_final: 0.7937 (tpm-80) REVERT: C 118 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7519 (tp) REVERT: B 14 MET cc_start: 0.8652 (mmm) cc_final: 0.8333 (mtp) outliers start: 167 outliers final: 59 residues processed: 422 average time/residue: 0.7555 time to fit residues: 392.3540 Evaluate side-chains 338 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 268 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 509 GLU Chi-restraints excluded: chain O residue 17 ARG Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain O residue 217 GLU Chi-restraints excluded: chain O residue 353 MET Chi-restraints excluded: chain O residue 386 THR Chi-restraints excluded: chain O residue 389 ASP Chi-restraints excluded: chain O residue 448 GLU Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain J residue 551 LYS Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 353 MET Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain G residue 487 LEU Chi-restraints excluded: chain G residue 514 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 409 optimal weight: 9.9990 chunk 431 optimal weight: 9.9990 chunk 394 optimal weight: 5.9990 chunk 122 optimal weight: 0.0470 chunk 482 optimal weight: 1.9990 chunk 538 optimal weight: 2.9990 chunk 452 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 428 optimal weight: 1.9990 chunk 315 optimal weight: 0.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 41 ASN ** K 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 285 ASN O 169 GLN D 277 GLN H 470 HIS ** L 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 169 GLN P 203 GLN C 277 GLN G 470 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.095869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.058892 restraints weight = 97265.928| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.61 r_work: 0.2787 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 44850 Z= 0.178 Angle : 0.540 11.318 60704 Z= 0.274 Chirality : 0.044 0.194 7054 Planarity : 0.004 0.059 7780 Dihedral : 6.569 165.704 6166 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.62 % Favored : 96.27 % Rotamer: Outliers : 3.28 % Allowed : 18.89 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.56 % 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: 0.67 (0.11), residues: 5574 helix: 1.54 (0.12), residues: 2014 sheet: -0.48 (0.19), residues: 816 loop : 0.02 (0.12), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 14 TYR 0.034 0.001 TYR J 583 PHE 0.020 0.001 PHE J 706 TRP 0.019 0.001 TRP I 628 HIS 0.007 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00419 (44850) covalent geometry : angle 0.53972 (60704) hydrogen bonds : bond 0.03783 ( 1849) hydrogen bonds : angle 4.32329 ( 5229) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 291 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 71 MET cc_start: 0.8873 (ptt) cc_final: 0.8479 (ptp) REVERT: F 320 MET cc_start: 0.8987 (tmm) cc_final: 0.8674 (tpt) REVERT: E 409 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7678 (pp) REVERT: K 18 ASP cc_start: 0.8068 (t0) cc_final: 0.7596 (t0) REVERT: K 155 HIS cc_start: 0.8377 (t-90) cc_final: 0.8135 (t-90) REVERT: K 196 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7820 (tm-30) REVERT: K 276 LYS cc_start: 0.8727 (tmmt) cc_final: 0.8464 (ttpp) REVERT: I 236 ASP cc_start: 0.7946 (p0) cc_final: 0.7737 (p0) REVERT: I 324 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: I 509 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: I 547 MET cc_start: 0.7086 (tmm) cc_final: 0.6415 (tmt) REVERT: I 668 MET cc_start: 0.8269 (ppp) cc_final: 0.7831 (pmm) REVERT: O 89 TYR cc_start: 0.6830 (m-10) cc_final: 0.5952 (m-10) REVERT: O 215 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8385 (p) REVERT: D 50 ARG cc_start: 0.8291 (tpp-160) cc_final: 0.7937 (tpm-80) REVERT: D 84 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8664 (mmp-170) REVERT: D 107 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: A 14 MET cc_start: 0.8625 (mmm) cc_final: 0.8291 (mtp) REVERT: A 41 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8772 (t) REVERT: A 264 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6584 (pm20) REVERT: M 19 ASN cc_start: 0.9327 (m-40) cc_final: 0.8887 (m-40) REVERT: N 18 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8112 (t80) REVERT: L 64 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8726 (ttp-170) REVERT: L 155 HIS cc_start: 0.8037 (t-90) cc_final: 0.7765 (t-170) REVERT: J 324 GLU cc_start: 0.9397 (OUTLIER) cc_final: 0.8314 (pm20) REVERT: J 551 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8870 (pttp) REVERT: P 89 TYR cc_start: 0.6724 (m-10) cc_final: 0.5918 (m-10) REVERT: P 96 CYS cc_start: 0.7956 (t) cc_final: 0.6720 (p) REVERT: P 204 TYR cc_start: 0.9075 (t80) cc_final: 0.8543 (t80) REVERT: C 118 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7553 (tp) REVERT: B 14 MET cc_start: 0.8631 (mmm) cc_final: 0.8316 (mtp) REVERT: B 202 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.7795 (tm-30) outliers start: 161 outliers final: 66 residues processed: 416 average time/residue: 0.6751 time to fit residues: 348.5175 Evaluate side-chains 348 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 268 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain I residue 509 GLU Chi-restraints excluded: chain I residue 596 LEU Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain O residue 217 GLU Chi-restraints excluded: chain O residue 386 THR Chi-restraints excluded: chain O residue 389 ASP Chi-restraints excluded: chain O residue 391 LYS Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain J residue 551 LYS Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 706 PHE Chi-restraints excluded: chain P residue 448 GLU Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain G residue 487 LEU Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 518 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 236 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 340 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 492 optimal weight: 3.9990 chunk 413 optimal weight: 8.9990 chunk 487 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 384 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 41 ASN ** K 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 169 GLN H 470 HIS ** L 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 169 GLN P 203 GLN G 470 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.095265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.058016 restraints weight = 96920.737| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.64 r_work: 0.2765 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 44850 Z= 0.212 Angle : 0.565 11.952 60704 Z= 0.286 Chirality : 0.045 0.180 7054 Planarity : 0.004 0.060 7780 Dihedral : 6.625 165.219 6166 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 3.47 % Allowed : 19.01 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.11), residues: 5574 helix: 1.46 (0.12), residues: 2018 sheet: -0.52 (0.19), residues: 810 loop : -0.01 (0.12), residues: 2746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 633 TYR 0.013 0.001 TYR P 102 PHE 0.020 0.001 PHE J 706 TRP 0.018 0.001 TRP I 628 HIS 0.008 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00503 (44850) covalent geometry : angle 0.56474 (60704) hydrogen bonds : bond 0.03945 ( 1849) hydrogen bonds : angle 4.35684 ( 5229) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 284 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 320 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8649 (tpt) REVERT: F 393 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.6206 (mtp) REVERT: E 409 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7588 (pp) REVERT: K 18 ASP cc_start: 0.8069 (t0) cc_final: 0.7547 (t0) REVERT: K 155 HIS cc_start: 0.8362 (t-90) cc_final: 0.8096 (t-90) REVERT: K 196 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7783 (tm-30) REVERT: K 276 LYS cc_start: 0.8717 (tmmt) cc_final: 0.8453 (ttpp) REVERT: I 324 GLU cc_start: 0.9402 (OUTLIER) cc_final: 0.8302 (pm20) REVERT: I 509 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6067 (mp0) REVERT: I 547 MET cc_start: 0.7142 (tmm) cc_final: 0.6463 (tmt) REVERT: I 668 MET cc_start: 0.8331 (ppp) cc_final: 0.7940 (pmm) REVERT: O 89 TYR cc_start: 0.6677 (m-10) cc_final: 0.5855 (m-10) REVERT: O 215 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8335 (p) REVERT: D 84 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8721 (mmp-170) REVERT: D 107 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: A 14 MET cc_start: 0.8613 (mmm) cc_final: 0.8270 (mtp) REVERT: A 41 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8724 (t) REVERT: A 264 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6539 (pm20) REVERT: H 481 SER cc_start: 0.9243 (OUTLIER) cc_final: 0.8899 (p) REVERT: N 18 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8154 (t80) REVERT: L 64 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8678 (ttp-170) REVERT: L 155 HIS cc_start: 0.8031 (t-90) cc_final: 0.7742 (t-170) REVERT: L 196 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7599 (tm-30) REVERT: J 324 GLU cc_start: 0.9414 (OUTLIER) cc_final: 0.8335 (pm20) REVERT: J 551 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8866 (pttp) REVERT: J 632 PHE cc_start: 0.8929 (m-80) cc_final: 0.8158 (m-80) REVERT: P 89 TYR cc_start: 0.6518 (m-10) cc_final: 0.5810 (m-10) REVERT: P 96 CYS cc_start: 0.7945 (t) cc_final: 0.6723 (p) REVERT: P 204 TYR cc_start: 0.9069 (t80) cc_final: 0.8573 (t80) REVERT: C 118 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7527 (tp) REVERT: C 145 GLU cc_start: 0.8236 (mp0) cc_final: 0.8009 (mm-30) REVERT: B 14 MET cc_start: 0.8604 (mmm) cc_final: 0.8265 (mtp) REVERT: B 202 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.7785 (tm-30) outliers start: 170 outliers final: 66 residues processed: 419 average time/residue: 0.5733 time to fit residues: 298.3517 Evaluate side-chains 354 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 271 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain I residue 509 GLU Chi-restraints excluded: chain I residue 596 LEU Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain O residue 217 GLU Chi-restraints excluded: chain O residue 386 THR Chi-restraints excluded: chain O residue 389 ASP Chi-restraints excluded: chain O residue 413 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain H residue 481 SER Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain L residue 7 ARG Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain J residue 551 LYS Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 706 PHE Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 212 GLN Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 518 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 412 optimal weight: 0.0000 chunk 85 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 chunk 273 optimal weight: 0.7980 chunk 435 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 301 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 169 GLN D 277 GLN H 470 HIS ** L 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 169 GLN P 203 GLN C 277 GLN G 470 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.096745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.059602 restraints weight = 96717.923| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.67 r_work: 0.2802 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 44850 Z= 0.113 Angle : 0.534 11.328 60704 Z= 0.269 Chirality : 0.043 0.183 7054 Planarity : 0.004 0.058 7780 Dihedral : 6.533 163.257 6166 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.38 % Rotamer: Outliers : 2.92 % Allowed : 19.85 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.56 % 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: 0.68 (0.11), residues: 5574 helix: 1.56 (0.12), residues: 2028 sheet: -0.43 (0.18), residues: 868 loop : 0.00 (0.12), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 633 TYR 0.020 0.001 TYR B 83 PHE 0.021 0.001 PHE J 706 TRP 0.021 0.001 TRP J 628 HIS 0.008 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00258 (44850) covalent geometry : angle 0.53426 (60704) hydrogen bonds : bond 0.03384 ( 1849) hydrogen bonds : angle 4.23266 ( 5229) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 295 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 69 MET cc_start: 0.7568 (pmm) cc_final: 0.6547 (ptp) REVERT: F 320 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8644 (tpt) REVERT: E 409 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7642 (pp) REVERT: K 18 ASP cc_start: 0.8111 (t0) cc_final: 0.7667 (t0) REVERT: K 155 HIS cc_start: 0.8350 (t-90) cc_final: 0.8055 (t-90) REVERT: K 196 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7820 (tm-30) REVERT: K 276 LYS cc_start: 0.8748 (tmmt) cc_final: 0.8499 (ttpp) REVERT: I 509 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: I 547 MET cc_start: 0.7075 (tmm) cc_final: 0.6456 (tmt) REVERT: I 668 MET cc_start: 0.8410 (ppp) cc_final: 0.8185 (pmm) REVERT: O 89 TYR cc_start: 0.6723 (m-10) cc_final: 0.5967 (m-10) REVERT: O 215 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8343 (p) REVERT: D 84 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8659 (mmp-170) REVERT: D 199 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8504 (mt0) REVERT: A 14 MET cc_start: 0.8659 (mmm) cc_final: 0.8316 (mtp) REVERT: A 41 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8715 (t) REVERT: A 95 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8395 (mp0) REVERT: A 202 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: A 264 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: N 18 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8150 (t80) REVERT: N 20 ILE cc_start: 0.9481 (mm) cc_final: 0.9216 (mm) REVERT: L 64 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8747 (ttp-170) REVERT: L 155 HIS cc_start: 0.8029 (t-90) cc_final: 0.7743 (t-170) REVERT: L 196 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7647 (tm-30) REVERT: L 276 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8267 (pptt) REVERT: J 280 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: J 632 PHE cc_start: 0.8867 (m-80) cc_final: 0.8154 (m-80) REVERT: P 89 TYR cc_start: 0.6539 (m-10) cc_final: 0.5848 (m-10) REVERT: P 96 CYS cc_start: 0.7958 (t) cc_final: 0.6725 (p) REVERT: P 204 TYR cc_start: 0.9075 (t80) cc_final: 0.8585 (t80) REVERT: C 50 ARG cc_start: 0.8202 (tpp-160) cc_final: 0.7812 (tpm-80) REVERT: C 118 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7539 (tp) REVERT: C 145 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: B 14 MET cc_start: 0.8647 (mmm) cc_final: 0.8334 (mtp) REVERT: B 95 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: G 481 SER cc_start: 0.9214 (OUTLIER) cc_final: 0.8956 (p) outliers start: 143 outliers final: 59 residues processed: 405 average time/residue: 0.5877 time to fit residues: 294.7959 Evaluate side-chains 347 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 270 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 509 GLU Chi-restraints excluded: chain I residue 596 LEU Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain O residue 217 GLU Chi-restraints excluded: chain O residue 386 THR Chi-restraints excluded: chain O residue 389 ASP Chi-restraints excluded: chain O residue 391 LYS Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 276 LYS Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 280 GLU Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 706 PHE Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 448 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 481 SER Chi-restraints excluded: chain G residue 514 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 199 optimal weight: 8.9990 chunk 281 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 315 optimal weight: 0.7980 chunk 360 optimal weight: 0.0870 chunk 291 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 145 optimal weight: 0.0570 chunk 63 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 169 GLN A 43 GLN H 470 HIS ** L 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 169 GLN P 203 GLN G 470 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.097177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.060158 restraints weight = 96320.117| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.66 r_work: 0.2817 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 44850 Z= 0.107 Angle : 0.541 11.068 60704 Z= 0.272 Chirality : 0.043 0.226 7054 Planarity : 0.004 0.058 7780 Dihedral : 6.441 161.949 6164 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 2.77 % Allowed : 20.30 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.56 % 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: 0.76 (0.11), residues: 5574 helix: 1.65 (0.12), residues: 2026 sheet: -0.36 (0.18), residues: 844 loop : 0.01 (0.12), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 633 TYR 0.021 0.001 TYR B 83 PHE 0.025 0.001 PHE I 653 TRP 0.021 0.001 TRP J 628 HIS 0.008 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00243 (44850) covalent geometry : angle 0.54061 (60704) hydrogen bonds : bond 0.03263 ( 1849) hydrogen bonds : angle 4.17578 ( 5229) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 283 time to evaluate : 1.078 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: F 71 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8441 (ptp) REVERT: F 320 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8653 (tpt) REVERT: E 409 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7532 (pp) REVERT: K 18 ASP cc_start: 0.8092 (t0) cc_final: 0.7660 (OUTLIER) REVERT: K 155 HIS cc_start: 0.8358 (t-90) cc_final: 0.8053 (t-90) REVERT: K 196 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7825 (tm-30) REVERT: K 276 LYS cc_start: 0.8720 (tmmt) cc_final: 0.8463 (ttpp) REVERT: I 236 ASP cc_start: 0.7904 (p0) cc_final: 0.7039 (p0) REVERT: I 509 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6223 (mp0) REVERT: I 547 MET cc_start: 0.7062 (tmm) cc_final: 0.6469 (tmt) REVERT: I 563 ARG cc_start: 0.7715 (ptt-90) cc_final: 0.7054 (ptt-90) REVERT: O 27 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8924 (tmmt) REVERT: O 89 TYR cc_start: 0.6713 (m-10) cc_final: 0.5925 (m-10) REVERT: O 204 TYR cc_start: 0.9168 (t80) cc_final: 0.8844 (t80) REVERT: O 215 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8349 (p) REVERT: D 50 ARG cc_start: 0.8241 (tpp-160) cc_final: 0.7841 (tpm-80) REVERT: D 84 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8678 (mmp-170) REVERT: D 199 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8468 (mt0) REVERT: A 14 MET cc_start: 0.8665 (mmm) cc_final: 0.8329 (mtp) REVERT: A 41 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8694 (t) REVERT: A 43 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: A 95 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: A 264 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: N 18 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8232 (t80) REVERT: L 64 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8733 (ttp-170) REVERT: L 155 HIS cc_start: 0.8031 (t-90) cc_final: 0.7769 (t70) REVERT: L 196 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7667 (tm-30) REVERT: L 276 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8246 (pptt) REVERT: J 632 PHE cc_start: 0.8817 (m-80) cc_final: 0.8120 (m-80) REVERT: P 89 TYR cc_start: 0.6534 (m-10) cc_final: 0.5824 (m-10) REVERT: P 96 CYS cc_start: 0.7965 (t) cc_final: 0.6734 (p) REVERT: P 126 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7448 (tp) REVERT: P 204 TYR cc_start: 0.9078 (t80) cc_final: 0.8637 (t80) REVERT: C 50 ARG cc_start: 0.8226 (tpp-160) cc_final: 0.7869 (tpm-80) REVERT: C 118 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7534 (tp) REVERT: C 145 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: B 14 MET cc_start: 0.8653 (mmm) cc_final: 0.8337 (mtp) REVERT: B 95 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: G 481 SER cc_start: 0.9196 (OUTLIER) cc_final: 0.8941 (p) outliers start: 136 outliers final: 65 residues processed: 392 average time/residue: 0.4561 time to fit residues: 223.4827 Evaluate side-chains 358 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 274 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain I residue 509 GLU Chi-restraints excluded: chain I residue 596 LEU Chi-restraints excluded: chain O residue 27 LYS Chi-restraints excluded: chain O residue 169 GLN Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain O residue 217 GLU Chi-restraints excluded: chain O residue 353 MET Chi-restraints excluded: chain O residue 386 THR Chi-restraints excluded: chain O residue 389 ASP Chi-restraints excluded: chain O residue 391 LYS Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 276 LYS Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 353 MET Chi-restraints excluded: chain P residue 448 GLU Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 481 SER Chi-restraints excluded: chain G residue 514 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 495 optimal weight: 0.8980 chunk 289 optimal weight: 0.7980 chunk 487 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 chunk 401 optimal weight: 5.9990 chunk 486 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 186 optimal weight: 0.0980 chunk 484 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 236 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 169 GLN D 277 GLN A 43 GLN H 470 HIS ** L 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 169 GLN P 203 GLN P 407 ASN C 277 GLN G 470 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.097163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.060035 restraints weight = 96943.276| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.67 r_work: 0.2813 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44850 Z= 0.118 Angle : 0.548 11.133 60704 Z= 0.276 Chirality : 0.043 0.225 7054 Planarity : 0.004 0.062 7780 Dihedral : 6.392 161.057 6164 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 2.59 % Allowed : 20.58 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.56 % 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: 0.77 (0.11), residues: 5574 helix: 1.66 (0.12), residues: 2024 sheet: -0.40 (0.18), residues: 854 loop : 0.04 (0.12), residues: 2696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 14 TYR 0.020 0.001 TYR I 583 PHE 0.026 0.001 PHE I 653 TRP 0.024 0.001 TRP J 628 HIS 0.008 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00274 (44850) covalent geometry : angle 0.54760 (60704) hydrogen bonds : bond 0.03295 ( 1849) hydrogen bonds : angle 4.17498 ( 5229) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 279 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 69 MET cc_start: 0.7547 (pmm) cc_final: 0.6473 (ptp) REVERT: E 409 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7612 (pp) REVERT: K 18 ASP cc_start: 0.8104 (t0) cc_final: 0.7671 (OUTLIER) REVERT: K 155 HIS cc_start: 0.8368 (t-90) cc_final: 0.8060 (t-90) REVERT: K 196 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7886 (tm-30) REVERT: K 276 LYS cc_start: 0.8720 (tmmt) cc_final: 0.8464 (ttpp) REVERT: I 236 ASP cc_start: 0.7873 (p0) cc_final: 0.7024 (p0) REVERT: I 324 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.8239 (pm20) REVERT: I 509 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6238 (mp0) REVERT: I 547 MET cc_start: 0.7075 (tmm) cc_final: 0.6483 (tmt) REVERT: I 668 MET cc_start: 0.8410 (ppp) cc_final: 0.8131 (pmm) REVERT: O 27 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8919 (tmmt) REVERT: O 89 TYR cc_start: 0.6730 (m-10) cc_final: 0.5943 (m-10) REVERT: O 204 TYR cc_start: 0.9177 (t80) cc_final: 0.8849 (t80) REVERT: O 215 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8341 (p) REVERT: D 50 ARG cc_start: 0.8247 (tpp-160) cc_final: 0.7861 (tpm-80) REVERT: D 84 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8677 (mmp-170) REVERT: A 14 MET cc_start: 0.8675 (mmm) cc_final: 0.8336 (mtp) REVERT: A 41 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8807 (t) REVERT: A 95 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: A 202 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: A 264 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6611 (pm20) REVERT: N 18 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8234 (t80) REVERT: L 64 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8707 (ttp-170) REVERT: L 155 HIS cc_start: 0.8030 (t-90) cc_final: 0.7773 (t70) REVERT: L 196 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7709 (tm-30) REVERT: L 276 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8280 (pptt) REVERT: J 324 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.8250 (pm20) REVERT: J 632 PHE cc_start: 0.8829 (m-80) cc_final: 0.8167 (m-80) REVERT: P 89 TYR cc_start: 0.6539 (m-10) cc_final: 0.5846 (m-10) REVERT: P 96 CYS cc_start: 0.7983 (t) cc_final: 0.6769 (p) REVERT: P 126 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7457 (tp) REVERT: P 204 TYR cc_start: 0.9090 (t80) cc_final: 0.8643 (t80) REVERT: C 50 ARG cc_start: 0.8214 (tpp-160) cc_final: 0.7873 (tpm-80) REVERT: C 118 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7471 (tp) REVERT: C 145 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8004 (mm-30) REVERT: B 14 MET cc_start: 0.8651 (mmm) cc_final: 0.8314 (mtp) REVERT: B 95 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: G 481 SER cc_start: 0.9200 (OUTLIER) cc_final: 0.8944 (p) outliers start: 127 outliers final: 71 residues processed: 380 average time/residue: 0.4767 time to fit residues: 225.9429 Evaluate side-chains 360 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 271 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 509 GLU Chi-restraints excluded: chain I residue 596 LEU Chi-restraints excluded: chain O residue 27 LYS Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain O residue 217 GLU Chi-restraints excluded: chain O residue 353 MET Chi-restraints excluded: chain O residue 386 THR Chi-restraints excluded: chain O residue 389 ASP Chi-restraints excluded: chain O residue 391 LYS Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 276 LYS Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain J residue 504 MET Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 169 GLN Chi-restraints excluded: chain P residue 353 MET Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 470 HIS Chi-restraints excluded: chain G residue 481 SER Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 518 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 532 optimal weight: 0.6980 chunk 357 optimal weight: 0.0870 chunk 546 optimal weight: 2.9990 chunk 172 optimal weight: 0.0010 chunk 443 optimal weight: 4.9990 chunk 542 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 176 optimal weight: 5.9990 chunk 446 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 0.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 169 GLN H 470 HIS ** L 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 503 ASN ** J 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 169 GLN P 203 GLN P 407 ASN G 470 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.097494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.060422 restraints weight = 96396.704| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.67 r_work: 0.2824 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 44850 Z= 0.109 Angle : 0.552 11.116 60704 Z= 0.277 Chirality : 0.043 0.217 7054 Planarity : 0.004 0.064 7780 Dihedral : 6.344 160.158 6164 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.30 % Favored : 96.59 % Rotamer: Outliers : 2.37 % Allowed : 20.69 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.56 % 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: 0.79 (0.11), residues: 5574 helix: 1.67 (0.12), residues: 2026 sheet: -0.36 (0.18), residues: 844 loop : 0.03 (0.12), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 633 TYR 0.020 0.001 TYR B 83 PHE 0.022 0.001 PHE I 653 TRP 0.042 0.001 TRP I 628 HIS 0.013 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00251 (44850) covalent geometry : angle 0.55192 (60704) hydrogen bonds : bond 0.03208 ( 1849) hydrogen bonds : angle 4.16713 ( 5229) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 281 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 69 MET cc_start: 0.7462 (pmm) cc_final: 0.6411 (ptp) REVERT: E 409 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7668 (pp) REVERT: K 18 ASP cc_start: 0.8009 (t0) cc_final: 0.7584 (OUTLIER) REVERT: K 155 HIS cc_start: 0.8339 (t-90) cc_final: 0.8026 (t-90) REVERT: K 196 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7849 (tm-30) REVERT: K 276 LYS cc_start: 0.8676 (tmmt) cc_final: 0.8415 (ttpp) REVERT: I 236 ASP cc_start: 0.7886 (p0) cc_final: 0.7029 (p0) REVERT: I 509 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6247 (mp0) REVERT: I 547 MET cc_start: 0.7019 (tmm) cc_final: 0.6424 (tmt) REVERT: I 583 TYR cc_start: 0.8343 (m-80) cc_final: 0.8076 (m-80) REVERT: I 668 MET cc_start: 0.8401 (ppp) cc_final: 0.8133 (pmm) REVERT: O 89 TYR cc_start: 0.6698 (m-10) cc_final: 0.5911 (m-10) REVERT: O 204 TYR cc_start: 0.9169 (t80) cc_final: 0.8860 (t80) REVERT: O 215 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8326 (p) REVERT: D 50 ARG cc_start: 0.8262 (tpp-160) cc_final: 0.7864 (tpm-80) REVERT: D 84 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8606 (mmp-170) REVERT: D 172 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7698 (mpp-170) REVERT: D 199 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8355 (mt0) REVERT: A 14 MET cc_start: 0.8647 (mmm) cc_final: 0.8301 (mtp) REVERT: A 41 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8661 (t) REVERT: A 95 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: A 202 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: A 264 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6654 (pm20) REVERT: N 18 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8315 (t80) REVERT: L 64 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8707 (ttp-170) REVERT: L 155 HIS cc_start: 0.7992 (t-90) cc_final: 0.7741 (t70) REVERT: L 276 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8242 (pptt) REVERT: P 89 TYR cc_start: 0.6494 (m-10) cc_final: 0.5779 (m-10) REVERT: P 96 CYS cc_start: 0.8000 (t) cc_final: 0.6765 (p) REVERT: P 126 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7344 (tp) REVERT: P 204 TYR cc_start: 0.9093 (t80) cc_final: 0.8657 (t80) REVERT: C 50 ARG cc_start: 0.8227 (tpp-160) cc_final: 0.7912 (tpm-80) REVERT: C 118 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7477 (tp) REVERT: C 145 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7955 (mm-30) REVERT: C 172 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7705 (mpp-170) REVERT: B 14 MET cc_start: 0.8618 (mmm) cc_final: 0.8283 (mtp) REVERT: B 95 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: G 481 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8870 (p) outliers start: 116 outliers final: 68 residues processed: 376 average time/residue: 0.4601 time to fit residues: 215.6235 Evaluate side-chains 359 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 273 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 509 GLU Chi-restraints excluded: chain I residue 558 LEU Chi-restraints excluded: chain I residue 596 LEU Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain O residue 217 GLU Chi-restraints excluded: chain O residue 353 MET Chi-restraints excluded: chain O residue 386 THR Chi-restraints excluded: chain O residue 389 ASP Chi-restraints excluded: chain O residue 391 LYS Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 470 HIS Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 276 LYS Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 169 GLN Chi-restraints excluded: chain P residue 353 MET Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 481 SER Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 518 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 95 optimal weight: 0.9990 chunk 237 optimal weight: 0.6980 chunk 286 optimal weight: 2.9990 chunk 376 optimal weight: 0.0970 chunk 312 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 429 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 462 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 169 GLN D 277 GLN H 470 HIS ** L 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 169 GLN P 203 GLN P 407 ASN C 277 GLN G 470 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.096898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.059759 restraints weight = 96757.440| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.67 r_work: 0.2807 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 44850 Z= 0.140 Angle : 0.571 12.692 60704 Z= 0.286 Chirality : 0.044 0.336 7054 Planarity : 0.004 0.066 7780 Dihedral : 6.338 159.811 6164 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.46 % Favored : 96.43 % Rotamer: Outliers : 2.16 % Allowed : 21.03 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.56 % 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: 0.77 (0.11), residues: 5574 helix: 1.66 (0.12), residues: 2020 sheet: -0.39 (0.18), residues: 850 loop : 0.03 (0.12), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 633 TYR 0.022 0.001 TYR B 83 PHE 0.020 0.001 PHE I 653 TRP 0.034 0.001 TRP I 628 HIS 0.012 0.001 HIS H 470 Details of bonding type rmsd covalent geometry : bond 0.00331 (44850) covalent geometry : angle 0.57093 (60704) hydrogen bonds : bond 0.03364 ( 1849) hydrogen bonds : angle 4.19242 ( 5229) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 285 time to evaluate : 1.055 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: E 409 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7743 (pp) REVERT: K 18 ASP cc_start: 0.8098 (t0) cc_final: 0.7674 (OUTLIER) REVERT: K 155 HIS cc_start: 0.8366 (t-90) cc_final: 0.8048 (t-90) REVERT: K 196 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7915 (tm-30) REVERT: K 276 LYS cc_start: 0.8729 (tmmt) cc_final: 0.8469 (ttpp) REVERT: I 236 ASP cc_start: 0.7846 (p0) cc_final: 0.6999 (p0) REVERT: I 504 MET cc_start: 0.6200 (tpt) cc_final: 0.5631 (tpp) REVERT: I 508 GLU cc_start: 0.2180 (pt0) cc_final: 0.1813 (pt0) REVERT: I 509 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6296 (mp0) REVERT: I 547 MET cc_start: 0.6947 (tmm) cc_final: 0.6338 (tmt) REVERT: I 583 TYR cc_start: 0.8390 (m-80) cc_final: 0.8099 (m-80) REVERT: I 668 MET cc_start: 0.8409 (ppp) cc_final: 0.8141 (pmm) REVERT: O 89 TYR cc_start: 0.6742 (m-10) cc_final: 0.5946 (m-10) REVERT: O 204 TYR cc_start: 0.9174 (t80) cc_final: 0.8853 (t80) REVERT: O 215 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8349 (p) REVERT: D 50 ARG cc_start: 0.8256 (tpp-160) cc_final: 0.7893 (tpm-80) REVERT: D 84 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8671 (mmp-170) REVERT: A 14 MET cc_start: 0.8689 (mmm) cc_final: 0.8352 (mtp) REVERT: A 41 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8663 (t) REVERT: A 202 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: A 264 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6616 (pm20) REVERT: N 18 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8314 (t80) REVERT: L 64 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8719 (ttp-170) REVERT: L 155 HIS cc_start: 0.8021 (t-90) cc_final: 0.7769 (t-170) REVERT: L 276 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8289 (pptt) REVERT: J 583 TYR cc_start: 0.8406 (m-80) cc_final: 0.8091 (m-80) REVERT: J 632 PHE cc_start: 0.8865 (m-80) cc_final: 0.8131 (m-80) REVERT: P 89 TYR cc_start: 0.6535 (m-10) cc_final: 0.5815 (m-10) REVERT: P 126 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7333 (tp) REVERT: P 204 TYR cc_start: 0.9105 (t80) cc_final: 0.8598 (t80) REVERT: C 50 ARG cc_start: 0.8222 (tpp-160) cc_final: 0.7958 (tpm-80) REVERT: C 118 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7492 (tp) REVERT: C 145 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8012 (mm-30) REVERT: B 14 MET cc_start: 0.8663 (mmm) cc_final: 0.8318 (mtp) REVERT: B 95 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: G 481 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8947 (p) outliers start: 106 outliers final: 68 residues processed: 369 average time/residue: 0.4535 time to fit residues: 208.8028 Evaluate side-chains 355 residues out of total 4904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 273 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 509 GLU Chi-restraints excluded: chain I residue 596 LEU Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain O residue 217 GLU Chi-restraints excluded: chain O residue 386 THR Chi-restraints excluded: chain O residue 389 ASP Chi-restraints excluded: chain O residue 391 LYS Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 276 LYS Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 470 HIS Chi-restraints excluded: chain G residue 481 SER Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 518 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 229 optimal weight: 0.3980 chunk 141 optimal weight: 0.2980 chunk 348 optimal weight: 0.9980 chunk 272 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 468 optimal weight: 0.0470 chunk 446 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 342 optimal weight: 0.8980 chunk 323 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 285 ASN ** I 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 169 GLN H 470 HIS ** L 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 272 GLN P 169 GLN P 203 GLN P 407 ASN G 470 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.097592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.060581 restraints weight = 96716.662| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.67 r_work: 0.2828 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 44850 Z= 0.108 Angle : 0.570 14.346 60704 Z= 0.284 Chirality : 0.043 0.212 7054 Planarity : 0.004 0.063 7780 Dihedral : 6.284 158.820 6164 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.35 % Favored : 96.54 % Rotamer: Outliers : 2.06 % Allowed : 21.13 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.56 % 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: 0.80 (0.11), residues: 5574 helix: 1.69 (0.12), residues: 2021 sheet: -0.35 (0.18), residues: 840 loop : 0.04 (0.12), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 633 TYR 0.022 0.001 TYR B 83 PHE 0.019 0.001 PHE I 653 TRP 0.033 0.001 TRP I 628 HIS 0.011 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00248 (44850) covalent geometry : angle 0.56993 (60704) hydrogen bonds : bond 0.03202 ( 1849) hydrogen bonds : angle 4.15597 ( 5229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16106.79 seconds wall clock time: 274 minutes 4.12 seconds (16444.12 seconds total)