Starting phenix.real_space_refine on Fri Mar 6 22:51:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nyu_12654/03_2026/7nyu_12654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nyu_12654/03_2026/7nyu_12654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nyu_12654/03_2026/7nyu_12654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nyu_12654/03_2026/7nyu_12654.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nyu_12654/03_2026/7nyu_12654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nyu_12654/03_2026/7nyu_12654.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.000 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 1 5.49 5 S 243 5.16 5 C 22719 2.51 5 N 5962 2.21 5 O 6270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35228 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 668 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1222 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 148} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 4725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4725 Classifications: {'peptide': 588} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 551} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3424 Classifications: {'peptide': 441} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 415} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 7044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 907, 7044 Classifications: {'peptide': 907} Link IDs: {'PTRANS': 41, 'TRANS': 865} Chain: "H" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1985 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 13, 'TRANS': 256} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TRP:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "I" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1220 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 144} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "J" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "L" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4126 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 18, 'TRANS': 593} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 777 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'HIS:plan': 8, 'GLU:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 5, 'PHE:plan': 11, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 3, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 268 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 21, 'TRANS': 482} Chain: "N" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3543 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 19, 'TRANS': 447} Chain breaks: 2 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1478 SG CYS B 158 178.846 106.982 66.831 1.00 55.34 S ATOM 849 SG CYS B 64 176.794 100.819 66.746 1.00 76.96 S ATOM 843 SG CYS B 63 173.647 103.866 63.422 1.00 85.99 S ATOM 1261 SG CYS B 129 173.764 106.920 68.492 1.00 61.52 S ATOM 7262 SG CYS E 92 223.218 165.181 64.042 1.00 51.70 S ATOM 7296 SG CYS E 97 225.783 165.122 62.378 1.00 52.28 S ATOM 7575 SG CYS E 133 219.999 168.265 62.280 1.00 52.38 S ATOM 7601 SG CYS E 137 221.711 169.036 60.577 1.00 58.19 S ATOM 10602 SG CYS F 357 203.759 158.585 62.650 1.00 43.95 S ATOM 10582 SG CYS F 354 199.126 158.487 63.464 1.00 58.94 S ATOM 10923 SG CYS F 398 201.561 163.884 62.380 1.00 55.89 S ATOM 10558 SG CYS F 351 201.874 161.611 67.783 1.00 42.95 S ATOM 11517 SG CYS G 34 188.365 156.183 66.734 1.00 61.68 S ATOM 11619 SG CYS G 48 186.534 155.642 62.509 1.00 60.11 S ATOM 11768 SG CYS G 67 186.366 158.000 64.685 1.00 51.83 S ATOM 11517 SG CYS G 34 188.365 156.183 66.734 1.00 61.68 S ATOM 11593 SG CYS G 45 190.071 153.438 65.721 1.00 52.73 S ATOM 12499 SG CYS G 157 193.913 153.193 79.122 1.00 62.67 S ATOM 12451 SG CYS G 151 197.426 149.653 75.374 1.00 43.68 S ATOM 12470 SG CYS G 154 191.585 151.346 73.586 1.00 47.53 S ATOM 12847 SG CYS G 201 191.873 147.151 77.719 1.00 52.17 S ATOM 12076 SG CYS G 106 192.914 138.097 77.156 1.00 47.70 S ATOM 12056 SG CYS G 103 194.074 135.673 71.359 1.00 55.35 S ATOM 12116 SG CYS G 112 190.171 140.631 72.748 1.00 52.04 S ATOM 13072 SG CYS G 228 173.876 147.447 93.163 1.00 52.88 S ATOM 13096 SG CYS G 231 173.284 151.589 95.206 1.00 46.39 S ATOM 13120 SG CYS G 235 173.805 150.859 90.135 1.00 40.39 S ATOM 13072 SG CYS G 228 173.876 147.447 93.163 1.00 52.88 S ATOM 13120 SG CYS G 235 173.805 150.859 90.135 1.00 40.39 S ATOM 13357 SG CYS G 263 178.125 151.010 92.504 1.00 37.17 S ATOM 20945 SG CYS I 109 194.239 121.443 73.280 1.00 49.73 S ATOM 20568 SG CYS I 60 193.443 121.524 79.854 1.00 51.19 S ATOM 20608 SG CYS I 66 188.536 120.586 76.316 1.00 62.78 S ATOM 20586 SG CYS I 63 191.458 125.864 75.278 1.00 52.06 S ATOM 20631 SG CYS I 70 181.725 116.609 72.890 1.00 64.48 S ATOM 20898 SG CYS I 102 183.550 114.722 67.973 1.00 55.99 S ATOM 20873 SG CYS I 99 184.134 110.475 73.128 1.00 45.52 S ATOM 20916 SG CYS I 105 187.926 115.648 71.434 1.00 52.41 S Time building chain proxies: 7.24, per 1000 atoms: 0.21 Number of scatterers: 35228 At special positions: 0 Unit cell: (252.888, 214.338, 138.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 243 16.00 P 1 15.00 O 6270 8.00 N 5962 7.00 C 22719 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: 2.89 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1001 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 45 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 34 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 67 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 48 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 502 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 351 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 357 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 354 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 154 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 157 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 201 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 151 " pdb=" SF4 G1003 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 103 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 106 " pdb="FE3 SF4 G1003 " - pdb=" NE2 HIS G 99 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 112 " pdb=" SF4 G1004 " pdb="FE4 SF4 G1004 " - pdb=" SG CYS G 263 " pdb="FE3 SF4 G1004 " - pdb=" SG CYS G 235 " pdb="FE1 SF4 G1004 " - pdb=" SG CYS G 228 " pdb="FE1 SF4 G1004 " - pdb=" SG CYS G 231 " pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 63 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 66 " pdb=" SF4 I 202 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 102 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 99 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 105 " Number of angles added : 95 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8440 Finding SS restraints... Secondary structure from input PDB file: 206 helices and 26 sheets defined 60.5% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 Processing helix chain 'A' and resid 69 through 89 removed outlier: 3.695A pdb=" N VAL A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 120 Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 64 through 76 removed outlier: 3.879A pdb=" N MET B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 117 removed outlier: 3.561A pdb=" N ILE B 110 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.645A pdb=" N LYS B 147 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 148 " --> pdb=" O VAL B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 148' Processing helix chain 'B' and resid 161 through 177 Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.601A pdb=" N LYS B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 removed outlier: 3.604A pdb=" N ALA B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 30 removed outlier: 3.587A pdb=" N GLY D 23 " --> pdb=" O ASP D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 129 through 141 removed outlier: 4.333A pdb=" N TYR D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.609A pdb=" N LYS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN D 186 " --> pdb=" O THR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 257 removed outlier: 3.805A pdb=" N GLU D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 269 removed outlier: 3.557A pdb=" N THR D 268 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP D 269 " --> pdb=" O ILE D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 264 through 269' Processing helix chain 'D' and resid 276 through 292 removed outlier: 3.610A pdb=" N GLU D 280 " --> pdb=" O GLY D 276 " (cutoff:3.500A) Proline residue: D 282 - end of helix Processing helix chain 'D' and resid 296 through 326 Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 333 through 350 removed outlier: 3.887A pdb=" N THR D 337 " --> pdb=" O PHE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 396 removed outlier: 3.784A pdb=" N LEU D 375 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Proline residue: D 384 - end of helix Processing helix chain 'D' and resid 398 through 404 Processing helix chain 'D' and resid 411 through 418 Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 433 through 438 Processing helix chain 'D' and resid 442 through 446 removed outlier: 3.668A pdb=" N ASN D 445 " --> pdb=" O GLY D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 483 Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 507 through 520 Processing helix chain 'D' and resid 559 through 572 removed outlier: 4.285A pdb=" N ALA D 563 " --> pdb=" O THR D 559 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 568 " --> pdb=" O HIS D 564 " (cutoff:3.500A) Proline residue: D 569 - end of helix Processing helix chain 'D' and resid 576 through 587 Processing helix chain 'D' and resid 590 through 596 Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 27 through 29 No H-bonds generated for 'chain 'E' and resid 27 through 29' Processing helix chain 'E' and resid 31 through 34 Processing helix chain 'E' and resid 35 through 48 Processing helix chain 'E' and resid 51 through 63 removed outlier: 3.879A pdb=" N ILE E 55 " --> pdb=" O PRO E 51 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 removed outlier: 3.630A pdb=" N VAL E 69 " --> pdb=" O PRO E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 101 Processing helix chain 'E' and resid 101 through 114 removed outlier: 4.118A pdb=" N ILE E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'E' and resid 157 through 166 removed outlier: 3.732A pdb=" N TYR E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 32 Processing helix chain 'F' and resid 35 through 45 Processing helix chain 'F' and resid 46 through 58 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 99 through 108 removed outlier: 4.205A pdb=" N LEU F 103 " --> pdb=" O TYR F 99 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.836A pdb=" N LEU F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 151 removed outlier: 3.536A pdb=" N ALA F 140 " --> pdb=" O TYR F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 177 through 181 Processing helix chain 'F' and resid 182 through 191 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 219 through 232 removed outlier: 3.836A pdb=" N VAL F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 232 through 238 removed outlier: 4.000A pdb=" N ASN F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 276 removed outlier: 3.685A pdb=" N ILE F 273 " --> pdb=" O THR F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 310 through 316 Processing helix chain 'F' and resid 334 through 349 Processing helix chain 'F' and resid 354 through 374 removed outlier: 3.816A pdb=" N LEU F 361 " --> pdb=" O CYS F 357 " (cutoff:3.500A) Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 379 through 391 Processing helix chain 'F' and resid 399 through 415 removed outlier: 3.582A pdb=" N GLY F 403 " --> pdb=" O ALA F 399 " (cutoff:3.500A) Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.823A pdb=" N PHE F 419 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 26 Processing helix chain 'G' and resid 81 through 97 Processing helix chain 'G' and resid 102 through 106 Processing helix chain 'G' and resid 112 through 122 Processing helix chain 'G' and resid 148 through 151 Processing helix chain 'G' and resid 155 through 162 Processing helix chain 'G' and resid 175 through 179 removed outlier: 3.977A pdb=" N VAL G 179 " --> pdb=" O HIS G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 201 Processing helix chain 'G' and resid 209 through 214 removed outlier: 4.410A pdb=" N ARG G 214 " --> pdb=" O THR G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 221 Processing helix chain 'G' and resid 263 through 269 Processing helix chain 'G' and resid 270 through 275 removed outlier: 3.621A pdb=" N LEU G 275 " --> pdb=" O TYR G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 309 Processing helix chain 'G' and resid 321 through 333 Processing helix chain 'G' and resid 342 through 359 Processing helix chain 'G' and resid 367 through 372 Processing helix chain 'G' and resid 386 through 398 removed outlier: 3.581A pdb=" N ALA G 390 " --> pdb=" O GLY G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 408 Processing helix chain 'G' and resid 414 through 423 removed outlier: 3.644A pdb=" N GLN G 423 " --> pdb=" O LEU G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 466 Processing helix chain 'G' and resid 476 through 492 Processing helix chain 'G' and resid 503 through 505 No H-bonds generated for 'chain 'G' and resid 503 through 505' Processing helix chain 'G' and resid 506 through 523 removed outlier: 3.892A pdb=" N ILE G 510 " --> pdb=" O SER G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 545 Processing helix chain 'G' and resid 548 through 558 Processing helix chain 'G' and resid 576 through 587 Processing helix chain 'G' and resid 598 through 602 removed outlier: 3.658A pdb=" N GLU G 602 " --> pdb=" O ALA G 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 612 through 616 Processing helix chain 'G' and resid 647 through 662 Processing helix chain 'G' and resid 668 through 680 removed outlier: 3.719A pdb=" N VAL G 672 " --> pdb=" O GLN G 668 " (cutoff:3.500A) Processing helix chain 'G' and resid 681 through 689 removed outlier: 5.104A pdb=" N GLY G 685 " --> pdb=" O GLU G 682 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE G 686 " --> pdb=" O LEU G 683 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS G 687 " --> pdb=" O ALA G 684 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 769 removed outlier: 3.731A pdb=" N GLN G 769 " --> pdb=" O ASN G 766 " (cutoff:3.500A) Processing helix chain 'G' and resid 824 through 832 Proline residue: G 829 - end of helix Processing helix chain 'G' and resid 843 through 851 Processing helix chain 'G' and resid 892 through 896 Processing helix chain 'H' and resid 56 through 68 removed outlier: 4.309A pdb=" N LEU H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 97 Proline residue: H 87 - end of helix removed outlier: 3.640A pdb=" N ALA H 90 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER H 93 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 101 removed outlier: 3.764A pdb=" N VAL H 101 " --> pdb=" O PHE H 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 98 through 101' Processing helix chain 'H' and resid 115 through 138 removed outlier: 4.409A pdb=" N VAL H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 157 Processing helix chain 'H' and resid 158 through 172 removed outlier: 4.322A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 183 removed outlier: 3.629A pdb=" N ILE H 179 " --> pdb=" O ASN H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 206 Processing helix chain 'H' and resid 231 through 256 removed outlier: 4.155A pdb=" N GLY H 235 " --> pdb=" O GLY H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 289 Processing helix chain 'H' and resid 293 through 300 Processing helix chain 'H' and resid 301 through 321 removed outlier: 3.585A pdb=" N CYS H 305 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU H 306 " --> pdb=" O TRP H 302 " (cutoff:3.500A) Proline residue: H 307 - end of helix removed outlier: 4.080A pdb=" N LEU H 321 " --> pdb=" O ALA H 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 29 Processing helix chain 'I' and resid 64 through 70 removed outlier: 3.651A pdb=" N VAL I 68 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 109 removed outlier: 3.591A pdb=" N GLU I 107 " --> pdb=" O GLY I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 129 Processing helix chain 'I' and resid 133 through 137 Processing helix chain 'I' and resid 149 through 154 removed outlier: 4.064A pdb=" N MET I 153 " --> pdb=" O ASN I 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 24 through 47 removed outlier: 3.669A pdb=" N ALA J 28 " --> pdb=" O ASN J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 59 removed outlier: 4.261A pdb=" N ALA J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU J 54 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE J 57 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 75 removed outlier: 3.830A pdb=" N ASN J 75 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 88 Processing helix chain 'J' and resid 89 through 112 removed outlier: 3.680A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.902A pdb=" N LEU J 99 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 133 removed outlier: 4.040A pdb=" N VAL J 129 " --> pdb=" O SER J 125 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE J 131 " --> pdb=" O LYS J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'K' and resid 3 through 25 removed outlier: 4.189A pdb=" N GLY K 7 " --> pdb=" O PRO K 3 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 53 removed outlier: 3.855A pdb=" N TRP K 53 " --> pdb=" O ALA K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 87 removed outlier: 3.704A pdb=" N TYR K 62 " --> pdb=" O GLY K 58 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE K 63 " --> pdb=" O GLN K 59 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU K 64 " --> pdb=" O VAL K 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 21 removed outlier: 3.652A pdb=" N LEU L 10 " --> pdb=" O LEU L 6 " (cutoff:3.500A) Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 26 through 55 removed outlier: 3.611A pdb=" N SER L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 107 removed outlier: 3.676A pdb=" N VAL L 92 " --> pdb=" O MET L 88 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 133 removed outlier: 3.801A pdb=" N ASN L 121 " --> pdb=" O PHE L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 155 Processing helix chain 'L' and resid 160 through 193 removed outlier: 3.574A pdb=" N GLY L 164 " --> pdb=" O ASP L 160 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA L 167 " --> pdb=" O ASN L 163 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N MET L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS L 169 " --> pdb=" O ALA L 165 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA L 170 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA L 184 " --> pdb=" O PHE L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 202 Processing helix chain 'L' and resid 203 through 208 Processing helix chain 'L' and resid 212 through 230 removed outlier: 4.033A pdb=" N MET L 216 " --> pdb=" O ASN L 212 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TRP L 217 " --> pdb=" O ASN L 213 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY L 228 " --> pdb=" O GLY L 224 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS L 229 " --> pdb=" O GLY L 225 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 236 Processing helix chain 'L' and resid 240 through 245 removed outlier: 3.826A pdb=" N GLY L 245 " --> pdb=" O ALA L 242 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 255 Processing helix chain 'L' and resid 261 through 269 removed outlier: 3.566A pdb=" N ILE L 266 " --> pdb=" O GLY L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 269 through 275 Processing helix chain 'L' and resid 276 through 295 removed outlier: 3.549A pdb=" N LEU L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL L 283 " --> pdb=" O VAL L 279 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY L 284 " --> pdb=" O LEU L 280 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU L 292 " --> pdb=" O ALA L 288 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU L 293 " --> pdb=" O VAL L 289 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY L 295 " --> pdb=" O LEU L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 301 removed outlier: 3.979A pdb=" N GLN L 301 " --> pdb=" O ALA L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 303 through 325 Processing helix chain 'L' and resid 327 through 357 removed outlier: 4.078A pdb=" N PHE L 340 " --> pdb=" O MET L 336 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE L 341 " --> pdb=" O THR L 337 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU L 344 " --> pdb=" O PHE L 340 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER L 349 " --> pdb=" O LEU L 345 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS L 357 " --> pdb=" O ILE L 353 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 387 removed outlier: 4.021A pdb=" N TYR L 376 " --> pdb=" O ILE L 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 410 Processing helix chain 'L' and resid 411 through 437 removed outlier: 4.349A pdb=" N PHE L 430 " --> pdb=" O SER L 426 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG L 431 " --> pdb=" O LEU L 427 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET L 432 " --> pdb=" O TYR L 428 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 450 through 465 Proline residue: L 456 - end of helix removed outlier: 3.699A pdb=" N THR L 465 " --> pdb=" O LEU L 461 " (cutoff:3.500A) Processing helix chain 'L' and resid 465 through 470 removed outlier: 3.674A pdb=" N ALA L 469 " --> pdb=" O THR L 465 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU L 470 " --> pdb=" O PHE L 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 465 through 470' Processing helix chain 'L' and resid 489 through 514 Processing helix chain 'L' and resid 516 through 523 Processing helix chain 'L' and resid 525 through 537 Processing helix chain 'L' and resid 540 through 548 Processing helix chain 'L' and resid 549 through 560 Processing helix chain 'L' and resid 563 through 569 removed outlier: 3.658A pdb=" N SER L 567 " --> pdb=" O ASP L 563 " (cutoff:3.500A) Processing helix chain 'L' and resid 570 through 587 removed outlier: 3.521A pdb=" N GLU L 587 " --> pdb=" O LEU L 583 " (cutoff:3.500A) Processing helix chain 'L' and resid 590 through 611 removed outlier: 3.643A pdb=" N TYR L 594 " --> pdb=" O TYR L 590 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 26 through 50 removed outlier: 4.167A pdb=" N TRP M 30 " --> pdb=" O LYS M 26 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE M 34 " --> pdb=" O TRP M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 105 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 135 through 146 Processing helix chain 'M' and resid 148 through 159 removed outlier: 3.804A pdb=" N PHE M 152 " --> pdb=" O VAL M 148 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N HIS M 159 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 167 removed outlier: 3.883A pdb=" N THR M 166 " --> pdb=" O ASP M 163 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG M 167 " --> pdb=" O GLY M 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 163 through 167' Processing helix chain 'M' and resid 169 through 200 removed outlier: 3.822A pdb=" N THR M 178 " --> pdb=" O PHE M 174 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER M 181 " --> pdb=" O TYR M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 211 Processing helix chain 'M' and resid 219 through 231 removed outlier: 3.765A pdb=" N LEU M 223 " --> pdb=" O VAL M 219 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA M 230 " --> pdb=" O GLY M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 251 removed outlier: 4.469A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 262 removed outlier: 3.781A pdb=" N ILE M 262 " --> pdb=" O ASP M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 274 removed outlier: 4.434A pdb=" N ALA M 268 " --> pdb=" O LEU M 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 331 removed outlier: 3.986A pdb=" N VAL M 320 " --> pdb=" O ALA M 316 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER M 321 " --> pdb=" O TYR M 317 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY M 324 " --> pdb=" O VAL M 320 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE M 325 " --> pdb=" O SER M 321 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL M 326 " --> pdb=" O HIS M 322 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 367 removed outlier: 3.515A pdb=" N TYR M 338 " --> pdb=" O SER M 334 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE M 343 " --> pdb=" O GLN M 339 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY M 354 " --> pdb=" O LEU M 350 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU M 355 " --> pdb=" O SER M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 383 through 396 removed outlier: 3.987A pdb=" N LEU M 396 " --> pdb=" O ALA M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 401 through 418 removed outlier: 4.131A pdb=" N VAL M 405 " --> pdb=" O THR M 401 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 426 removed outlier: 4.096A pdb=" N THR M 422 " --> pdb=" O VAL M 418 " (cutoff:3.500A) Processing helix chain 'M' and resid 427 through 444 Processing helix chain 'M' and resid 447 through 456 removed outlier: 3.751A pdb=" N GLN M 451 " --> pdb=" O ALA M 448 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE M 452 " --> pdb=" O LYS M 449 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA M 453 " --> pdb=" O SER M 450 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN M 455 " --> pdb=" O ILE M 452 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU M 456 " --> pdb=" O ALA M 453 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 481 removed outlier: 3.625A pdb=" N LEU M 465 " --> pdb=" O SER M 461 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU M 471 " --> pdb=" O MET M 467 " (cutoff:3.500A) Processing helix chain 'M' and resid 482 through 503 removed outlier: 5.119A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 11 Processing helix chain 'N' and resid 11 through 31 removed outlier: 3.589A pdb=" N GLY N 18 " --> pdb=" O LEU N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 58 removed outlier: 4.105A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA N 58 " --> pdb=" O PHE N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 96 removed outlier: 3.539A pdb=" N LEU N 75 " --> pdb=" O GLY N 71 " (cutoff:3.500A) Proline residue: N 93 - end of helix Processing helix chain 'N' and resid 103 through 120 removed outlier: 4.338A pdb=" N LEU N 107 " --> pdb=" O ASP N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 142 removed outlier: 3.575A pdb=" N PHE N 129 " --> pdb=" O LEU N 125 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 151 through 179 removed outlier: 3.698A pdb=" N TYR N 178 " --> pdb=" O MET N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 216 Processing helix chain 'N' and resid 220 through 224 removed outlier: 3.972A pdb=" N HIS N 224 " --> pdb=" O VAL N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 234 removed outlier: 4.455A pdb=" N ASP N 229 " --> pdb=" O LEU N 225 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR N 231 " --> pdb=" O THR N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 235 through 244 removed outlier: 3.613A pdb=" N PHE N 241 " --> pdb=" O PRO N 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 244 through 261 removed outlier: 3.676A pdb=" N GLY N 252 " --> pdb=" O ILE N 248 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL N 253 " --> pdb=" O ALA N 249 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE N 258 " --> pdb=" O VAL N 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 Processing helix chain 'N' and resid 266 through 286 removed outlier: 3.652A pdb=" N ARG N 270 " --> pdb=" O SER N 266 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL N 272 " --> pdb=" O ALA N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 314 removed outlier: 3.825A pdb=" N ILE N 303 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER N 304 " --> pdb=" O TYR N 300 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 348 removed outlier: 3.731A pdb=" N SER N 348 " --> pdb=" O VAL N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 369 through 385 removed outlier: 3.848A pdb=" N ALA N 384 " --> pdb=" O MET N 380 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY N 385 " --> pdb=" O LEU N 381 " (cutoff:3.500A) Processing helix chain 'N' and resid 389 through 405 removed outlier: 3.926A pdb=" N ILE N 393 " --> pdb=" O THR N 389 " (cutoff:3.500A) Processing helix chain 'N' and resid 407 through 432 removed outlier: 4.655A pdb=" N TYR N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR N 425 " --> pdb=" O GLY N 421 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU N 432 " --> pdb=" O VAL N 428 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 470 Processing helix chain 'N' and resid 471 through 482 removed outlier: 3.550A pdb=" N ILE N 475 " --> pdb=" O PRO N 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.409A pdb=" N MET B 96 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N MET B 126 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 98 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 153 " --> pdb=" O VAL B 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 45 through 47 removed outlier: 6.656A pdb=" N ILE D 99 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU D 70 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.795A pdb=" N VAL D 120 " --> pdb=" O THR D 144 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP D 146 " --> pdb=" O VAL D 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 212 through 214 removed outlier: 3.852A pdb=" N ARG D 228 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP D 240 " --> pdb=" O GLN D 232 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASP D 234 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 359 through 360 Processing sheet with id=AA6, first strand: chain 'D' and resid 528 through 534 Processing sheet with id=AA7, first strand: chain 'E' and resid 126 through 131 removed outlier: 6.465A pdb=" N HIS E 87 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU E 129 " --> pdb=" O HIS E 87 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE E 89 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR E 131 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N TYR E 91 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 168 through 173 removed outlier: 6.503A pdb=" N LEU F 87 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N PHE F 131 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N CYS F 89 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CSX F 215 " --> pdb=" O TYR F 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 260 through 265 removed outlier: 7.644A pdb=" N ALA F 326 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY F 251 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ALA F 328 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N SER F 253 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ASP F 330 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 9 through 13 removed outlier: 9.251A pdb=" N ILE G 77 " --> pdb=" O THR G 3 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS G 5 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE G 76 " --> pdb=" O TYR G 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 144 through 146 Processing sheet with id=AB3, first strand: chain 'G' and resid 171 through 173 Processing sheet with id=AB4, first strand: chain 'G' and resid 222 through 223 Processing sheet with id=AB5, first strand: chain 'G' and resid 222 through 223 removed outlier: 8.441A pdb=" N ASN G 236 " --> pdb=" O ASN G 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ASN G 251 " --> pdb=" O ASN G 236 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER G 238 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE G 249 " --> pdb=" O SER G 238 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY G 240 " --> pdb=" O ARG G 247 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG G 242 " --> pdb=" O GLU G 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 289 through 292 removed outlier: 3.507A pdb=" N LEU G 606 " --> pdb=" O VAL G 590 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP G 594 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL G 564 " --> pdb=" O MET G 591 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL G 593 " --> pdb=" O VAL G 564 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL G 566 " --> pdb=" O VAL G 593 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE G 313 " --> pdb=" O VAL G 565 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU G 567 " --> pdb=" O ILE G 313 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE G 315 " --> pdb=" O LEU G 567 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N TYR G 338 " --> pdb=" O VAL G 312 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY G 314 " --> pdb=" O TYR G 338 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 445 through 448 removed outlier: 6.298A pdb=" N ALA G 374 " --> pdb=" O LEU G 497 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE G 499 " --> pdb=" O ALA G 374 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU G 376 " --> pdb=" O ILE G 499 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLY G 501 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU G 378 " --> pdb=" O GLY G 501 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 618 through 621 removed outlier: 3.669A pdb=" N VAL G 783 " --> pdb=" O ALA G 627 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 702 through 703 removed outlier: 6.474A pdb=" N LEU G 702 " --> pdb=" O THR G 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 811 through 815 removed outlier: 6.327A pdb=" N ARG G 811 " --> pdb=" O VAL G 882 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU G 884 " --> pdb=" O ARG G 811 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA G 813 " --> pdb=" O LEU G 884 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 840 through 842 removed outlier: 5.789A pdb=" N ILE G 840 " --> pdb=" O GLU G 872 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU G 869 " --> pdb=" O VAL G 858 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP G 902 " --> pdb=" O SER G 861 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 48 through 50 Processing sheet with id=AC4, first strand: chain 'I' and resid 75 through 81 removed outlier: 6.831A pdb=" N SER I 76 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE I 92 " --> pdb=" O SER I 76 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLN I 78 " --> pdb=" O GLU I 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 60 through 70 removed outlier: 8.401A pdb=" N GLN L 62 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU L 81 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU L 64 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N LEU L 79 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR L 66 " --> pdb=" O PHE L 77 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N PHE L 77 " --> pdb=" O THR L 66 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 65 through 66 removed outlier: 4.050A pdb=" N SER M 65 " --> pdb=" O ILE M 83 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 70 through 72 Processing sheet with id=AC8, first strand: chain 'N' and resid 61 through 62 1908 hydrogen bonds defined for protein. 5490 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: 7.85 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 15288 1.43 - 1.65: 20342 1.65 - 1.86: 365 1.86 - 2.07: 1 2.07 - 2.29: 92 Bond restraints: 36088 Sorted by residual: bond pdb=" C4 FMN F 501 " pdb=" C4A FMN F 501 " ideal model delta sigma weight residual 1.485 1.386 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" CB CSX F 215 " pdb=" SG CSX F 215 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB CSX B 102 " pdb=" SG CSX B 102 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C4A FMN F 501 " pdb=" N5 FMN F 501 " ideal model delta sigma weight residual 1.300 1.370 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" CB CSX E 132 " pdb=" SG CSX E 132 " ideal model delta sigma weight residual 1.831 1.762 0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 36083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 46362 1.70 - 3.41: 2272 3.41 - 5.11: 400 5.11 - 6.82: 69 6.82 - 8.52: 12 Bond angle restraints: 49115 Sorted by residual: angle pdb=" CA TYR M 435 " pdb=" CB TYR M 435 " pdb=" CG TYR M 435 " ideal model delta sigma weight residual 113.90 120.46 -6.56 1.80e+00 3.09e-01 1.33e+01 angle pdb=" N GLY L 317 " pdb=" CA GLY L 317 " pdb=" C GLY L 317 " ideal model delta sigma weight residual 113.37 108.51 4.86 1.34e+00 5.57e-01 1.32e+01 angle pdb=" CA PHE L 341 " pdb=" CB PHE L 341 " pdb=" CG PHE L 341 " ideal model delta sigma weight residual 113.80 117.10 -3.30 1.00e+00 1.00e+00 1.09e+01 angle pdb=" N VAL N 221 " pdb=" CA VAL N 221 " pdb=" C VAL N 221 " ideal model delta sigma weight residual 108.88 115.92 -7.04 2.16e+00 2.14e-01 1.06e+01 angle pdb=" CA CYS G 228 " pdb=" CB CYS G 228 " pdb=" SG CYS G 228 " ideal model delta sigma weight residual 114.40 121.41 -7.01 2.30e+00 1.89e-01 9.28e+00 ... (remaining 49110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 19135 17.90 - 35.80: 1621 35.80 - 53.70: 280 53.70 - 71.60: 50 71.60 - 89.50: 19 Dihedral angle restraints: 21105 sinusoidal: 7917 harmonic: 13188 Sorted by residual: dihedral pdb=" CA TRP L 535 " pdb=" C TRP L 535 " pdb=" N TYR L 536 " pdb=" CA TYR L 536 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA VAL K 23 " pdb=" C VAL K 23 " pdb=" N ILE K 24 " pdb=" CA ILE K 24 " ideal model delta harmonic sigma weight residual -180.00 -154.03 -25.97 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA THR L 237 " pdb=" C THR L 237 " pdb=" N TRP L 238 " pdb=" CA TRP L 238 " ideal model delta harmonic sigma weight residual -180.00 -154.20 -25.80 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 21102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 4268 0.052 - 0.104: 1091 0.104 - 0.157: 177 0.157 - 0.209: 15 0.209 - 0.261: 3 Chirality restraints: 5554 Sorted by residual: chirality pdb=" CA PHE L 341 " pdb=" N PHE L 341 " pdb=" C PHE L 341 " pdb=" CB PHE L 341 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL L 35 " pdb=" CA VAL L 35 " pdb=" CG1 VAL L 35 " pdb=" CG2 VAL L 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU L 299 " pdb=" CB LEU L 299 " pdb=" CD1 LEU L 299 " pdb=" CD2 LEU L 299 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 5551 not shown) Planarity restraints: 6256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO F 356 " 0.021 2.00e-02 2.50e+03 4.17e-02 1.74e+01 pdb=" C PRO F 356 " -0.072 2.00e-02 2.50e+03 pdb=" O PRO F 356 " 0.026 2.00e-02 2.50e+03 pdb=" N CYS F 357 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 457 " -0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LEU G 457 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU G 457 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY G 458 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 30 " 0.031 2.00e-02 2.50e+03 2.31e-02 1.34e+01 pdb=" CG TRP M 30 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP M 30 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP M 30 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP M 30 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TRP M 30 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP M 30 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 30 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 30 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP M 30 " 0.004 2.00e-02 2.50e+03 ... (remaining 6253 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 436 2.66 - 3.22: 33617 3.22 - 3.78: 55432 3.78 - 4.34: 75640 4.34 - 4.90: 123735 Nonbonded interactions: 288860 Sorted by model distance: nonbonded pdb=" OG SER D 100 " pdb=" OD1 ASP D 102 " model vdw 2.097 3.040 nonbonded pdb=" OE2 GLU G 647 " pdb="CA CA G1005 " model vdw 2.184 2.510 nonbonded pdb=" NH2 ARG E 125 " pdb=" O TYR E 165 " model vdw 2.196 3.120 nonbonded pdb=" NH1 ARG A 63 " pdb=" O ASP D 210 " model vdw 2.196 3.120 nonbonded pdb=" OD1 ASP N 265 " pdb=" NE2 GLN N 317 " model vdw 2.217 3.120 ... (remaining 288855 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 36.140 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.276 36124 Z= 0.236 Angle : 1.531 83.184 49210 Z= 0.470 Chirality : 0.047 0.261 5554 Planarity : 0.006 0.083 6256 Dihedral : 13.873 89.505 12665 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.82 % Allowed : 2.83 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.11), residues: 4573 helix: -0.91 (0.09), residues: 2470 sheet: -0.36 (0.29), residues: 311 loop : -1.35 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 597 TYR 0.054 0.003 TYR N 397 PHE 0.046 0.003 PHE N 396 TRP 0.061 0.002 TRP M 30 HIS 0.011 0.002 HIS F 400 Details of bonding type rmsd covalent geometry : bond 0.00525 (36088) covalent geometry : angle 0.85957 (49115) hydrogen bonds : bond 0.18208 ( 1906) hydrogen bonds : angle 6.74155 ( 5490) metal coordination : bond 0.06543 ( 36) metal coordination : angle 28.84700 ( 95) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 1377 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.7433 (mp) cc_final: 0.6791 (mt) REVERT: D 87 LEU cc_start: 0.6386 (mp) cc_final: 0.5894 (mp) REVERT: D 141 PHE cc_start: 0.6907 (m-80) cc_final: 0.6293 (m-80) REVERT: D 255 MET cc_start: 0.7378 (tpp) cc_final: 0.7099 (tpp) REVERT: D 281 MET cc_start: 0.7285 (tpp) cc_final: 0.7061 (tpp) REVERT: D 301 VAL cc_start: 0.8589 (t) cc_final: 0.8129 (m) REVERT: D 417 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6177 (tp30) REVERT: D 485 PRO cc_start: 0.4439 (Cg_endo) cc_final: 0.4179 (Cg_exo) REVERT: D 509 GLU cc_start: 0.8153 (pm20) cc_final: 0.7205 (mp0) REVERT: E 75 PHE cc_start: 0.9275 (t80) cc_final: 0.9067 (t80) REVERT: E 161 LEU cc_start: 0.7248 (tp) cc_final: 0.6011 (mm) REVERT: F 53 GLN cc_start: 0.7492 (mt0) cc_final: 0.6936 (tp-100) REVERT: F 71 LEU cc_start: 0.7637 (tt) cc_final: 0.7243 (tp) REVERT: F 89 CYS cc_start: 0.8373 (t) cc_final: 0.6887 (p) REVERT: F 212 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8188 (mmtm) REVERT: F 235 TRP cc_start: 0.5888 (t60) cc_final: 0.5033 (t-100) REVERT: F 274 LEU cc_start: 0.8366 (tp) cc_final: 0.8033 (tp) REVERT: F 291 GLN cc_start: 0.4383 (mt0) cc_final: 0.4035 (mt0) REVERT: F 349 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6597 (mm-30) REVERT: F 437 GLN cc_start: 0.7037 (mt0) cc_final: 0.6602 (mt0) REVERT: G 17 ASP cc_start: 0.5298 (m-30) cc_final: 0.3711 (m-30) REVERT: G 245 GLU cc_start: 0.6972 (pt0) cc_final: 0.6152 (pt0) REVERT: G 299 MET cc_start: 0.6472 (mmp) cc_final: 0.5766 (ttm) REVERT: G 326 PHE cc_start: 0.7040 (t80) cc_final: 0.6398 (t80) REVERT: G 424 ARG cc_start: 0.7523 (ptp-170) cc_final: 0.7294 (ptp-170) REVERT: G 435 ASP cc_start: 0.6996 (t0) cc_final: 0.6355 (t0) REVERT: G 453 ASP cc_start: 0.7026 (m-30) cc_final: 0.6359 (m-30) REVERT: G 589 LEU cc_start: 0.8202 (tp) cc_final: 0.7150 (tt) REVERT: G 624 GLU cc_start: 0.5448 (tt0) cc_final: 0.5109 (mm-30) REVERT: G 644 VAL cc_start: 0.7354 (t) cc_final: 0.6697 (t) REVERT: G 654 SER cc_start: 0.8190 (t) cc_final: 0.7774 (p) REVERT: G 658 THR cc_start: 0.8660 (m) cc_final: 0.8055 (t) REVERT: G 731 ASP cc_start: 0.7590 (m-30) cc_final: 0.7389 (m-30) REVERT: G 842 LEU cc_start: 0.8070 (mt) cc_final: 0.7801 (mt) REVERT: G 849 LYS cc_start: 0.7334 (ptpp) cc_final: 0.6456 (tmmt) REVERT: H 236 LEU cc_start: 0.6693 (mp) cc_final: 0.6028 (tp) REVERT: H 265 LEU cc_start: 0.5451 (pp) cc_final: 0.3971 (mt) REVERT: I 53 ASP cc_start: 0.6479 (t70) cc_final: 0.6158 (t0) REVERT: I 101 PHE cc_start: 0.7879 (m-80) cc_final: 0.7666 (m-80) REVERT: I 124 GLU cc_start: 0.8195 (tp30) cc_final: 0.7933 (mm-30) REVERT: J 64 MET cc_start: 0.7343 (mmm) cc_final: 0.7134 (tpp) REVERT: K 2 ILE cc_start: 0.1437 (mm) cc_final: 0.1167 (mm) REVERT: L 1 MET cc_start: -0.1084 (ptt) cc_final: -0.2843 (ptt) REVERT: L 73 PHE cc_start: 0.5110 (t80) cc_final: 0.4888 (t80) REVERT: L 98 LEU cc_start: 0.8228 (mt) cc_final: 0.8018 (mt) REVERT: L 214 MET cc_start: 0.0095 (ppp) cc_final: -0.1898 (pmm) REVERT: L 554 LEU cc_start: 0.6852 (mm) cc_final: 0.5298 (tp) REVERT: M 72 ILE cc_start: 0.7957 (mt) cc_final: 0.7661 (mm) REVERT: M 118 LEU cc_start: 0.2383 (pp) cc_final: 0.1562 (tp) REVERT: M 156 LEU cc_start: 0.5676 (tp) cc_final: 0.5247 (tp) REVERT: M 195 VAL cc_start: 0.7051 (m) cc_final: 0.6676 (p) REVERT: N 74 MET cc_start: 0.3162 (mtp) cc_final: 0.1824 (mtt) REVERT: N 125 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7208 (mp) REVERT: N 174 MET cc_start: 0.5855 (OUTLIER) cc_final: 0.5604 (ttt) REVERT: N 184 LEU cc_start: 0.7994 (mp) cc_final: 0.7269 (mp) REVERT: N 185 SER cc_start: 0.7387 (t) cc_final: 0.7177 (t) REVERT: N 283 PHE cc_start: 0.7292 (m-80) cc_final: 0.6825 (m-80) REVERT: N 379 MET cc_start: 0.5583 (mmt) cc_final: 0.4316 (mmm) REVERT: N 396 PHE cc_start: 0.7544 (t80) cc_final: 0.7293 (t80) outliers start: 29 outliers final: 7 residues processed: 1394 average time/residue: 0.2238 time to fit residues: 492.8870 Evaluate side-chains 1077 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1067 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 174 MET Chi-restraints excluded: chain N residue 187 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 173 GLN D 37 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN D 163 HIS ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN E 150 HIS F 52 ASN F 172 HIS ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN G 115 GLN ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 653 HIS G 671 HIS G 747 HIS G 763 GLN G 766 ASN H 152 GLN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 HIS J 24 ASN ** J 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 254 HIS ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN N 37 ASN N 232 GLN N 406 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.244077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.204233 restraints weight = 60779.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.205013 restraints weight = 77242.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.206673 restraints weight = 40582.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.206360 restraints weight = 28201.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.207540 restraints weight = 23769.848| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 36124 Z= 0.228 Angle : 1.280 73.004 49210 Z= 0.401 Chirality : 0.046 0.260 5554 Planarity : 0.006 0.066 6256 Dihedral : 5.497 77.889 5005 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.12 % Allowed : 15.67 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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 (0.12), residues: 4573 helix: 0.06 (0.10), residues: 2536 sheet: -0.38 (0.28), residues: 337 loop : -1.07 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 306 TYR 0.034 0.003 TYR M 435 PHE 0.037 0.002 PHE N 186 TRP 0.040 0.002 TRP L 143 HIS 0.026 0.002 HIS M 322 Details of bonding type rmsd covalent geometry : bond 0.00497 (36088) covalent geometry : angle 0.75453 (49115) hydrogen bonds : bond 0.05230 ( 1906) hydrogen bonds : angle 5.05420 ( 5490) metal coordination : bond 0.01982 ( 36) metal coordination : angle 23.55541 ( 95) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1097 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 TYR cc_start: 0.7337 (m-80) cc_final: 0.6934 (m-80) REVERT: B 159 PRO cc_start: 0.9163 (Cg_endo) cc_final: 0.8845 (Cg_exo) REVERT: B 197 MET cc_start: 0.5640 (mpp) cc_final: 0.5240 (mpp) REVERT: D 71 PHE cc_start: 0.6838 (t80) cc_final: 0.6587 (t80) REVERT: D 141 PHE cc_start: 0.7238 (m-80) cc_final: 0.6753 (m-80) REVERT: D 213 PHE cc_start: 0.7174 (p90) cc_final: 0.6930 (p90) REVERT: D 228 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.5580 (mtp85) REVERT: D 290 LEU cc_start: 0.8754 (mt) cc_final: 0.7894 (tp) REVERT: D 318 TYR cc_start: 0.6770 (t80) cc_final: 0.6441 (t80) REVERT: D 417 GLU cc_start: 0.6867 (pt0) cc_final: 0.6632 (pt0) REVERT: D 436 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7503 (mtmt) REVERT: E 99 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7234 (tt) REVERT: F 53 GLN cc_start: 0.7490 (mt0) cc_final: 0.6775 (tp-100) REVERT: F 235 TRP cc_start: 0.6356 (t60) cc_final: 0.6134 (t60) REVERT: F 236 TYR cc_start: 0.6578 (t80) cc_final: 0.6137 (t80) REVERT: F 237 GLN cc_start: 0.6829 (OUTLIER) cc_final: 0.6611 (pm20) REVERT: G 88 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7821 (mtm-85) REVERT: G 99 HIS cc_start: 0.8488 (t70) cc_final: 0.8174 (t70) REVERT: G 116 ASP cc_start: 0.8221 (m-30) cc_final: 0.7805 (m-30) REVERT: G 147 GLU cc_start: 0.6067 (mm-30) cc_final: 0.5815 (mm-30) REVERT: G 408 GLN cc_start: 0.7749 (tp-100) cc_final: 0.7528 (tp-100) REVERT: G 420 ASN cc_start: 0.7410 (t0) cc_final: 0.7002 (t0) REVERT: G 424 ARG cc_start: 0.7268 (ptp-170) cc_final: 0.6817 (ptp-170) REVERT: G 440 ASP cc_start: 0.6557 (m-30) cc_final: 0.6348 (m-30) REVERT: G 453 ASP cc_start: 0.7478 (m-30) cc_final: 0.6969 (m-30) REVERT: G 640 ASP cc_start: 0.7694 (t0) cc_final: 0.7120 (t0) REVERT: G 683 LEU cc_start: 0.6961 (mt) cc_final: 0.6516 (mt) REVERT: G 760 ASN cc_start: 0.8014 (m-40) cc_final: 0.7798 (m-40) REVERT: G 769 GLN cc_start: 0.7869 (mt0) cc_final: 0.7657 (mt0) REVERT: G 849 LYS cc_start: 0.6450 (ptpp) cc_final: 0.5886 (tmmt) REVERT: H 236 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.5820 (tp) REVERT: H 267 PRO cc_start: 0.8054 (Cg_endo) cc_final: 0.7339 (Cg_exo) REVERT: K 53 TRP cc_start: 0.6323 (m100) cc_final: 0.5893 (m100) REVERT: L 214 MET cc_start: 0.0996 (ppp) cc_final: -0.1172 (pmm) REVERT: M 54 LEU cc_start: 0.3162 (pt) cc_final: 0.0741 (tp) REVERT: M 69 MET cc_start: 0.7622 (ppp) cc_final: 0.6120 (mtt) REVERT: M 131 PHE cc_start: 0.5712 (m-10) cc_final: 0.5369 (m-10) REVERT: M 189 ILE cc_start: 0.6631 (mt) cc_final: 0.6425 (mt) REVERT: M 223 LEU cc_start: 0.4524 (tt) cc_final: 0.4076 (mt) REVERT: M 235 MET cc_start: 0.5417 (mmt) cc_final: 0.5037 (ppp) REVERT: M 243 TRP cc_start: 0.5596 (p-90) cc_final: 0.5324 (p-90) REVERT: M 323 MET cc_start: 0.3524 (mmp) cc_final: 0.3205 (mmp) REVERT: M 345 MET cc_start: 0.4894 (mmm) cc_final: 0.4540 (mmm) REVERT: M 361 GLN cc_start: 0.5713 (OUTLIER) cc_final: 0.5377 (tp-100) REVERT: N 52 LEU cc_start: 0.6053 (tp) cc_final: 0.5781 (tt) REVERT: N 74 MET cc_start: 0.2878 (mtp) cc_final: 0.2275 (mtt) REVERT: N 95 LEU cc_start: 0.4973 (mt) cc_final: 0.4576 (mt) REVERT: N 202 LEU cc_start: 0.4689 (mp) cc_final: 0.3754 (tp) REVERT: N 260 TYR cc_start: 0.6800 (m-10) cc_final: 0.6581 (m-80) REVERT: N 297 LEU cc_start: 0.8343 (tt) cc_final: 0.8075 (tt) REVERT: N 379 MET cc_start: 0.5227 (mmt) cc_final: 0.4418 (mmm) REVERT: N 396 PHE cc_start: 0.7674 (t80) cc_final: 0.7389 (t80) REVERT: N 427 ARG cc_start: 0.7548 (mmp80) cc_final: 0.6163 (ttp80) outliers start: 110 outliers final: 63 residues processed: 1145 average time/residue: 0.2044 time to fit residues: 379.8213 Evaluate side-chains 1088 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 1020 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 856 THR Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 590 TYR Chi-restraints excluded: chain M residue 63 TRP Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 221 TYR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 361 GLN Chi-restraints excluded: chain M residue 452 ILE Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 35 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 353 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 328 optimal weight: 8.9990 chunk 373 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 344 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 173 GLN B 213 ASN D 224 HIS ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 GLN ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 HIS ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 GLN G 503 ASN ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 742 ASN H 183 GLN H 188 ASN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 GLN K 84 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 451 GLN N 149 GLN N 199 ASN N 406 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.243971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.204590 restraints weight = 60626.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.207636 restraints weight = 77086.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.208271 restraints weight = 35750.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.207768 restraints weight = 29873.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.209104 restraints weight = 22810.264| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 36124 Z= 0.171 Angle : 1.172 71.470 49210 Z= 0.363 Chirality : 0.044 0.173 5554 Planarity : 0.005 0.054 6256 Dihedral : 5.076 76.427 4988 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.00 % Allowed : 17.91 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.28 (0.12), residues: 4573 helix: 0.44 (0.10), residues: 2542 sheet: -0.16 (0.29), residues: 314 loop : -1.03 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 573 TYR 0.031 0.002 TYR M 435 PHE 0.044 0.002 PHE B 59 TRP 0.048 0.002 TRP L 143 HIS 0.012 0.001 HIS M 322 Details of bonding type rmsd covalent geometry : bond 0.00380 (36088) covalent geometry : angle 0.69233 (49115) hydrogen bonds : bond 0.04481 ( 1906) hydrogen bonds : angle 4.78669 ( 5490) metal coordination : bond 0.01473 ( 36) metal coordination : angle 21.52447 ( 95) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1049 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7404 (m-10) cc_final: 0.6968 (m-80) REVERT: B 45 MET cc_start: 0.7363 (mmm) cc_final: 0.7003 (mmm) REVERT: B 117 MET cc_start: 0.7221 (ppp) cc_final: 0.6792 (ppp) REVERT: B 173 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: B 197 MET cc_start: 0.6035 (mpp) cc_final: 0.5465 (mpp) REVERT: D 78 GLU cc_start: 0.6697 (tp30) cc_final: 0.6311 (tm-30) REVERT: D 97 HIS cc_start: 0.7519 (t-90) cc_final: 0.7292 (t-90) REVERT: D 199 GLU cc_start: 0.7422 (pm20) cc_final: 0.7130 (pm20) REVERT: D 228 ARG cc_start: 0.6242 (mtp85) cc_final: 0.5760 (mtp85) REVERT: D 318 TYR cc_start: 0.6602 (t80) cc_final: 0.6061 (t80) REVERT: D 417 GLU cc_start: 0.7000 (pt0) cc_final: 0.6755 (pt0) REVERT: D 436 LYS cc_start: 0.7815 (mmtt) cc_final: 0.7344 (mttt) REVERT: D 591 MET cc_start: 0.5102 (tpp) cc_final: 0.4772 (tpt) REVERT: F 53 GLN cc_start: 0.7517 (mt0) cc_final: 0.6794 (tp-100) REVERT: F 94 MET cc_start: 0.7724 (tpp) cc_final: 0.7315 (tpp) REVERT: F 235 TRP cc_start: 0.6387 (t60) cc_final: 0.6158 (t60) REVERT: F 236 TYR cc_start: 0.6416 (t80) cc_final: 0.5991 (t80) REVERT: F 237 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6138 (tm-30) REVERT: F 252 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.5717 (t80) REVERT: G 88 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.7609 (mtm-85) REVERT: G 99 HIS cc_start: 0.8499 (t70) cc_final: 0.8175 (t70) REVERT: G 116 ASP cc_start: 0.8268 (m-30) cc_final: 0.7481 (m-30) REVERT: G 148 MET cc_start: 0.8593 (tpp) cc_final: 0.7785 (tpp) REVERT: G 408 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7713 (tp-100) REVERT: G 420 ASN cc_start: 0.7475 (t0) cc_final: 0.7031 (t0) REVERT: G 440 ASP cc_start: 0.6402 (m-30) cc_final: 0.6136 (m-30) REVERT: G 453 ASP cc_start: 0.7575 (m-30) cc_final: 0.7365 (m-30) REVERT: G 629 ARG cc_start: 0.6576 (tpp80) cc_final: 0.6242 (tpp80) REVERT: G 640 ASP cc_start: 0.7640 (t0) cc_final: 0.6953 (t0) REVERT: G 654 SER cc_start: 0.7947 (t) cc_final: 0.7552 (p) REVERT: G 671 HIS cc_start: 0.6209 (OUTLIER) cc_final: 0.5511 (t-90) REVERT: G 734 PHE cc_start: 0.6721 (m-80) cc_final: 0.6465 (m-80) REVERT: G 849 LYS cc_start: 0.6444 (ptpp) cc_final: 0.5838 (tmmt) REVERT: H 131 LEU cc_start: 0.7651 (mt) cc_final: 0.7148 (mt) REVERT: H 236 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5468 (tp) REVERT: K 53 TRP cc_start: 0.6350 (m100) cc_final: 0.5981 (m100) REVERT: L 243 MET cc_start: 0.2500 (mmm) cc_final: 0.1787 (ptp) REVERT: L 258 MET cc_start: -0.3155 (tmt) cc_final: -0.3909 (tmt) REVERT: L 275 MET cc_start: -0.1430 (mtp) cc_final: -0.1633 (ttt) REVERT: M 42 LEU cc_start: 0.6883 (mt) cc_final: 0.6328 (tp) REVERT: M 54 LEU cc_start: 0.3038 (pt) cc_final: 0.0381 (tp) REVERT: M 77 ILE cc_start: 0.8494 (mt) cc_final: 0.7858 (tt) REVERT: M 90 MET cc_start: 0.7319 (mmt) cc_final: 0.7040 (mmt) REVERT: M 205 PHE cc_start: 0.4558 (m-10) cc_final: 0.4164 (m-80) REVERT: M 235 MET cc_start: 0.5595 (mmt) cc_final: 0.5026 (ppp) REVERT: M 299 PHE cc_start: 0.6552 (m-10) cc_final: 0.5858 (m-80) REVERT: M 323 MET cc_start: 0.3549 (mmp) cc_final: 0.3082 (mmp) REVERT: M 345 MET cc_start: 0.4826 (mmm) cc_final: 0.4485 (mmm) REVERT: N 52 LEU cc_start: 0.5901 (tp) cc_final: 0.5670 (tt) REVERT: N 74 MET cc_start: 0.2926 (mtp) cc_final: 0.2227 (mtt) REVERT: N 202 LEU cc_start: 0.4619 (mp) cc_final: 0.3629 (tp) REVERT: N 297 LEU cc_start: 0.8359 (tt) cc_final: 0.8120 (tt) REVERT: N 359 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5688 (tt) REVERT: N 380 MET cc_start: 0.6969 (tmm) cc_final: 0.6658 (tmm) REVERT: N 427 ARG cc_start: 0.7277 (mmp80) cc_final: 0.6095 (ttp80) outliers start: 141 outliers final: 94 residues processed: 1101 average time/residue: 0.2085 time to fit residues: 372.5705 Evaluate side-chains 1091 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 991 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 281 GLN Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 619 THR Chi-restraints excluded: chain G residue 671 HIS Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 825 SER Chi-restraints excluded: chain G residue 856 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain M residue 63 TRP Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 434 optimal weight: 6.9990 chunk 353 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 294 optimal weight: 6.9990 chunk 441 optimal weight: 0.9990 chunk 230 optimal weight: 0.0370 chunk 309 optimal weight: 7.9990 chunk 298 optimal weight: 6.9990 chunk 235 optimal weight: 0.2980 chunk 216 optimal weight: 0.9990 chunk 360 optimal weight: 0.9980 overall best weight: 0.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN D 37 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN D 279 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 HIS F 341 ASN ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 742 ASN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 HIS ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN N 406 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.245014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.205994 restraints weight = 60509.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.208270 restraints weight = 73516.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.207983 restraints weight = 41342.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.208052 restraints weight = 27139.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.208852 restraints weight = 21899.693| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36124 Z= 0.144 Angle : 1.087 69.942 49210 Z= 0.347 Chirality : 0.042 0.168 5554 Planarity : 0.005 0.061 6256 Dihedral : 4.939 76.878 4988 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.28 % Allowed : 19.81 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.12), residues: 4573 helix: 0.66 (0.10), residues: 2546 sheet: -0.16 (0.29), residues: 326 loop : -0.94 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 386 TYR 0.028 0.002 TYR M 435 PHE 0.031 0.002 PHE B 103 TRP 0.043 0.002 TRP L 143 HIS 0.009 0.001 HIS G 259 Details of bonding type rmsd covalent geometry : bond 0.00321 (36088) covalent geometry : angle 0.66602 (49115) hydrogen bonds : bond 0.04098 ( 1906) hydrogen bonds : angle 4.63677 ( 5490) metal coordination : bond 0.01178 ( 36) metal coordination : angle 19.55666 ( 95) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 1024 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7266 (m-10) cc_final: 0.6841 (m-80) REVERT: B 45 MET cc_start: 0.7369 (mmm) cc_final: 0.6954 (mmm) REVERT: B 117 MET cc_start: 0.6886 (ppp) cc_final: 0.6617 (ppp) REVERT: B 136 TYR cc_start: 0.7272 (m-80) cc_final: 0.6897 (m-80) REVERT: B 197 MET cc_start: 0.5948 (mpp) cc_final: 0.5487 (mpp) REVERT: D 228 ARG cc_start: 0.6190 (mtp85) cc_final: 0.5824 (mtp85) REVERT: D 290 LEU cc_start: 0.8882 (mt) cc_final: 0.8076 (tp) REVERT: D 318 TYR cc_start: 0.6825 (t80) cc_final: 0.6241 (t80) REVERT: D 436 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7315 (mtmt) REVERT: D 464 MET cc_start: 0.6508 (tmm) cc_final: 0.6141 (tmm) REVERT: F 53 GLN cc_start: 0.7545 (mt0) cc_final: 0.6798 (tp-100) REVERT: F 94 MET cc_start: 0.7765 (tpp) cc_final: 0.7017 (tpp) REVERT: F 235 TRP cc_start: 0.6382 (t60) cc_final: 0.6167 (t60) REVERT: F 236 TYR cc_start: 0.6316 (t80) cc_final: 0.5868 (t80) REVERT: F 237 GLN cc_start: 0.6577 (OUTLIER) cc_final: 0.5860 (tm-30) REVERT: F 252 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.5331 (t80) REVERT: F 262 TRP cc_start: 0.8002 (m-90) cc_final: 0.7453 (m-90) REVERT: F 344 GLU cc_start: 0.7348 (tp30) cc_final: 0.6657 (tp30) REVERT: G 99 HIS cc_start: 0.8595 (t70) cc_final: 0.8098 (t70) REVERT: G 116 ASP cc_start: 0.8021 (m-30) cc_final: 0.7604 (m-30) REVERT: G 148 MET cc_start: 0.8447 (tpp) cc_final: 0.7346 (tpp) REVERT: G 209 LYS cc_start: 0.8731 (tttp) cc_final: 0.8227 (mtpt) REVERT: G 215 TYR cc_start: 0.8633 (t80) cc_final: 0.8115 (t80) REVERT: G 261 PHE cc_start: 0.8419 (m-10) cc_final: 0.8187 (m-10) REVERT: G 420 ASN cc_start: 0.7362 (t0) cc_final: 0.6928 (t0) REVERT: G 453 ASP cc_start: 0.7249 (m-30) cc_final: 0.6726 (m-30) REVERT: G 486 ILE cc_start: 0.8019 (mt) cc_final: 0.7742 (mt) REVERT: G 629 ARG cc_start: 0.6657 (tpp80) cc_final: 0.6319 (tpp80) REVERT: G 640 ASP cc_start: 0.7493 (t0) cc_final: 0.6698 (t70) REVERT: G 644 VAL cc_start: 0.7365 (OUTLIER) cc_final: 0.6782 (t) REVERT: G 671 HIS cc_start: 0.6636 (OUTLIER) cc_final: 0.6078 (t-90) REVERT: G 903 LEU cc_start: 0.7583 (pt) cc_final: 0.7336 (pp) REVERT: H 131 LEU cc_start: 0.7611 (mt) cc_final: 0.7262 (mt) REVERT: H 236 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5512 (tp) REVERT: H 298 MET cc_start: 0.5213 (ptp) cc_final: 0.3915 (ppp) REVERT: I 162 ASP cc_start: 0.7821 (t0) cc_final: 0.7537 (t70) REVERT: I 173 ILE cc_start: 0.7655 (mp) cc_final: 0.7438 (mm) REVERT: K 98 MET cc_start: 0.1337 (mtm) cc_final: 0.0102 (mtp) REVERT: L 144 GLU cc_start: 0.1684 (OUTLIER) cc_final: 0.1478 (mm-30) REVERT: L 258 MET cc_start: -0.3387 (tmt) cc_final: -0.3885 (tmt) REVERT: L 272 LEU cc_start: 0.3701 (mp) cc_final: 0.2198 (mt) REVERT: M 42 LEU cc_start: 0.6840 (mt) cc_final: 0.6147 (tp) REVERT: M 54 LEU cc_start: 0.3049 (pt) cc_final: 0.0410 (tp) REVERT: M 69 MET cc_start: 0.7410 (ppp) cc_final: 0.5984 (mtt) REVERT: M 71 TRP cc_start: 0.6724 (t60) cc_final: 0.6467 (t60) REVERT: M 74 ARG cc_start: 0.5895 (tpt90) cc_final: 0.5634 (mtp85) REVERT: M 90 MET cc_start: 0.7078 (mmt) cc_final: 0.6745 (mmt) REVERT: M 112 TYR cc_start: 0.1406 (p90) cc_final: 0.1134 (p90) REVERT: M 156 LEU cc_start: 0.5142 (tp) cc_final: 0.4820 (tp) REVERT: M 235 MET cc_start: 0.5430 (mmt) cc_final: 0.5046 (ppp) REVERT: M 323 MET cc_start: 0.3359 (mmp) cc_final: 0.2973 (mmp) REVERT: M 336 LEU cc_start: 0.8469 (tt) cc_final: 0.7988 (mm) REVERT: M 345 MET cc_start: 0.4867 (mmm) cc_final: 0.4231 (mmm) REVERT: M 465 LEU cc_start: 0.3889 (mt) cc_final: 0.2787 (tp) REVERT: N 52 LEU cc_start: 0.5898 (tp) cc_final: 0.5698 (mt) REVERT: N 74 MET cc_start: 0.2771 (mtp) cc_final: 0.1995 (mtt) REVERT: N 180 GLN cc_start: 0.5451 (pt0) cc_final: 0.4861 (pt0) REVERT: N 202 LEU cc_start: 0.4582 (mp) cc_final: 0.3733 (tp) REVERT: N 204 LEU cc_start: 0.5754 (pp) cc_final: 0.5440 (mp) REVERT: N 260 TYR cc_start: 0.6762 (m-80) cc_final: 0.6231 (m-10) REVERT: N 283 PHE cc_start: 0.6896 (m-80) cc_final: 0.6548 (m-80) REVERT: N 287 MET cc_start: 0.4729 (tmm) cc_final: 0.4409 (tmm) REVERT: N 297 LEU cc_start: 0.8372 (tt) cc_final: 0.8131 (tt) REVERT: N 359 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5672 (tt) REVERT: N 379 MET cc_start: 0.5956 (tpp) cc_final: 0.5179 (tpp) REVERT: N 380 MET cc_start: 0.7075 (tmm) cc_final: 0.6499 (tmm) REVERT: N 427 ARG cc_start: 0.7196 (mmp80) cc_final: 0.6211 (ttp80) outliers start: 151 outliers final: 90 residues processed: 1079 average time/residue: 0.2052 time to fit residues: 358.8128 Evaluate side-chains 1071 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 974 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 619 THR Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 671 HIS Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 856 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 187 TRP Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain M residue 63 TRP Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 221 TYR Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 340 optimal weight: 9.9990 chunk 341 optimal weight: 30.0000 chunk 263 optimal weight: 0.0040 chunk 327 optimal weight: 7.9990 chunk 367 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 chunk 345 optimal weight: 20.0000 chunk 271 optimal weight: 0.0170 chunk 362 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 342 optimal weight: 10.0000 overall best weight: 1.1832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN D 37 GLN D 104 ASN F 172 HIS F 196 ASN F 341 ASN ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 GLN ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 653 HIS G 742 ASN G 769 GLN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 HIS L 135 ASN ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 416 GLN ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 HIS N 37 ASN N 406 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.242999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.204630 restraints weight = 60349.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.210247 restraints weight = 67669.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.207467 restraints weight = 24849.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.208252 restraints weight = 25978.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.208464 restraints weight = 17380.878| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 36124 Z= 0.168 Angle : 1.096 69.029 49210 Z= 0.356 Chirality : 0.043 0.190 5554 Planarity : 0.005 0.062 6256 Dihedral : 4.946 73.726 4988 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.48 % Allowed : 21.09 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 4573 helix: 0.74 (0.10), residues: 2549 sheet: -0.07 (0.29), residues: 323 loop : -0.96 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 306 TYR 0.028 0.002 TYR N 333 PHE 0.043 0.002 PHE M 142 TRP 0.043 0.002 TRP L 143 HIS 0.013 0.001 HIS G 653 Details of bonding type rmsd covalent geometry : bond 0.00377 (36088) covalent geometry : angle 0.67854 (49115) hydrogen bonds : bond 0.04149 ( 1906) hydrogen bonds : angle 4.62864 ( 5490) metal coordination : bond 0.01442 ( 36) metal coordination : angle 19.59161 ( 95) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 986 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.7389 (mmm) cc_final: 0.6960 (mmm) REVERT: B 117 MET cc_start: 0.6747 (ppp) cc_final: 0.6404 (ppp) REVERT: B 136 TYR cc_start: 0.7309 (m-80) cc_final: 0.6875 (m-80) REVERT: B 197 MET cc_start: 0.5978 (mpp) cc_final: 0.5614 (mpp) REVERT: D 228 ARG cc_start: 0.6142 (mtp85) cc_final: 0.5848 (mtp85) REVERT: D 318 TYR cc_start: 0.6956 (t80) cc_final: 0.6343 (t80) REVERT: D 417 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6350 (tm-30) REVERT: D 436 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7381 (mtmt) REVERT: D 464 MET cc_start: 0.6609 (tmm) cc_final: 0.6221 (tmm) REVERT: F 15 TRP cc_start: 0.7328 (p-90) cc_final: 0.2819 (t60) REVERT: F 53 GLN cc_start: 0.7612 (mt0) cc_final: 0.6884 (tp-100) REVERT: F 236 TYR cc_start: 0.6448 (t80) cc_final: 0.6064 (t80) REVERT: F 237 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.5857 (tm-30) REVERT: F 252 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.5647 (t80) REVERT: F 262 TRP cc_start: 0.8010 (m-90) cc_final: 0.7287 (m-90) REVERT: G 147 GLU cc_start: 0.5911 (mm-30) cc_final: 0.5635 (mm-30) REVERT: G 148 MET cc_start: 0.8384 (tpp) cc_final: 0.7091 (tpp) REVERT: G 420 ASN cc_start: 0.7411 (t0) cc_final: 0.6868 (t0) REVERT: G 453 ASP cc_start: 0.7348 (m-30) cc_final: 0.6864 (m-30) REVERT: G 551 GLU cc_start: 0.6885 (mp0) cc_final: 0.6175 (tp30) REVERT: G 554 THR cc_start: 0.7556 (p) cc_final: 0.7283 (p) REVERT: G 640 ASP cc_start: 0.7647 (t0) cc_final: 0.6829 (t70) REVERT: G 644 VAL cc_start: 0.7375 (OUTLIER) cc_final: 0.6799 (t) REVERT: G 671 HIS cc_start: 0.6818 (OUTLIER) cc_final: 0.6315 (t-90) REVERT: G 903 LEU cc_start: 0.7433 (pt) cc_final: 0.7143 (pp) REVERT: H 131 LEU cc_start: 0.7766 (mt) cc_final: 0.7244 (mt) REVERT: H 236 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5416 (tp) REVERT: H 298 MET cc_start: 0.5150 (ptp) cc_final: 0.3958 (ppp) REVERT: J 1 MET cc_start: 0.2954 (tpp) cc_final: 0.2186 (tpp) REVERT: K 25 ARG cc_start: 0.6902 (tpm170) cc_final: 0.6448 (tpm170) REVERT: K 31 MET cc_start: 0.5866 (mpp) cc_final: 0.5568 (tpp) REVERT: K 52 TYR cc_start: 0.5295 (t80) cc_final: 0.4986 (t80) REVERT: K 98 MET cc_start: 0.1316 (mtm) cc_final: 0.0480 (mtp) REVERT: L 243 MET cc_start: 0.2941 (mmm) cc_final: 0.0881 (ptp) REVERT: L 258 MET cc_start: -0.3201 (tmt) cc_final: -0.3822 (tmt) REVERT: L 275 MET cc_start: -0.2102 (mtp) cc_final: -0.2351 (mtp) REVERT: L 305 LYS cc_start: 0.7193 (mmmm) cc_final: 0.6918 (mmmm) REVERT: M 42 LEU cc_start: 0.6576 (mt) cc_final: 0.6065 (mt) REVERT: M 54 LEU cc_start: 0.3112 (pt) cc_final: 0.0704 (tp) REVERT: M 69 MET cc_start: 0.7191 (ppp) cc_final: 0.5982 (mtt) REVERT: M 71 TRP cc_start: 0.6897 (t60) cc_final: 0.6608 (t60) REVERT: M 77 ILE cc_start: 0.8332 (mt) cc_final: 0.7768 (tt) REVERT: M 90 MET cc_start: 0.7026 (mmt) cc_final: 0.6529 (mmt) REVERT: M 112 TYR cc_start: 0.1232 (p90) cc_final: 0.1025 (p90) REVERT: M 156 LEU cc_start: 0.5415 (tp) cc_final: 0.5121 (tp) REVERT: M 224 MET cc_start: 0.5093 (ptt) cc_final: 0.2569 (ptt) REVERT: M 235 MET cc_start: 0.5514 (mmt) cc_final: 0.5235 (ppp) REVERT: M 323 MET cc_start: 0.3619 (mmp) cc_final: 0.3142 (mmp) REVERT: M 345 MET cc_start: 0.5262 (mmm) cc_final: 0.4858 (mmm) REVERT: M 366 ILE cc_start: 0.3045 (OUTLIER) cc_final: 0.2367 (tt) REVERT: M 374 MET cc_start: -0.0797 (mtt) cc_final: -0.1197 (mmt) REVERT: M 465 LEU cc_start: 0.3817 (mt) cc_final: 0.1926 (tp) REVERT: N 74 MET cc_start: 0.2842 (mtp) cc_final: 0.1994 (mtt) REVERT: N 204 LEU cc_start: 0.5877 (pp) cc_final: 0.5526 (mp) REVERT: N 287 MET cc_start: 0.4904 (tmm) cc_final: 0.4217 (tmm) REVERT: N 359 LEU cc_start: 0.6088 (tt) cc_final: 0.5636 (tt) REVERT: N 379 MET cc_start: 0.5759 (tpp) cc_final: 0.4985 (tpp) REVERT: N 380 MET cc_start: 0.6993 (tmm) cc_final: 0.6313 (tmm) REVERT: N 397 TYR cc_start: 0.6335 (OUTLIER) cc_final: 0.5652 (m-10) REVERT: N 427 ARG cc_start: 0.7038 (mmp80) cc_final: 0.6552 (ttp80) outliers start: 158 outliers final: 113 residues processed: 1048 average time/residue: 0.2026 time to fit residues: 344.2522 Evaluate side-chains 1076 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 955 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 408 GLN Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 619 THR Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 671 HIS Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 825 SER Chi-restraints excluded: chain G residue 856 THR Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 187 TRP Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain M residue 377 LEU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 175 optimal weight: 0.8980 chunk 419 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 384 optimal weight: 7.9990 chunk 388 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 330 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN D 37 GLN D 104 ASN D 279 ASN ** F 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 341 ASN ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 GLN ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 HIS ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 406 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.241692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.202581 restraints weight = 59782.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.208226 restraints weight = 66738.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.205500 restraints weight = 24802.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.206349 restraints weight = 24581.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.206509 restraints weight = 16843.896| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 36124 Z= 0.178 Angle : 1.106 68.372 49210 Z= 0.361 Chirality : 0.044 0.223 5554 Planarity : 0.005 0.063 6256 Dihedral : 4.967 71.169 4988 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.59 % Allowed : 21.83 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 4573 helix: 0.76 (0.10), residues: 2563 sheet: -0.07 (0.28), residues: 332 loop : -1.03 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 159 TYR 0.029 0.002 TYR N 333 PHE 0.038 0.002 PHE D 489 TRP 0.043 0.002 TRP L 143 HIS 0.010 0.001 HIS G 653 Details of bonding type rmsd covalent geometry : bond 0.00400 (36088) covalent geometry : angle 0.69432 (49115) hydrogen bonds : bond 0.04097 ( 1906) hydrogen bonds : angle 4.67714 ( 5490) metal coordination : bond 0.01546 ( 36) metal coordination : angle 19.61705 ( 95) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 994 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.7295 (mmm) cc_final: 0.6812 (mmm) REVERT: B 106 MET cc_start: 0.8060 (tpt) cc_final: 0.7740 (tpt) REVERT: B 117 MET cc_start: 0.6733 (ppp) cc_final: 0.6306 (ppp) REVERT: B 136 TYR cc_start: 0.7421 (m-80) cc_final: 0.7103 (m-80) REVERT: B 197 MET cc_start: 0.5998 (mpp) cc_final: 0.5685 (mpp) REVERT: D 199 GLU cc_start: 0.7348 (pm20) cc_final: 0.6976 (mm-30) REVERT: D 228 ARG cc_start: 0.6111 (mtp85) cc_final: 0.5897 (mtp85) REVERT: D 318 TYR cc_start: 0.6909 (t80) cc_final: 0.6338 (t80) REVERT: D 417 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6396 (tm-30) REVERT: D 436 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7466 (mttt) REVERT: D 464 MET cc_start: 0.6480 (tmm) cc_final: 0.6008 (tmm) REVERT: D 537 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7654 (ptpp) REVERT: D 558 ARG cc_start: 0.7476 (tpt-90) cc_final: 0.7217 (tmt-80) REVERT: D 591 MET cc_start: 0.5138 (tpp) cc_final: 0.4844 (tpt) REVERT: F 11 HIS cc_start: 0.8305 (m90) cc_final: 0.8031 (m90) REVERT: F 15 TRP cc_start: 0.7407 (p-90) cc_final: 0.3961 (t60) REVERT: F 53 GLN cc_start: 0.7802 (mt0) cc_final: 0.6842 (tp-100) REVERT: F 237 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.5934 (tm-30) REVERT: F 252 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.5825 (t80) REVERT: F 262 TRP cc_start: 0.8039 (m-90) cc_final: 0.7199 (m-90) REVERT: G 148 MET cc_start: 0.8414 (tpp) cc_final: 0.7187 (tpp) REVERT: G 245 GLU cc_start: 0.8015 (pm20) cc_final: 0.7773 (pm20) REVERT: G 420 ASN cc_start: 0.7377 (t0) cc_final: 0.7012 (t0) REVERT: G 453 ASP cc_start: 0.7363 (m-30) cc_final: 0.6885 (m-30) REVERT: G 551 GLU cc_start: 0.6870 (mp0) cc_final: 0.6225 (tp30) REVERT: G 589 LEU cc_start: 0.8624 (tp) cc_final: 0.8384 (tp) REVERT: G 640 ASP cc_start: 0.7588 (t0) cc_final: 0.6753 (t0) REVERT: G 644 VAL cc_start: 0.7171 (OUTLIER) cc_final: 0.6452 (t) REVERT: G 671 HIS cc_start: 0.7579 (OUTLIER) cc_final: 0.7090 (t-90) REVERT: G 767 LYS cc_start: 0.8510 (mppt) cc_final: 0.8137 (mptt) REVERT: G 888 MET cc_start: 0.5404 (ppp) cc_final: 0.5044 (ppp) REVERT: H 131 LEU cc_start: 0.7896 (mt) cc_final: 0.7266 (mt) REVERT: H 236 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5448 (tp) REVERT: H 237 PHE cc_start: 0.7746 (t80) cc_final: 0.7449 (t80) REVERT: H 298 MET cc_start: 0.5261 (ptp) cc_final: 0.3980 (ppp) REVERT: J 74 LEU cc_start: 0.8458 (mt) cc_final: 0.8220 (tt) REVERT: K 52 TYR cc_start: 0.5752 (t80) cc_final: 0.5486 (t80) REVERT: K 98 MET cc_start: 0.1028 (mtm) cc_final: -0.0029 (mtp) REVERT: L 1 MET cc_start: 0.2081 (ptt) cc_final: -0.0815 (ppp) REVERT: L 16 VAL cc_start: 0.8369 (t) cc_final: 0.8077 (t) REVERT: L 258 MET cc_start: -0.3191 (tmt) cc_final: -0.3836 (tmt) REVERT: L 305 LYS cc_start: 0.7176 (mmmm) cc_final: 0.6969 (mmmm) REVERT: M 54 LEU cc_start: 0.3203 (pt) cc_final: 0.1129 (tp) REVERT: M 69 MET cc_start: 0.7196 (ppp) cc_final: 0.6270 (mtt) REVERT: M 77 ILE cc_start: 0.8280 (mt) cc_final: 0.7641 (tt) REVERT: M 90 MET cc_start: 0.6358 (mmt) cc_final: 0.5584 (mmt) REVERT: M 210 LEU cc_start: 0.5685 (mt) cc_final: 0.5413 (mt) REVERT: M 222 LEU cc_start: 0.6353 (mp) cc_final: 0.5678 (tp) REVERT: M 224 MET cc_start: 0.4758 (ptt) cc_final: 0.4099 (ptm) REVERT: M 235 MET cc_start: 0.5040 (mmt) cc_final: 0.4829 (ptm) REVERT: M 299 PHE cc_start: 0.5749 (m-10) cc_final: 0.4920 (m-80) REVERT: M 323 MET cc_start: 0.4053 (mmp) cc_final: 0.3330 (mmp) REVERT: M 345 MET cc_start: 0.5311 (mmm) cc_final: 0.4964 (mmm) REVERT: M 366 ILE cc_start: 0.3135 (OUTLIER) cc_final: 0.0588 (mt) REVERT: M 374 MET cc_start: -0.1058 (mtt) cc_final: -0.1500 (mmt) REVERT: M 460 MET cc_start: 0.2087 (ptt) cc_final: 0.1727 (ptt) REVERT: M 465 LEU cc_start: 0.4000 (mt) cc_final: 0.3743 (tp) REVERT: M 466 PHE cc_start: 0.4215 (OUTLIER) cc_final: 0.3201 (t80) REVERT: N 74 MET cc_start: 0.2967 (mtp) cc_final: 0.2082 (mtt) REVERT: N 204 LEU cc_start: 0.6150 (pp) cc_final: 0.5699 (mp) REVERT: N 359 LEU cc_start: 0.5762 (tt) cc_final: 0.5405 (tt) REVERT: N 379 MET cc_start: 0.5419 (tpp) cc_final: 0.4629 (tpp) REVERT: N 380 MET cc_start: 0.6873 (tmm) cc_final: 0.6173 (tmm) REVERT: N 397 TYR cc_start: 0.6202 (OUTLIER) cc_final: 0.5660 (m-10) REVERT: N 427 ARG cc_start: 0.7228 (mmp80) cc_final: 0.6623 (ttp80) outliers start: 162 outliers final: 118 residues processed: 1065 average time/residue: 0.2026 time to fit residues: 352.5518 Evaluate side-chains 1089 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 962 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 408 GLN Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 619 THR Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 671 HIS Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 748 ARG Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 825 SER Chi-restraints excluded: chain G residue 856 THR Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 187 TRP Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 143 TRP Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 327 LEU Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 249 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 170 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 267 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 308 optimal weight: 30.0000 chunk 289 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 104 ASN D 279 ASN F 172 HIS F 341 ASN F 437 GLN ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 GLN ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN K 84 HIS L 236 GLN ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 198 ASN ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN N 406 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.242703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.201593 restraints weight = 60022.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.207264 restraints weight = 65943.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.205222 restraints weight = 24192.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.205878 restraints weight = 27414.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.206052 restraints weight = 19638.527| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 36124 Z= 0.157 Angle : 1.078 68.916 49210 Z= 0.358 Chirality : 0.044 0.207 5554 Planarity : 0.005 0.053 6256 Dihedral : 4.935 72.246 4988 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.28 % Allowed : 22.85 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.10 (0.13), residues: 4573 helix: 0.81 (0.10), residues: 2565 sheet: 0.06 (0.30), residues: 305 loop : -1.02 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 159 TYR 0.026 0.002 TYR M 435 PHE 0.046 0.002 PHE M 142 TRP 0.043 0.002 TRP L 143 HIS 0.009 0.001 HIS G 259 Details of bonding type rmsd covalent geometry : bond 0.00356 (36088) covalent geometry : angle 0.69726 (49115) hydrogen bonds : bond 0.03971 ( 1906) hydrogen bonds : angle 4.62164 ( 5490) metal coordination : bond 0.01321 ( 36) metal coordination : angle 18.72165 ( 95) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1129 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 978 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.7287 (mmm) cc_final: 0.6940 (mmm) REVERT: B 59 PHE cc_start: 0.7318 (t80) cc_final: 0.7096 (t80) REVERT: B 106 MET cc_start: 0.8037 (tpt) cc_final: 0.7720 (tpt) REVERT: B 136 TYR cc_start: 0.7415 (m-80) cc_final: 0.7100 (m-80) REVERT: B 215 ARG cc_start: 0.7936 (ttp-170) cc_final: 0.7718 (ttp-170) REVERT: D 199 GLU cc_start: 0.7280 (pm20) cc_final: 0.7050 (pm20) REVERT: D 228 ARG cc_start: 0.6136 (mtp85) cc_final: 0.5923 (mtp85) REVERT: D 318 TYR cc_start: 0.6903 (t80) cc_final: 0.6355 (t80) REVERT: D 385 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6528 (mmtm) REVERT: D 410 TYR cc_start: 0.4403 (p90) cc_final: 0.4059 (p90) REVERT: D 436 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7430 (mtmt) REVERT: D 464 MET cc_start: 0.6448 (tmm) cc_final: 0.6025 (tmm) REVERT: E 52 ASP cc_start: 0.6781 (m-30) cc_final: 0.6528 (m-30) REVERT: F 11 HIS cc_start: 0.8248 (m90) cc_final: 0.7981 (m90) REVERT: F 15 TRP cc_start: 0.7360 (p-90) cc_final: 0.3954 (t60) REVERT: F 53 GLN cc_start: 0.7606 (mt0) cc_final: 0.6752 (tp-100) REVERT: F 237 GLN cc_start: 0.6393 (OUTLIER) cc_final: 0.5871 (tm-30) REVERT: F 252 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.5893 (t80) REVERT: F 262 TRP cc_start: 0.8013 (m-90) cc_final: 0.7025 (m-90) REVERT: G 147 GLU cc_start: 0.5845 (mm-30) cc_final: 0.5577 (mm-30) REVERT: G 148 MET cc_start: 0.8440 (tpp) cc_final: 0.7217 (tpp) REVERT: G 209 LYS cc_start: 0.8641 (tmmt) cc_final: 0.8214 (mtpt) REVERT: G 245 GLU cc_start: 0.7958 (pm20) cc_final: 0.7738 (pm20) REVERT: G 408 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7512 (tp-100) REVERT: G 420 ASN cc_start: 0.7302 (t0) cc_final: 0.7004 (t0) REVERT: G 453 ASP cc_start: 0.7315 (m-30) cc_final: 0.6822 (m-30) REVERT: G 495 LYS cc_start: 0.7957 (mttt) cc_final: 0.7533 (mtmm) REVERT: G 644 VAL cc_start: 0.7048 (OUTLIER) cc_final: 0.6468 (t) REVERT: G 671 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.7132 (t-90) REVERT: G 748 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.6936 (pmt-80) REVERT: G 767 LYS cc_start: 0.8581 (mppt) cc_final: 0.8072 (mppt) REVERT: G 841 LYS cc_start: 0.6650 (mmmt) cc_final: 0.6113 (mmmt) REVERT: H 131 LEU cc_start: 0.7889 (mt) cc_final: 0.7262 (mt) REVERT: H 236 LEU cc_start: 0.5758 (OUTLIER) cc_final: 0.5160 (tp) REVERT: H 298 MET cc_start: 0.5136 (ptp) cc_final: 0.4015 (ppp) REVERT: I 53 ASP cc_start: 0.6190 (t70) cc_final: 0.5520 (t0) REVERT: J 74 LEU cc_start: 0.8441 (mt) cc_final: 0.8194 (tt) REVERT: K 25 ARG cc_start: 0.6911 (tpm170) cc_final: 0.6344 (tpm170) REVERT: K 31 MET cc_start: 0.6116 (mpp) cc_final: 0.5769 (tpp) REVERT: K 98 MET cc_start: 0.0965 (mtm) cc_final: -0.0119 (mtp) REVERT: L 1 MET cc_start: 0.2252 (ptt) cc_final: -0.0695 (ppp) REVERT: L 68 MET cc_start: 0.6101 (ppp) cc_final: 0.5451 (ppp) REVERT: L 234 PRO cc_start: 0.5633 (Cg_exo) cc_final: 0.5418 (Cg_endo) REVERT: L 243 MET cc_start: 0.1279 (mmm) cc_final: -0.0151 (ptp) REVERT: L 258 MET cc_start: -0.3325 (tmt) cc_final: -0.3843 (tmt) REVERT: L 272 LEU cc_start: 0.3411 (mp) cc_final: 0.1870 (mt) REVERT: L 275 MET cc_start: -0.1438 (ttt) cc_final: -0.1684 (mtp) REVERT: L 305 LYS cc_start: 0.7201 (mmmm) cc_final: 0.6994 (mmmm) REVERT: M 15 PHE cc_start: 0.5378 (m-80) cc_final: 0.4924 (m-10) REVERT: M 54 LEU cc_start: 0.3189 (pt) cc_final: 0.1157 (tp) REVERT: M 69 MET cc_start: 0.6963 (ppp) cc_final: 0.6233 (mtt) REVERT: M 90 MET cc_start: 0.6290 (mmt) cc_final: 0.5800 (mmt) REVERT: M 224 MET cc_start: 0.4771 (ptt) cc_final: 0.4502 (ptm) REVERT: M 279 PHE cc_start: 0.5694 (p90) cc_final: 0.5456 (p90) REVERT: M 299 PHE cc_start: 0.5898 (m-10) cc_final: 0.5022 (m-80) REVERT: M 345 MET cc_start: 0.5060 (mmm) cc_final: 0.4785 (mmm) REVERT: M 366 ILE cc_start: 0.3666 (OUTLIER) cc_final: 0.2843 (tt) REVERT: M 374 MET cc_start: -0.0652 (mtt) cc_final: -0.1728 (mmt) REVERT: M 460 MET cc_start: 0.1976 (ptt) cc_final: 0.1740 (ptt) REVERT: M 465 LEU cc_start: 0.3754 (mt) cc_final: 0.3481 (tp) REVERT: M 466 PHE cc_start: 0.4577 (OUTLIER) cc_final: 0.3631 (t80) REVERT: N 52 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5521 (mt) REVERT: N 74 MET cc_start: 0.2453 (mtp) cc_final: 0.1925 (mtt) REVERT: N 176 LEU cc_start: 0.5188 (mt) cc_final: 0.4549 (tt) REVERT: N 204 LEU cc_start: 0.6242 (pp) cc_final: 0.5770 (mp) REVERT: N 359 LEU cc_start: 0.5410 (tt) cc_final: 0.4827 (tt) REVERT: N 379 MET cc_start: 0.5273 (tpp) cc_final: 0.4560 (tpp) REVERT: N 380 MET cc_start: 0.6907 (tmm) cc_final: 0.6151 (tmm) REVERT: N 395 LYS cc_start: 0.6345 (mtpt) cc_final: 0.6134 (mtmt) REVERT: N 397 TYR cc_start: 0.6277 (OUTLIER) cc_final: 0.5805 (m-10) REVERT: N 427 ARG cc_start: 0.7152 (mmp80) cc_final: 0.6576 (ttp80) outliers start: 151 outliers final: 111 residues processed: 1045 average time/residue: 0.2010 time to fit residues: 342.7683 Evaluate side-chains 1068 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 945 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 385 LYS Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 408 GLN Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 482 LYS Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 619 THR Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 671 HIS Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 748 ARG Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 825 SER Chi-restraints excluded: chain G residue 856 THR Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 187 TRP Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 143 TRP Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 360 PHE Chi-restraints excluded: chain N residue 362 TYR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 282 optimal weight: 30.0000 chunk 316 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 362 optimal weight: 0.0060 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 104 ASN D 279 ASN F 172 HIS F 304 HIS F 341 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 763 GLN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 HIS L 236 GLN ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 198 ASN M 348 HIS N 406 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.243722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.204821 restraints weight = 60467.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.206735 restraints weight = 77551.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.206492 restraints weight = 43850.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.206755 restraints weight = 28075.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.207454 restraints weight = 22516.427| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36124 Z= 0.140 Angle : 1.033 69.311 49210 Z= 0.359 Chirality : 0.044 0.284 5554 Planarity : 0.004 0.054 6256 Dihedral : 4.875 72.810 4988 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.00 % Allowed : 24.18 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.16 (0.13), residues: 4573 helix: 0.87 (0.10), residues: 2567 sheet: -0.08 (0.30), residues: 309 loop : -0.97 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 159 TYR 0.043 0.002 TYR K 52 PHE 0.058 0.002 PHE M 286 TRP 0.063 0.002 TRP M 122 HIS 0.027 0.001 HIS M 117 Details of bonding type rmsd covalent geometry : bond 0.00318 (36088) covalent geometry : angle 0.70305 (49115) hydrogen bonds : bond 0.03831 ( 1906) hydrogen bonds : angle 4.57115 ( 5490) metal coordination : bond 0.01080 ( 36) metal coordination : angle 17.23928 ( 95) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 963 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.7343 (mmm) cc_final: 0.6780 (mmm) REVERT: B 59 PHE cc_start: 0.7050 (t80) cc_final: 0.6780 (t80) REVERT: B 106 MET cc_start: 0.8088 (tpt) cc_final: 0.7884 (tpt) REVERT: B 117 MET cc_start: 0.6466 (ppp) cc_final: 0.6151 (ppp) REVERT: B 136 TYR cc_start: 0.7423 (m-80) cc_final: 0.7090 (m-80) REVERT: D 199 GLU cc_start: 0.7332 (pm20) cc_final: 0.7059 (pm20) REVERT: D 228 ARG cc_start: 0.6054 (mtp85) cc_final: 0.5853 (mtp85) REVERT: D 318 TYR cc_start: 0.6960 (t80) cc_final: 0.6378 (t80) REVERT: D 354 MET cc_start: 0.5375 (pmm) cc_final: 0.4158 (ttp) REVERT: D 385 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6485 (mmtm) REVERT: D 410 TYR cc_start: 0.4403 (p90) cc_final: 0.4097 (p90) REVERT: D 417 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6409 (tm-30) REVERT: D 436 LYS cc_start: 0.7948 (mmtt) cc_final: 0.7425 (mtmt) REVERT: D 464 MET cc_start: 0.6405 (tmm) cc_final: 0.6044 (tmm) REVERT: D 537 LYS cc_start: 0.7706 (ptpp) cc_final: 0.7125 (ptpp) REVERT: F 53 GLN cc_start: 0.7684 (mt0) cc_final: 0.6784 (tp-100) REVERT: F 237 GLN cc_start: 0.6365 (OUTLIER) cc_final: 0.5915 (tm-30) REVERT: F 252 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.5770 (t80) REVERT: F 262 TRP cc_start: 0.7995 (m-90) cc_final: 0.6942 (m-90) REVERT: G 147 GLU cc_start: 0.5986 (mm-30) cc_final: 0.5625 (mm-30) REVERT: G 148 MET cc_start: 0.8509 (tpp) cc_final: 0.7136 (tpp) REVERT: G 209 LYS cc_start: 0.8836 (tmmt) cc_final: 0.8175 (mtpt) REVERT: G 215 TYR cc_start: 0.8657 (t80) cc_final: 0.8302 (t80) REVERT: G 420 ASN cc_start: 0.7349 (t0) cc_final: 0.6832 (t0) REVERT: G 453 ASP cc_start: 0.7214 (m-30) cc_final: 0.6675 (m-30) REVERT: G 454 GLN cc_start: 0.7257 (mm-40) cc_final: 0.6681 (mm-40) REVERT: G 495 LYS cc_start: 0.7995 (mttt) cc_final: 0.7574 (mtmm) REVERT: G 551 GLU cc_start: 0.6699 (mp0) cc_final: 0.5841 (tp30) REVERT: G 644 VAL cc_start: 0.7265 (OUTLIER) cc_final: 0.6724 (t) REVERT: G 671 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.7159 (t-90) REVERT: G 695 PHE cc_start: 0.6829 (t80) cc_final: 0.6616 (t80) REVERT: G 767 LYS cc_start: 0.8559 (mppt) cc_final: 0.8040 (mppt) REVERT: H 131 LEU cc_start: 0.7847 (mt) cc_final: 0.7253 (mt) REVERT: H 236 LEU cc_start: 0.5684 (mp) cc_final: 0.5120 (tp) REVERT: H 298 MET cc_start: 0.5173 (ptp) cc_final: 0.4081 (ppp) REVERT: I 53 ASP cc_start: 0.6222 (OUTLIER) cc_final: 0.5527 (t0) REVERT: J 74 LEU cc_start: 0.8394 (mt) cc_final: 0.8146 (tt) REVERT: K 25 ARG cc_start: 0.6838 (tpm170) cc_final: 0.6277 (tpm170) REVERT: K 31 MET cc_start: 0.6245 (mpp) cc_final: 0.5913 (tpp) REVERT: K 53 TRP cc_start: 0.6182 (m100) cc_final: 0.5885 (m-10) REVERT: K 57 ASP cc_start: 0.5839 (p0) cc_final: 0.5271 (p0) REVERT: K 98 MET cc_start: 0.0631 (mtm) cc_final: -0.0395 (mtp) REVERT: L 1 MET cc_start: 0.2496 (ptt) cc_final: -0.0491 (ppp) REVERT: L 24 ARG cc_start: 0.3056 (ptt90) cc_final: 0.1319 (ptt180) REVERT: L 68 MET cc_start: 0.6515 (ppp) cc_final: 0.5951 (ppp) REVERT: L 243 MET cc_start: 0.1102 (mmm) cc_final: -0.0172 (ptp) REVERT: L 258 MET cc_start: -0.3636 (tmt) cc_final: -0.3989 (tmt) REVERT: L 272 LEU cc_start: 0.3919 (mp) cc_final: 0.2486 (mt) REVERT: L 305 LYS cc_start: 0.7678 (mmmm) cc_final: 0.7455 (mmmm) REVERT: M 69 MET cc_start: 0.6807 (ppp) cc_final: 0.6223 (mtt) REVERT: M 90 MET cc_start: 0.6555 (mmt) cc_final: 0.5969 (mmt) REVERT: M 174 PHE cc_start: 0.5010 (OUTLIER) cc_final: 0.3284 (t80) REVERT: M 185 MET cc_start: 0.4270 (ppp) cc_final: 0.4043 (ppp) REVERT: M 209 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6827 (tm-30) REVERT: M 299 PHE cc_start: 0.6070 (m-10) cc_final: 0.5410 (m-80) REVERT: M 345 MET cc_start: 0.5330 (mmm) cc_final: 0.4918 (mmm) REVERT: M 366 ILE cc_start: 0.3525 (OUTLIER) cc_final: 0.0993 (mt) REVERT: M 466 PHE cc_start: 0.4745 (t80) cc_final: 0.3906 (t80) REVERT: N 52 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.5971 (mt) REVERT: N 74 MET cc_start: 0.2514 (mtp) cc_final: 0.2178 (mtt) REVERT: N 94 TRP cc_start: 0.5532 (t-100) cc_final: 0.4032 (t-100) REVERT: N 176 LEU cc_start: 0.5122 (mt) cc_final: 0.4598 (tt) REVERT: N 204 LEU cc_start: 0.6634 (pp) cc_final: 0.6152 (mp) REVERT: N 359 LEU cc_start: 0.5358 (tt) cc_final: 0.4826 (tt) REVERT: N 379 MET cc_start: 0.4900 (tpp) cc_final: 0.4219 (tpp) REVERT: N 380 MET cc_start: 0.6895 (tmm) cc_final: 0.6108 (tmm) REVERT: N 397 TYR cc_start: 0.6307 (OUTLIER) cc_final: 0.5831 (m-10) REVERT: N 427 ARG cc_start: 0.7048 (mmp80) cc_final: 0.6534 (ttp80) outliers start: 141 outliers final: 109 residues processed: 1027 average time/residue: 0.2063 time to fit residues: 344.5113 Evaluate side-chains 1066 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 946 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 385 LYS Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 408 GLN Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 482 LYS Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 619 THR Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 671 HIS Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 825 SER Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 187 TRP Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 591 LEU Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 143 TRP Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 327 LEU Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 360 PHE Chi-restraints excluded: chain N residue 362 TYR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 359 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 246 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 388 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 51 optimal weight: 0.0270 chunk 71 optimal weight: 5.9990 chunk 282 optimal weight: 30.0000 chunk 420 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 overall best weight: 1.0840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 104 ASN D 540 ASN ** F 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 341 ASN ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 GLN ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 747 HIS ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 HIS L 236 GLN ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 198 ASN N 406 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.241055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.203587 restraints weight = 59614.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.207675 restraints weight = 66155.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.204405 restraints weight = 25236.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.205315 restraints weight = 27863.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.205301 restraints weight = 17773.891| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36124 Z= 0.163 Angle : 1.069 70.616 49210 Z= 0.375 Chirality : 0.045 0.285 5554 Planarity : 0.005 0.056 6256 Dihedral : 4.952 70.809 4988 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 3.83 % Allowed : 24.49 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.12 (0.13), residues: 4573 helix: 0.86 (0.10), residues: 2566 sheet: -0.21 (0.30), residues: 304 loop : -1.01 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 159 TYR 0.037 0.002 TYR N 308 PHE 0.039 0.002 PHE M 142 TRP 0.091 0.002 TRP M 122 HIS 0.012 0.001 HIS M 117 Details of bonding type rmsd covalent geometry : bond 0.00370 (36088) covalent geometry : angle 0.73368 (49115) hydrogen bonds : bond 0.03918 ( 1906) hydrogen bonds : angle 4.59049 ( 5490) metal coordination : bond 0.01377 ( 36) metal coordination : angle 17.72557 ( 95) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 967 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.7204 (mmm) cc_final: 0.6863 (mmm) REVERT: B 106 MET cc_start: 0.7647 (tpt) cc_final: 0.7380 (tpt) REVERT: B 136 TYR cc_start: 0.7521 (m-80) cc_final: 0.7308 (m-80) REVERT: D 318 TYR cc_start: 0.7009 (t80) cc_final: 0.6420 (t80) REVERT: D 385 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6453 (mmtm) REVERT: D 410 TYR cc_start: 0.4624 (p90) cc_final: 0.4154 (p90) REVERT: D 417 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6358 (pt0) REVERT: D 436 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7373 (mtmt) REVERT: D 464 MET cc_start: 0.6357 (tmm) cc_final: 0.6057 (tmm) REVERT: D 537 LYS cc_start: 0.7655 (ptpp) cc_final: 0.7036 (ptpp) REVERT: F 11 HIS cc_start: 0.8023 (m90) cc_final: 0.7652 (m-70) REVERT: F 15 TRP cc_start: 0.7442 (p-90) cc_final: 0.3924 (t60) REVERT: F 53 GLN cc_start: 0.7684 (mt0) cc_final: 0.6840 (tp-100) REVERT: F 198 ARG cc_start: 0.8398 (mtt180) cc_final: 0.7913 (mtp180) REVERT: F 237 GLN cc_start: 0.6497 (OUTLIER) cc_final: 0.5991 (tm-30) REVERT: F 252 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.5752 (t80) REVERT: F 262 TRP cc_start: 0.8037 (m-90) cc_final: 0.6979 (m-90) REVERT: G 147 GLU cc_start: 0.5991 (mm-30) cc_final: 0.5656 (mm-30) REVERT: G 148 MET cc_start: 0.8440 (tpp) cc_final: 0.7253 (tpp) REVERT: G 420 ASN cc_start: 0.7352 (t0) cc_final: 0.6942 (t0) REVERT: G 424 ARG cc_start: 0.7229 (ptm160) cc_final: 0.6924 (ptp-170) REVERT: G 453 ASP cc_start: 0.7291 (m-30) cc_final: 0.6756 (m-30) REVERT: G 495 LYS cc_start: 0.7880 (mttt) cc_final: 0.7419 (mtmm) REVERT: G 551 GLU cc_start: 0.6656 (mp0) cc_final: 0.6183 (tp30) REVERT: G 644 VAL cc_start: 0.7082 (OUTLIER) cc_final: 0.6543 (t) REVERT: G 671 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.7177 (t-90) REVERT: G 748 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6895 (pmt-80) REVERT: G 767 LYS cc_start: 0.8536 (mppt) cc_final: 0.8203 (mptt) REVERT: G 841 LYS cc_start: 0.6741 (mmmt) cc_final: 0.6161 (mmmt) REVERT: H 131 LEU cc_start: 0.7877 (mt) cc_final: 0.7274 (mt) REVERT: H 236 LEU cc_start: 0.5750 (mp) cc_final: 0.5167 (tp) REVERT: H 298 MET cc_start: 0.4982 (ptp) cc_final: 0.3870 (ppp) REVERT: I 53 ASP cc_start: 0.6275 (OUTLIER) cc_final: 0.5619 (t0) REVERT: J 1 MET cc_start: 0.0774 (tpt) cc_final: 0.0537 (tpp) REVERT: J 74 LEU cc_start: 0.8441 (mt) cc_final: 0.8201 (tt) REVERT: K 25 ARG cc_start: 0.6796 (tpm170) cc_final: 0.6214 (tpm170) REVERT: K 31 MET cc_start: 0.6146 (mpp) cc_final: 0.5822 (tpp) REVERT: K 57 ASP cc_start: 0.5980 (p0) cc_final: 0.5333 (p0) REVERT: K 98 MET cc_start: 0.1072 (mtm) cc_final: 0.0029 (mtp) REVERT: L 1 MET cc_start: 0.2321 (ptt) cc_final: -0.0687 (ppp) REVERT: L 13 ILE cc_start: -0.0473 (tt) cc_final: -0.1016 (mt) REVERT: L 24 ARG cc_start: 0.2627 (ptt90) cc_final: 0.1175 (ptt180) REVERT: L 68 MET cc_start: 0.6217 (ppp) cc_final: 0.5859 (ppp) REVERT: L 243 MET cc_start: 0.0978 (mmm) cc_final: -0.0156 (ptp) REVERT: L 258 MET cc_start: -0.3325 (tmt) cc_final: -0.3883 (tmt) REVERT: L 272 LEU cc_start: 0.3691 (mp) cc_final: 0.2246 (mt) REVERT: M 15 PHE cc_start: 0.5002 (m-80) cc_final: 0.4709 (m-10) REVERT: M 54 LEU cc_start: 0.3811 (pt) cc_final: 0.2154 (mt) REVERT: M 69 MET cc_start: 0.6786 (ppp) cc_final: 0.6228 (mtt) REVERT: M 77 ILE cc_start: 0.7729 (mp) cc_final: 0.6995 (tt) REVERT: M 90 MET cc_start: 0.6233 (mmt) cc_final: 0.5718 (mmt) REVERT: M 174 PHE cc_start: 0.4940 (OUTLIER) cc_final: 0.3136 (t80) REVERT: M 185 MET cc_start: 0.4240 (ppp) cc_final: 0.4014 (ppp) REVERT: M 299 PHE cc_start: 0.5822 (m-10) cc_final: 0.4939 (m-80) REVERT: M 323 MET cc_start: 0.3777 (mmp) cc_final: 0.2933 (mmp) REVERT: M 345 MET cc_start: 0.5307 (mmm) cc_final: 0.4883 (mmm) REVERT: M 366 ILE cc_start: 0.3753 (pt) cc_final: 0.1412 (mt) REVERT: M 462 LEU cc_start: 0.7429 (mm) cc_final: 0.6327 (pp) REVERT: M 465 LEU cc_start: 0.3791 (mt) cc_final: 0.2715 (tp) REVERT: M 486 LEU cc_start: 0.7447 (tp) cc_final: 0.6577 (mt) REVERT: N 74 MET cc_start: 0.2659 (mtp) cc_final: 0.2196 (mtt) REVERT: N 94 TRP cc_start: 0.5232 (t-100) cc_final: 0.4606 (t-100) REVERT: N 176 LEU cc_start: 0.5126 (mt) cc_final: 0.4529 (tt) REVERT: N 204 LEU cc_start: 0.6720 (pp) cc_final: 0.6206 (mp) REVERT: N 359 LEU cc_start: 0.5288 (tt) cc_final: 0.4686 (tt) REVERT: N 379 MET cc_start: 0.4896 (tpp) cc_final: 0.4295 (tpp) REVERT: N 380 MET cc_start: 0.6810 (tmm) cc_final: 0.6044 (tmm) REVERT: N 397 TYR cc_start: 0.6182 (OUTLIER) cc_final: 0.5798 (m-10) REVERT: N 427 ARG cc_start: 0.7110 (mmp80) cc_final: 0.6758 (ttp80) outliers start: 135 outliers final: 110 residues processed: 1031 average time/residue: 0.2062 time to fit residues: 344.6942 Evaluate side-chains 1078 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 958 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 385 LYS Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 389 ARG Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 619 THR Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 671 HIS Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 748 ARG Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 825 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 187 TRP Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain L residue 236 GLN Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 143 TRP Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 327 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 347 MET Chi-restraints excluded: chain N residue 360 PHE Chi-restraints excluded: chain N residue 362 TYR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 34 optimal weight: 0.8980 chunk 443 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 chunk 133 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 359 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 182 optimal weight: 0.5980 chunk 162 optimal weight: 0.5980 chunk 326 optimal weight: 7.9990 chunk 335 optimal weight: 0.0010 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 104 ASN D 279 ASN F 304 HIS F 341 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 GLN ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 HIS ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 HIS L 236 GLN ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 406 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.244668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.205648 restraints weight = 60575.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.206544 restraints weight = 75854.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.208295 restraints weight = 40093.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.207694 restraints weight = 28928.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.208894 restraints weight = 23736.587| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36124 Z= 0.139 Angle : 1.018 70.384 49210 Z= 0.376 Chirality : 0.044 0.266 5554 Planarity : 0.005 0.071 6256 Dihedral : 4.891 73.147 4988 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.30 % Favored : 96.68 % Rotamer: Outliers : 3.20 % Allowed : 25.60 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.13), residues: 4573 helix: 0.96 (0.10), residues: 2562 sheet: -0.09 (0.31), residues: 283 loop : -0.96 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 105 TYR 0.037 0.002 TYR N 308 PHE 0.034 0.002 PHE M 480 TRP 0.110 0.002 TRP M 122 HIS 0.009 0.001 HIS G 259 Details of bonding type rmsd covalent geometry : bond 0.00314 (36088) covalent geometry : angle 0.73975 (49115) hydrogen bonds : bond 0.03794 ( 1906) hydrogen bonds : angle 4.54400 ( 5490) metal coordination : bond 0.01012 ( 36) metal coordination : angle 15.91884 ( 95) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 982 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.7172 (mmm) cc_final: 0.6891 (mmm) REVERT: B 48 TRP cc_start: 0.5913 (t-100) cc_final: 0.5262 (t60) REVERT: B 59 PHE cc_start: 0.6966 (t80) cc_final: 0.6737 (t80) REVERT: B 106 MET cc_start: 0.7636 (tpt) cc_final: 0.7282 (tpt) REVERT: B 204 LYS cc_start: 0.7196 (tppt) cc_final: 0.6756 (tptp) REVERT: D 76 MET cc_start: 0.7059 (ppp) cc_final: 0.6775 (ppp) REVERT: D 199 GLU cc_start: 0.7260 (pm20) cc_final: 0.6369 (mp0) REVERT: D 228 ARG cc_start: 0.6014 (mtp85) cc_final: 0.5751 (mtp85) REVERT: D 318 TYR cc_start: 0.6943 (t80) cc_final: 0.6336 (t80) REVERT: D 354 MET cc_start: 0.5245 (pmm) cc_final: 0.4084 (ttp) REVERT: D 410 TYR cc_start: 0.4560 (p90) cc_final: 0.4185 (p90) REVERT: D 436 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7367 (mtmt) REVERT: D 464 MET cc_start: 0.6305 (tmm) cc_final: 0.5140 (tmm) REVERT: D 532 MET cc_start: 0.6104 (mmp) cc_final: 0.5643 (mmm) REVERT: D 537 LYS cc_start: 0.7754 (ptpp) cc_final: 0.7218 (ptpp) REVERT: E 31 ASP cc_start: 0.6678 (t0) cc_final: 0.5936 (m-30) REVERT: F 53 GLN cc_start: 0.7596 (mt0) cc_final: 0.6830 (tp-100) REVERT: F 198 ARG cc_start: 0.8204 (mtt180) cc_final: 0.7619 (mtp180) REVERT: F 237 GLN cc_start: 0.6321 (OUTLIER) cc_final: 0.5756 (tm-30) REVERT: F 252 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.5301 (t80) REVERT: F 262 TRP cc_start: 0.7836 (m-90) cc_final: 0.6860 (m-90) REVERT: F 341 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7821 (t160) REVERT: F 344 GLU cc_start: 0.7439 (tp30) cc_final: 0.7157 (tp30) REVERT: G 148 MET cc_start: 0.8451 (tpp) cc_final: 0.7177 (tpp) REVERT: G 169 ASP cc_start: 0.7771 (p0) cc_final: 0.7510 (p0) REVERT: G 215 TYR cc_start: 0.8439 (t80) cc_final: 0.8139 (t80) REVERT: G 420 ASN cc_start: 0.7239 (t0) cc_final: 0.6845 (t0) REVERT: G 453 ASP cc_start: 0.7107 (m-30) cc_final: 0.6531 (m-30) REVERT: G 454 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6962 (mm-40) REVERT: G 495 LYS cc_start: 0.7939 (mttt) cc_final: 0.7563 (mtmm) REVERT: G 551 GLU cc_start: 0.6558 (mp0) cc_final: 0.5596 (tp30) REVERT: G 644 VAL cc_start: 0.7063 (OUTLIER) cc_final: 0.6497 (t) REVERT: G 671 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.7201 (t-90) REVERT: G 734 PHE cc_start: 0.7231 (m-80) cc_final: 0.6701 (m-80) REVERT: G 748 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6875 (pmt-80) REVERT: G 767 LYS cc_start: 0.8595 (mppt) cc_final: 0.8217 (mptt) REVERT: H 131 LEU cc_start: 0.7936 (mt) cc_final: 0.7386 (mt) REVERT: H 236 LEU cc_start: 0.5688 (mp) cc_final: 0.5108 (tp) REVERT: H 245 ILE cc_start: 0.3979 (tp) cc_final: 0.3764 (tp) REVERT: H 298 MET cc_start: 0.5029 (ptp) cc_final: 0.3930 (ppp) REVERT: I 53 ASP cc_start: 0.6433 (OUTLIER) cc_final: 0.6049 (t0) REVERT: J 74 LEU cc_start: 0.8406 (mt) cc_final: 0.8176 (tt) REVERT: K 31 MET cc_start: 0.6080 (mpp) cc_final: 0.5798 (tpp) REVERT: K 52 TYR cc_start: 0.4827 (t80) cc_final: 0.4392 (t80) REVERT: K 98 MET cc_start: 0.0744 (mtm) cc_final: -0.0298 (mtp) REVERT: L 1 MET cc_start: 0.2525 (ptt) cc_final: -0.0880 (tmm) REVERT: L 13 ILE cc_start: -0.0529 (tt) cc_final: -0.1084 (mt) REVERT: L 24 ARG cc_start: 0.2909 (ptt90) cc_final: 0.1444 (ptt180) REVERT: L 68 MET cc_start: 0.6594 (ppp) cc_final: 0.6253 (ppp) REVERT: L 234 PRO cc_start: 0.5820 (Cg_exo) cc_final: 0.5608 (Cg_endo) REVERT: L 258 MET cc_start: -0.3784 (tmt) cc_final: -0.4020 (tmt) REVERT: L 272 LEU cc_start: 0.3968 (mp) cc_final: 0.2502 (mt) REVERT: M 15 PHE cc_start: 0.5019 (m-80) cc_final: 0.4703 (m-10) REVERT: M 54 LEU cc_start: 0.3986 (pt) cc_final: 0.2139 (mt) REVERT: M 69 MET cc_start: 0.6586 (ppp) cc_final: 0.6345 (mtt) REVERT: M 90 MET cc_start: 0.6331 (mmt) cc_final: 0.5827 (mmt) REVERT: M 121 MET cc_start: 0.4218 (pmm) cc_final: 0.3163 (pmm) REVERT: M 174 PHE cc_start: 0.4489 (OUTLIER) cc_final: 0.2758 (t80) REVERT: M 185 MET cc_start: 0.4166 (ppp) cc_final: 0.3858 (ppp) REVERT: M 223 LEU cc_start: 0.6390 (tt) cc_final: 0.4694 (mt) REVERT: M 299 PHE cc_start: 0.6144 (m-10) cc_final: 0.5412 (m-80) REVERT: M 323 MET cc_start: 0.3543 (mmp) cc_final: 0.2509 (mmp) REVERT: M 345 MET cc_start: 0.5279 (mmm) cc_final: 0.4837 (mmm) REVERT: M 374 MET cc_start: -0.0506 (mtt) cc_final: -0.1194 (mtt) REVERT: M 460 MET cc_start: 0.1832 (ptt) cc_final: 0.1279 (ptt) REVERT: M 462 LEU cc_start: 0.7439 (mm) cc_final: 0.6327 (pp) REVERT: M 486 LEU cc_start: 0.7700 (tp) cc_final: 0.6684 (mt) REVERT: N 74 MET cc_start: 0.2977 (mtp) cc_final: 0.2040 (mtt) REVERT: N 94 TRP cc_start: 0.5350 (t-100) cc_final: 0.4644 (t-100) REVERT: N 204 LEU cc_start: 0.6660 (pp) cc_final: 0.6169 (mp) REVERT: N 359 LEU cc_start: 0.5135 (tt) cc_final: 0.4869 (tt) REVERT: N 379 MET cc_start: 0.4750 (tpp) cc_final: 0.4152 (tpp) REVERT: N 380 MET cc_start: 0.6839 (tmm) cc_final: 0.6081 (tmm) REVERT: N 397 TYR cc_start: 0.6213 (OUTLIER) cc_final: 0.5811 (m-10) outliers start: 113 outliers final: 91 residues processed: 1030 average time/residue: 0.2076 time to fit residues: 347.1025 Evaluate side-chains 1046 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 946 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 341 ASN Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 389 ARG Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 408 GLN Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 482 LYS Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 619 THR Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 671 HIS Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 748 ARG Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 825 SER Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 187 TRP Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain L residue 236 GLN Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 122 TRP Chi-restraints excluded: chain M residue 143 TRP Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 327 LEU Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 347 MET Chi-restraints excluded: chain N residue 360 PHE Chi-restraints excluded: chain N residue 362 TYR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 9 optimal weight: 0.5980 chunk 280 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 220 optimal weight: 1.9990 chunk 361 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 396 optimal weight: 20.0000 chunk 263 optimal weight: 0.0870 chunk 34 optimal weight: 0.8980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 HIS F 341 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 GLN ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 HIS L 135 ASN L 236 GLN ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 198 ASN N 406 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.242358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.202080 restraints weight = 59682.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.206407 restraints weight = 71242.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.205808 restraints weight = 27169.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.206341 restraints weight = 21909.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.206573 restraints weight = 17553.569| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36124 Z= 0.153 Angle : 1.032 71.401 49210 Z= 0.382 Chirality : 0.045 0.286 5554 Planarity : 0.005 0.063 6256 Dihedral : 4.872 72.686 4987 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 3.17 % Allowed : 25.68 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.13), residues: 4573 helix: 0.96 (0.10), residues: 2562 sheet: -0.23 (0.30), residues: 297 loop : -0.94 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 105 TYR 0.039 0.002 TYR N 308 PHE 0.036 0.002 PHE G 337 TRP 0.106 0.002 TRP M 122 HIS 0.008 0.001 HIS G 259 Details of bonding type rmsd covalent geometry : bond 0.00347 (36088) covalent geometry : angle 0.75433 (49115) hydrogen bonds : bond 0.03850 ( 1906) hydrogen bonds : angle 4.57454 ( 5490) metal coordination : bond 0.01266 ( 36) metal coordination : angle 16.05713 ( 95) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7661.96 seconds wall clock time: 132 minutes 7.68 seconds (7927.68 seconds total)