Starting phenix.real_space_refine on Sun Sep 29 00:39:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/09_2024/6b6h_7059_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/09_2024/6b6h_7059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/09_2024/6b6h_7059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/09_2024/6b6h_7059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/09_2024/6b6h_7059_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/09_2024/6b6h_7059_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.022 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 183 5.49 5 Mg 1 5.21 5 S 149 5.16 5 C 22425 2.51 5 N 6502 2.21 5 O 7408 1.98 5 H 35400 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 72070 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3599 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3556 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 21152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 21152 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 21010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 21010 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "E" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1261 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 8105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 8105 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 15, 'TRANS': 481} Chain breaks: 1 Chain: "G" Number of atoms: 3219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3219 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 196} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3223 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 196} Chain: "I" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1198 Classifications: {'peptide': 75} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 69} Chain: "1" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 2796 Classifications: {'DNA': 88} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 87} Chain: "2" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 2805 Classifications: {'DNA': 88} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 87} Chain: "3" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 99 Unusual residues: {'GTP': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="GTP 3 1 " pdbres=" A 3 2 " Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29207 SG CYS D 70 137.197 63.206 64.179 1.00 20.00 S ATOM 29236 SG CYS D 72 139.792 65.051 62.894 1.00 20.00 S ATOM 29466 SG CYS D 85 140.409 61.675 63.220 1.00 20.00 S ATOM 29513 SG CYS D 88 141.285 62.722 66.424 1.00 20.00 S ATOM 41046 SG CYS D 814 116.790 25.113 117.696 1.00 20.00 S ATOM 42183 SG CYS D 888 119.056 27.662 117.182 1.00 20.00 S ATOM 42312 SG CYS D 898 115.608 27.633 120.215 1.00 20.00 S Time building chain proxies: 24.41, per 1000 atoms: 0.34 Number of scatterers: 72070 At special positions: 0 Unit cell: (221.4, 164.7, 189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 149 16.00 P 183 15.00 Mg 1 11.99 O 7408 8.00 N 6502 7.00 C 22425 6.00 H 35400 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.12 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 6 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7774 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 56 sheets defined 44.1% alpha, 13.5% beta 65 base pairs and 140 stacking pairs defined. Time for finding SS restraints: 26.15 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.808A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 4.214A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.589A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 51 removed outlier: 3.870A pdb=" N MET B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.860A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 233 removed outlier: 5.736A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.858A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.610A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY C 89 " --> pdb=" O CYS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.150A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.702A pdb=" N LEU C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 319 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 391 removed outlier: 3.586A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 removed outlier: 3.620A pdb=" N GLY C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.711A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.576A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 609 through 614 removed outlier: 4.175A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 609 through 614' Processing helix chain 'C' and resid 662 through 668 removed outlier: 3.537A pdb=" N ILE C 668 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.649A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.716A pdb=" N LEU C 946 " --> pdb=" O ASP C 942 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1038 removed outlier: 3.646A pdb=" N GLN C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.535A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.714A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1261 through 1265 Processing helix chain 'C' and resid 1272 through 1282 removed outlier: 4.145A pdb=" N LEU C1278 " --> pdb=" O GLU C1274 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1293 Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.923A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.679A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.620A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 173 removed outlier: 3.876A pdb=" N ASP D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 208 removed outlier: 4.154A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.065A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.762A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.524A pdb=" N GLN D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.003A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.725A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 540 removed outlier: 4.055A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.837A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 593 Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.616A pdb=" N VAL D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 671 Processing helix chain 'D' and resid 675 through 700 Processing helix chain 'D' and resid 720 through 729 removed outlier: 3.870A pdb=" N GLY D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 788 removed outlier: 4.406A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 804 Processing helix chain 'D' and resid 805 through 807 No H-bonds generated for 'chain 'D' and resid 805 through 807' Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 931 removed outlier: 4.124A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Proline residue: D 926 - end of helix removed outlier: 5.375A pdb=" N GLN D 929 " --> pdb=" O GLU D 925 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 930 " --> pdb=" O PRO D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.589A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 4.008A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1259 removed outlier: 3.541A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1288 Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 3.649A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D1315 " --> pdb=" O LYS D1311 " (cutoff:3.500A) Processing helix chain 'D' and resid 1321 through 1326 removed outlier: 4.362A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1321 through 1326' Processing helix chain 'D' and resid 1327 through 1338 removed outlier: 4.034A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1353 removed outlier: 4.069A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1375 removed outlier: 4.252A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.592A pdb=" N VAL E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 32 removed outlier: 3.846A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.719A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 80 removed outlier: 3.581A pdb=" N LEU E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 91 removed outlier: 3.501A pdb=" N SER F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.705A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 136 Processing helix chain 'F' and resid 138 through 153 removed outlier: 4.153A pdb=" N THR F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 165 removed outlier: 3.551A pdb=" N THR F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 236 removed outlier: 3.869A pdb=" N ALA F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG F 225 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 258 removed outlier: 3.961A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 296 removed outlier: 3.906A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 309 removed outlier: 3.754A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 322 removed outlier: 3.984A pdb=" N ASN F 317 " --> pdb=" O ASP F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 329 removed outlier: 3.836A pdb=" N GLU F 328 " --> pdb=" O LYS F 324 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS F 329 " --> pdb=" O PRO F 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 324 through 329' Processing helix chain 'F' and resid 330 through 352 removed outlier: 4.753A pdb=" N GLU F 335 " --> pdb=" O HIS F 331 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU F 336 " --> pdb=" O ASP F 332 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 392 removed outlier: 4.559A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 419 removed outlier: 3.574A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.330A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA F 444 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 removed outlier: 3.871A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 487 Processing helix chain 'F' and resid 490 through 501 removed outlier: 3.606A pdb=" N ILE F 494 " --> pdb=" O PRO F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 Processing helix chain 'F' and resid 530 through 549 Processing helix chain 'F' and resid 552 through 562 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 584 through 600 removed outlier: 3.563A pdb=" N ARG F 588 " --> pdb=" O ARG F 584 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS F 600 " --> pdb=" O ARG F 596 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 609 removed outlier: 4.346A pdb=" N LEU F 607 " --> pdb=" O ARG F 603 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER F 609 " --> pdb=" O GLU F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 610 through 613 Processing helix chain 'G' and resid 10 through 16 removed outlier: 3.534A pdb=" N PHE G 14 " --> pdb=" O THR G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 76 removed outlier: 3.546A pdb=" N LEU G 75 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE G 76 " --> pdb=" O LEU G 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 72 through 76' Processing helix chain 'G' and resid 99 through 109 removed outlier: 4.026A pdb=" N GLN G 104 " --> pdb=" O LYS G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 136 Processing helix chain 'G' and resid 138 through 151 Processing helix chain 'G' and resid 168 through 177 Processing helix chain 'G' and resid 179 through 193 Processing helix chain 'H' and resid 10 through 16 Processing helix chain 'H' and resid 98 through 108 Processing helix chain 'H' and resid 110 through 137 removed outlier: 4.165A pdb=" N PHE H 136 " --> pdb=" O GLY H 132 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU H 137 " --> pdb=" O ASN H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 153 Processing helix chain 'H' and resid 168 through 177 removed outlier: 3.700A pdb=" N ILE H 172 " --> pdb=" O THR H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 193 removed outlier: 3.643A pdb=" N VAL H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 261 Processing helix chain 'I' and resid 263 through 273 removed outlier: 3.507A pdb=" N GLU I 273 " --> pdb=" O CYS I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 284 removed outlier: 3.510A pdb=" N GLN I 283 " --> pdb=" O GLY I 279 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG I 284 " --> pdb=" O ASP I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 297 through 310 removed outlier: 3.534A pdb=" N THR I 301 " --> pdb=" O LYS I 297 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.797A pdb=" N GLU A 29 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.372A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 147 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 55 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 18 removed outlier: 4.608A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP B 197 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA B 190 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP B 199 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU B 188 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU B 201 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN B 186 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE B 203 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA B 184 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N MET B 205 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG B 182 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR B 207 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 180 " --> pdb=" O THR B 207 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 6.346A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.530A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.387A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 4.771A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB6, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.877A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 161 Processing sheet with id=AB8, first strand: chain 'C' and resid 230 through 233 removed outlier: 3.731A pdb=" N LYS C 236 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 256 Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.944A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.944A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 722 through 726 removed outlier: 5.632A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC5, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 4.938A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 804 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 6.316A pdb=" N LEU C1212 " --> pdb=" O PHE C1221 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG C1223 " --> pdb=" O ILE C1210 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE C1210 " --> pdb=" O ARG C1223 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 831 Processing sheet with id=AD1, first strand: chain 'C' and resid 835 through 841 removed outlier: 3.744A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD3, first strand: chain 'C' and resid 876 through 878 Processing sheet with id=AD4, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.421A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 5.976A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.722A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1335 through 1341 removed outlier: 3.519A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.107A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.526A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.584A pdb=" N LEU D 160 " --> pdb=" O TYR D 144 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL D 146 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS D 179 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AE3, first strand: chain 'D' and resid 526 through 527 removed outlier: 6.807A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE5, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE6, first strand: chain 'D' and resid 901 through 902 removed outlier: 3.568A pdb=" N HIS D 907 " --> pdb=" O ASP D 902 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 950 through 952 removed outlier: 5.984A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE9, first strand: chain 'D' and resid 981 through 985 removed outlier: 6.721A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1028 through 1029 Processing sheet with id=AF2, first strand: chain 'D' and resid 1079 through 1081 removed outlier: 4.030A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1047 through 1050 removed outlier: 4.510A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1106 through 1107 Processing sheet with id=AF5, first strand: chain 'D' and resid 1177 through 1178 Processing sheet with id=AF6, first strand: chain 'G' and resid 19 through 23 removed outlier: 6.353A pdb=" N ALA G 95 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE G 42 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE G 97 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR G 40 " --> pdb=" O ILE G 97 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 28 through 30 removed outlier: 7.294A pdb=" N VAL G 86 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE G 51 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE G 60 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 157 through 159 Processing sheet with id=AF9, first strand: chain 'H' and resid 19 through 23 removed outlier: 3.802A pdb=" N HIS H 19 " --> pdb=" O GLU H 96 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU H 93 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR H 41 " --> pdb=" O ALA H 95 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 28 through 30 removed outlier: 6.311A pdb=" N VAL H 86 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL H 47 " --> pdb=" O TYR H 63 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR H 63 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL H 49 " --> pdb=" O LEU H 61 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 157 through 159 1432 hydrogen bonds defined for protein. 4038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 159 hydrogen bonds 314 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 140 stacking parallelities Total time for adding SS restraints: 33.43 Time building geometry restraints manager: 17.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 35369 1.03 - 1.23: 397 1.23 - 1.43: 15238 1.43 - 1.63: 21738 1.63 - 1.83: 260 Bond restraints: 73002 Sorted by residual: bond pdb=" C5 GTP 3 1 " pdb=" C6 GTP 3 1 " ideal model delta sigma weight residual 1.390 1.474 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C4 GTP 3 1 " pdb=" C5 GTP 3 1 " ideal model delta sigma weight residual 1.390 1.459 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1' DC 1 18 " pdb=" N1 DC 1 18 " ideal model delta sigma weight residual 1.490 1.565 -0.075 3.00e-02 1.11e+03 6.20e+00 bond pdb=" CA VAL F 166 " pdb=" CB VAL F 166 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.36e-02 5.41e+03 6.01e+00 bond pdb=" C4 GTP 3 1 " pdb=" N9 GTP 3 1 " ideal model delta sigma weight residual 1.375 1.326 0.049 2.00e-02 2.50e+03 5.97e+00 ... (remaining 72997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 129406 2.33 - 4.67: 2811 4.67 - 7.00: 181 7.00 - 9.33: 17 9.33 - 11.67: 11 Bond angle restraints: 132426 Sorted by residual: angle pdb=" N SER F 602 " pdb=" CA SER F 602 " pdb=" C SER F 602 " ideal model delta sigma weight residual 114.04 107.14 6.90 1.24e+00 6.50e-01 3.10e+01 angle pdb=" N VAL D1017 " pdb=" CA VAL D1017 " pdb=" C VAL D1017 " ideal model delta sigma weight residual 110.82 106.12 4.70 9.70e-01 1.06e+00 2.35e+01 angle pdb=" N GLU C1005 " pdb=" CA GLU C1005 " pdb=" C GLU C1005 " ideal model delta sigma weight residual 110.80 120.84 -10.04 2.13e+00 2.20e-01 2.22e+01 angle pdb=" C THR F 112 " pdb=" N ARG F 113 " pdb=" CA ARG F 113 " ideal model delta sigma weight residual 121.54 130.06 -8.52 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C ILE D 619 " pdb=" N PHE D 620 " pdb=" CA PHE D 620 " ideal model delta sigma weight residual 120.82 127.36 -6.54 1.50e+00 4.44e-01 1.90e+01 ... (remaining 132421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 31772 35.63 - 71.26: 1402 71.26 - 106.89: 30 106.89 - 142.51: 5 142.51 - 178.14: 7 Dihedral angle restraints: 33216 sinusoidal: 19824 harmonic: 13392 Sorted by residual: dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual -180.00 -113.91 -66.09 0 5.00e+00 4.00e-02 1.75e+02 dihedral pdb=" CA PHE F 165 " pdb=" C PHE F 165 " pdb=" N VAL F 166 " pdb=" CA VAL F 166 " ideal model delta harmonic sigma weight residual -180.00 -125.67 -54.33 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA ASP C1004 " pdb=" C ASP C1004 " pdb=" N GLU C1005 " pdb=" CA GLU C1005 " ideal model delta harmonic sigma weight residual -180.00 -133.02 -46.98 0 5.00e+00 4.00e-02 8.83e+01 ... (remaining 33213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3896 0.045 - 0.090: 1473 0.090 - 0.134: 436 0.134 - 0.179: 60 0.179 - 0.224: 6 Chirality restraints: 5871 Sorted by residual: chirality pdb=" C2' GTP 3 1 " pdb=" C1' GTP 3 1 " pdb=" C3' GTP 3 1 " pdb=" O2' GTP 3 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE D 754 " pdb=" CA ILE D 754 " pdb=" CG1 ILE D 754 " pdb=" CG2 ILE D 754 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE H 106 " pdb=" CA ILE H 106 " pdb=" CG1 ILE H 106 " pdb=" CG2 ILE H 106 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.53e-01 ... (remaining 5868 not shown) Planarity restraints: 10222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 568 " 0.228 2.00e-02 2.50e+03 3.77e-01 2.14e+03 pdb=" CG ASN C 568 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN C 568 " -0.220 2.00e-02 2.50e+03 pdb=" ND2 ASN C 568 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 568 " -0.613 2.00e-02 2.50e+03 pdb="HD22 ASN C 568 " 0.615 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 424 " 0.246 2.00e-02 2.50e+03 3.32e-01 1.66e+03 pdb=" CG ASN D 424 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN D 424 " -0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN D 424 " -0.006 2.00e-02 2.50e+03 pdb="HD21 ASN D 424 " -0.508 2.00e-02 2.50e+03 pdb="HD22 ASN D 424 " 0.539 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 400 " 0.232 2.00e-02 2.50e+03 2.88e-01 1.24e+03 pdb=" CD GLN F 400 " -0.025 2.00e-02 2.50e+03 pdb=" OE1 GLN F 400 " -0.219 2.00e-02 2.50e+03 pdb=" NE2 GLN F 400 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN F 400 " -0.436 2.00e-02 2.50e+03 pdb="HE22 GLN F 400 " 0.451 2.00e-02 2.50e+03 ... (remaining 10219 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 7227 2.23 - 2.83: 162696 2.83 - 3.42: 183291 3.42 - 4.01: 252057 4.01 - 4.60: 387043 Nonbonded interactions: 992314 Sorted by model distance: nonbonded pdb=" O GLU C 985 " pdb=" H LEU C 989 " model vdw 1.643 2.450 nonbonded pdb=" O LEU C 699 " pdb=" H ILE C1182 " model vdw 1.644 2.450 nonbonded pdb=" H VAL D1035 " pdb=" O VAL D1113 " model vdw 1.653 2.450 nonbonded pdb=" H ASN C 582 " pdb=" O PHE C 586 " model vdw 1.654 2.450 nonbonded pdb=" OD1 ASP D 986 " pdb=" H GLY D 989 " model vdw 1.655 2.450 ... (remaining 992309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } ncs_group { reference = chain 'G' selection = (chain 'H' and ((resid 9 and (name CA or name C or name O or name CB or name CG \ or name CD or name HB2 or name HB3 or name HG2 or name HG3)) or resid 10 through \ 209 or resid 301)) } 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: 0.010 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.960 Extract box with map and model: 2.000 Check model and map are aligned: 0.420 Set scattering table: 0.510 Process input model: 168.200 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4724 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 : 0.008 0.084 37602 Z= 0.542 Angle : 0.960 11.668 51553 Z= 0.530 Chirality : 0.050 0.224 5871 Planarity : 0.006 0.075 6078 Dihedral : 16.110 178.143 14889 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.86 % Favored : 90.97 % Rotamer: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.10), residues: 4164 helix: -3.00 (0.09), residues: 1587 sheet: -3.27 (0.19), residues: 419 loop : -2.87 (0.12), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 85 HIS 0.014 0.003 HIS B 132 PHE 0.043 0.003 PHE D 620 TYR 0.029 0.003 TYR C1229 ARG 0.015 0.002 ARG C1301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 4.084 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: F 297 MET cc_start: 0.2476 (ptt) cc_final: 0.0090 (mtt) REVERT: H 51 ILE cc_start: 0.5139 (tp) cc_final: 0.4919 (tt) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 1.2276 time to fit residues: 479.3149 Evaluate side-chains 186 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 4.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 363 optimal weight: 10.0000 chunk 326 optimal weight: 40.0000 chunk 181 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 220 optimal weight: 0.0870 chunk 174 optimal weight: 6.9990 chunk 337 optimal weight: 30.0000 chunk 130 optimal weight: 20.0000 chunk 205 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 391 optimal weight: 50.0000 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN C 406 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1264 GLN C1313 HIS D 341 ASN D 651 HIS D 665 GLN D 700 ASN D 805 GLN D 910 ASN D1218 HIS H 21 HIS I 268 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4766 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37602 Z= 0.246 Angle : 0.693 9.996 51553 Z= 0.383 Chirality : 0.043 0.210 5871 Planarity : 0.006 0.095 6078 Dihedral : 20.480 177.411 6597 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.19 % Favored : 91.64 % Rotamer: Outliers : 0.53 % Allowed : 4.02 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.11), residues: 4164 helix: -1.43 (0.11), residues: 1641 sheet: -2.80 (0.20), residues: 430 loop : -2.54 (0.12), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 868 HIS 0.010 0.002 HIS D 80 PHE 0.026 0.002 PHE D 620 TYR 0.015 0.002 TYR D 679 ARG 0.010 0.001 ARG F 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 4.035 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: D 1095 MET cc_start: 0.3378 (mtm) cc_final: 0.2533 (mtt) REVERT: F 297 MET cc_start: 0.1914 (ptt) cc_final: 0.1325 (tmm) REVERT: G 59 MET cc_start: 0.0422 (tpt) cc_final: 0.0057 (tpt) REVERT: G 72 GLU cc_start: 0.0403 (pm20) cc_final: -0.0396 (mp0) outliers start: 19 outliers final: 11 residues processed: 205 average time/residue: 1.0193 time to fit residues: 332.8702 Evaluate side-chains 193 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 4.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 190 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 217 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 266 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 392 optimal weight: 50.0000 chunk 423 optimal weight: 20.0000 chunk 349 optimal weight: 9.9990 chunk 388 optimal weight: 50.0000 chunk 133 optimal weight: 9.9990 chunk 314 optimal weight: 20.0000 overall best weight: 8.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 651 HIS D1279 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4892 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 37602 Z= 0.348 Angle : 0.717 10.116 51553 Z= 0.396 Chirality : 0.044 0.263 5871 Planarity : 0.005 0.065 6078 Dihedral : 20.264 175.044 6597 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.92 % Favored : 89.99 % Rotamer: Outliers : 1.12 % Allowed : 4.55 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.12), residues: 4164 helix: -0.90 (0.12), residues: 1655 sheet: -2.76 (0.20), residues: 467 loop : -2.48 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 85 HIS 0.019 0.002 HIS D 651 PHE 0.028 0.002 PHE D 620 TYR 0.017 0.002 TYR D 679 ARG 0.007 0.001 ARG F 422 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 187 time to evaluate : 4.046 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: C 459 MET cc_start: 0.6559 (mtt) cc_final: 0.6355 (mtm) REVERT: C 922 ASN cc_start: 0.5338 (t0) cc_final: 0.5051 (t0) REVERT: D 1095 MET cc_start: 0.3768 (mtm) cc_final: 0.3016 (mtt) REVERT: E 71 GLU cc_start: 0.5516 (OUTLIER) cc_final: 0.5164 (pm20) REVERT: F 273 MET cc_start: 0.0373 (mtp) cc_final: 0.0003 (mtt) REVERT: F 297 MET cc_start: 0.2726 (ptt) cc_final: 0.1312 (tmm) REVERT: F 561 MET cc_start: 0.4686 (mmm) cc_final: 0.4376 (mmm) REVERT: G 59 MET cc_start: 0.0464 (tpt) cc_final: -0.0068 (tpt) REVERT: G 72 GLU cc_start: 0.0448 (pm20) cc_final: -0.0619 (mp0) outliers start: 40 outliers final: 23 residues processed: 214 average time/residue: 1.0115 time to fit residues: 342.4270 Evaluate side-chains 202 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 4.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain H residue 190 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 387 optimal weight: 0.9980 chunk 294 optimal weight: 20.0000 chunk 203 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 393 optimal weight: 20.0000 chunk 416 optimal weight: 60.0000 chunk 205 optimal weight: 7.9990 chunk 372 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN D1108 GLN F 518 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4863 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 37602 Z= 0.228 Angle : 0.629 10.136 51553 Z= 0.347 Chirality : 0.042 0.221 5871 Planarity : 0.005 0.061 6078 Dihedral : 20.040 173.335 6597 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.80 % Favored : 92.15 % Rotamer: Outliers : 0.89 % Allowed : 5.24 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.12), residues: 4164 helix: -0.38 (0.12), residues: 1665 sheet: -2.54 (0.21), residues: 476 loop : -2.29 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 85 HIS 0.009 0.001 HIS D 80 PHE 0.019 0.001 PHE D 620 TYR 0.015 0.001 TYR C1229 ARG 0.008 0.000 ARG C 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 181 time to evaluate : 4.139 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: C 800 MET cc_start: 0.7712 (pmm) cc_final: 0.7070 (pmm) REVERT: C 922 ASN cc_start: 0.5119 (t0) cc_final: 0.4864 (t0) REVERT: D 1095 MET cc_start: 0.3840 (mtm) cc_final: 0.3257 (mtt) REVERT: F 273 MET cc_start: 0.0422 (mtp) cc_final: 0.0198 (mtt) REVERT: F 297 MET cc_start: 0.2519 (ptt) cc_final: 0.1225 (tmm) outliers start: 32 outliers final: 16 residues processed: 205 average time/residue: 1.0341 time to fit residues: 334.2749 Evaluate side-chains 190 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 4.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 384 LYS Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 530 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 346 optimal weight: 9.9990 chunk 236 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 310 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 355 optimal weight: 5.9990 chunk 287 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 373 optimal weight: 50.0000 chunk 105 optimal weight: 10.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4898 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37602 Z= 0.254 Angle : 0.623 10.295 51553 Z= 0.345 Chirality : 0.042 0.226 5871 Planarity : 0.004 0.057 6078 Dihedral : 19.956 173.683 6597 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.34 % Favored : 90.61 % Rotamer: Outliers : 0.70 % Allowed : 5.94 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.12), residues: 4164 helix: -0.15 (0.12), residues: 1671 sheet: -2.39 (0.22), residues: 454 loop : -2.24 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 85 HIS 0.008 0.001 HIS D 80 PHE 0.018 0.001 PHE D 620 TYR 0.013 0.001 TYR D 679 ARG 0.005 0.000 ARG D 692 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 4.088 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: C 922 ASN cc_start: 0.5189 (t0) cc_final: 0.4924 (t0) REVERT: C 1017 GLN cc_start: 0.4190 (mm-40) cc_final: 0.3962 (mm-40) REVERT: C 1304 MET cc_start: 0.7609 (tpp) cc_final: 0.7374 (tpp) REVERT: D 1040 MET cc_start: 0.2677 (mtp) cc_final: 0.2373 (mtp) REVERT: D 1095 MET cc_start: 0.3911 (mtm) cc_final: 0.3244 (mtt) REVERT: D 1174 ARG cc_start: 0.5844 (OUTLIER) cc_final: 0.5102 (mtt90) REVERT: F 273 MET cc_start: 0.0610 (mtp) cc_final: 0.0256 (mtt) REVERT: F 297 MET cc_start: 0.2704 (ptt) cc_final: 0.1320 (tmm) outliers start: 25 outliers final: 21 residues processed: 192 average time/residue: 0.9880 time to fit residues: 303.1154 Evaluate side-chains 193 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 4.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 1174 ARG Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain H residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 140 optimal weight: 10.0000 chunk 375 optimal weight: 50.0000 chunk 82 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 417 optimal weight: 30.0000 chunk 346 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 137 optimal weight: 0.0870 chunk 218 optimal weight: 6.9990 overall best weight: 7.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4950 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 37602 Z= 0.293 Angle : 0.652 10.180 51553 Z= 0.360 Chirality : 0.043 0.230 5871 Planarity : 0.005 0.056 6078 Dihedral : 19.941 172.574 6597 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.56 % Favored : 90.39 % Rotamer: Outliers : 1.20 % Allowed : 6.02 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.12), residues: 4164 helix: -0.06 (0.12), residues: 1664 sheet: -2.35 (0.22), residues: 462 loop : -2.24 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 85 HIS 0.007 0.002 HIS D 80 PHE 0.019 0.002 PHE D 620 TYR 0.013 0.002 TYR D 679 ARG 0.006 0.001 ARG F 554 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 170 time to evaluate : 4.083 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: C 488 MET cc_start: 0.6912 (mmt) cc_final: 0.6689 (mmt) REVERT: C 685 MET cc_start: 0.7386 (ptp) cc_final: 0.7144 (ptp) REVERT: C 1017 GLN cc_start: 0.4236 (mm-40) cc_final: 0.4002 (mm-40) REVERT: D 1040 MET cc_start: 0.3025 (mtp) cc_final: 0.2687 (mtp) REVERT: D 1095 MET cc_start: 0.4060 (mtm) cc_final: 0.3366 (mtt) REVERT: D 1174 ARG cc_start: 0.5958 (OUTLIER) cc_final: 0.4935 (mtt90) REVERT: F 297 MET cc_start: 0.2743 (ptt) cc_final: 0.1434 (tmm) outliers start: 43 outliers final: 29 residues processed: 203 average time/residue: 0.9600 time to fit residues: 315.0590 Evaluate side-chains 196 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 166 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 1174 ARG Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 402 optimal weight: 50.0000 chunk 47 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 chunk 304 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 351 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 415 optimal weight: 70.0000 chunk 259 optimal weight: 20.0000 chunk 253 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4953 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 37602 Z= 0.259 Angle : 0.627 10.353 51553 Z= 0.345 Chirality : 0.042 0.225 5871 Planarity : 0.005 0.177 6078 Dihedral : 19.895 172.546 6597 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.77 % Favored : 91.19 % Rotamer: Outliers : 1.03 % Allowed : 6.94 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.12), residues: 4164 helix: 0.08 (0.12), residues: 1672 sheet: -2.03 (0.23), residues: 432 loop : -2.20 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 85 HIS 0.008 0.001 HIS B 160 PHE 0.016 0.002 PHE D 620 TYR 0.012 0.001 TYR B 68 ARG 0.022 0.000 ARG D1290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 166 time to evaluate : 4.154 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: C 488 MET cc_start: 0.7316 (mmt) cc_final: 0.7106 (mmt) REVERT: C 685 MET cc_start: 0.7293 (ptp) cc_final: 0.7056 (ptp) REVERT: C 1017 GLN cc_start: 0.4175 (mm-40) cc_final: 0.3946 (mm-40) REVERT: D 466 MET cc_start: 0.8096 (mtp) cc_final: 0.7531 (ttm) REVERT: D 1095 MET cc_start: 0.3541 (mtm) cc_final: 0.3201 (mtt) REVERT: D 1174 ARG cc_start: 0.5984 (OUTLIER) cc_final: 0.5015 (mtt90) REVERT: F 297 MET cc_start: 0.2837 (ptt) cc_final: 0.1543 (tmm) REVERT: H 163 MET cc_start: -0.0660 (mtm) cc_final: -0.1175 (mtt) outliers start: 37 outliers final: 30 residues processed: 194 average time/residue: 0.9472 time to fit residues: 298.2684 Evaluate side-chains 193 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 162 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1174 ARG Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 256 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 283 optimal weight: 0.6980 chunk 205 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 326 optimal weight: 40.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1146 GLN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4961 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 37602 Z= 0.252 Angle : 0.619 10.098 51553 Z= 0.342 Chirality : 0.042 0.225 5871 Planarity : 0.004 0.053 6078 Dihedral : 19.850 172.573 6597 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.27 % Favored : 90.68 % Rotamer: Outliers : 0.98 % Allowed : 7.28 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.13), residues: 4164 helix: 0.21 (0.12), residues: 1669 sheet: -2.09 (0.23), residues: 443 loop : -2.13 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 85 HIS 0.007 0.001 HIS D 651 PHE 0.016 0.001 PHE D 620 TYR 0.011 0.001 TYR D1282 ARG 0.012 0.000 ARG D1290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 166 time to evaluate : 4.037 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: C 685 MET cc_start: 0.7317 (ptp) cc_final: 0.7092 (ptp) REVERT: C 800 MET cc_start: 0.7720 (pmm) cc_final: 0.6952 (pmm) REVERT: C 826 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: C 1017 GLN cc_start: 0.4001 (mm-40) cc_final: 0.3768 (mm-40) REVERT: D 204 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.5795 (tm-30) REVERT: D 1095 MET cc_start: 0.3323 (mtm) cc_final: 0.2960 (mtt) REVERT: D 1174 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.5012 (mtt90) REVERT: E 71 GLU cc_start: 0.5215 (OUTLIER) cc_final: 0.4874 (pm20) REVERT: F 297 MET cc_start: 0.2591 (ptt) cc_final: 0.1454 (tmm) outliers start: 35 outliers final: 28 residues processed: 192 average time/residue: 0.9719 time to fit residues: 303.2785 Evaluate side-chains 196 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 4.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1174 ARG Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 377 optimal weight: 50.0000 chunk 397 optimal weight: 20.0000 chunk 363 optimal weight: 9.9990 chunk 387 optimal weight: 50.0000 chunk 232 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 349 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 385 optimal weight: 4.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 GLN ** F 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5032 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 37602 Z= 0.343 Angle : 0.694 9.897 51553 Z= 0.384 Chirality : 0.044 0.247 5871 Planarity : 0.005 0.127 6078 Dihedral : 19.916 172.207 6597 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.93 % Favored : 89.00 % Rotamer: Outliers : 0.98 % Allowed : 7.45 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.12), residues: 4164 helix: -0.07 (0.12), residues: 1669 sheet: -2.30 (0.22), residues: 470 loop : -2.30 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 85 HIS 0.010 0.002 HIS D 545 PHE 0.019 0.002 PHE D 773 TYR 0.017 0.002 TYR D1282 ARG 0.009 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 165 time to evaluate : 4.136 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: C 488 MET cc_start: 0.7465 (mmt) cc_final: 0.6286 (mmm) REVERT: C 922 ASN cc_start: 0.5415 (t0) cc_final: 0.5215 (t0) REVERT: C 1017 GLN cc_start: 0.4379 (mm-40) cc_final: 0.4137 (mm-40) REVERT: D 172 PHE cc_start: 0.5917 (OUTLIER) cc_final: 0.4474 (m-80) REVERT: D 204 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.5842 (tm-30) REVERT: D 466 MET cc_start: 0.8173 (mtp) cc_final: 0.7854 (ttm) REVERT: D 1095 MET cc_start: 0.3767 (mtm) cc_final: 0.3350 (mtt) REVERT: D 1174 ARG cc_start: 0.5904 (OUTLIER) cc_final: 0.4917 (mtt90) REVERT: E 71 GLU cc_start: 0.5608 (OUTLIER) cc_final: 0.5306 (pm20) REVERT: F 273 MET cc_start: 0.0295 (mtt) cc_final: 0.0077 (mtt) REVERT: F 297 MET cc_start: 0.2797 (ptt) cc_final: 0.1668 (tmm) REVERT: F 360 ASP cc_start: 0.5407 (OUTLIER) cc_final: 0.5171 (t70) REVERT: F 561 MET cc_start: 0.5507 (mmm) cc_final: 0.5292 (mmm) REVERT: G 157 MET cc_start: 0.1478 (mmm) cc_final: 0.1106 (mmm) REVERT: H 114 MET cc_start: 0.2671 (mtp) cc_final: 0.1978 (mtm) REVERT: I 316 MET cc_start: 0.4021 (mmt) cc_final: 0.3732 (mmm) outliers start: 35 outliers final: 28 residues processed: 192 average time/residue: 0.9477 time to fit residues: 297.7191 Evaluate side-chains 194 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1174 ARG Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 204 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 254 optimal weight: 9.9990 chunk 409 optimal weight: 20.0000 chunk 249 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 284 optimal weight: 9.9990 chunk 429 optimal weight: 30.0000 chunk 395 optimal weight: 40.0000 chunk 341 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 264 optimal weight: 9.9990 chunk 209 optimal weight: 0.0970 overall best weight: 6.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4997 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 37602 Z= 0.249 Angle : 0.629 9.937 51553 Z= 0.347 Chirality : 0.042 0.232 5871 Planarity : 0.005 0.081 6078 Dihedral : 19.842 171.885 6597 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.22 % Favored : 90.73 % Rotamer: Outliers : 0.89 % Allowed : 7.67 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 4164 helix: 0.23 (0.13), residues: 1649 sheet: -2.18 (0.23), residues: 454 loop : -2.16 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 85 HIS 0.007 0.001 HIS D 651 PHE 0.015 0.002 PHE D 620 TYR 0.013 0.001 TYR B 68 ARG 0.010 0.000 ARG D1290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 4.079 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: C 488 MET cc_start: 0.7489 (mmt) cc_final: 0.6977 (mmm) REVERT: C 685 MET cc_start: 0.7536 (ptp) cc_final: 0.7279 (ptp) REVERT: C 826 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7447 (m-30) REVERT: C 922 ASN cc_start: 0.5392 (t0) cc_final: 0.5188 (t0) REVERT: D 172 PHE cc_start: 0.5681 (OUTLIER) cc_final: 0.4403 (m-80) REVERT: D 204 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.5737 (tm-30) REVERT: D 1095 MET cc_start: 0.3524 (mtm) cc_final: 0.1052 (ttt) REVERT: D 1174 ARG cc_start: 0.5856 (OUTLIER) cc_final: 0.4679 (mtt90) REVERT: E 71 GLU cc_start: 0.5516 (OUTLIER) cc_final: 0.5238 (pm20) REVERT: F 360 ASP cc_start: 0.5362 (OUTLIER) cc_final: 0.5128 (t70) REVERT: G 157 MET cc_start: 0.1476 (mmm) cc_final: 0.1128 (mmm) outliers start: 32 outliers final: 26 residues processed: 198 average time/residue: 0.9550 time to fit residues: 307.8441 Evaluate side-chains 201 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 4.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1174 ARG Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 271 optimal weight: 20.0000 chunk 364 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 342 optimal weight: 0.0170 chunk 143 optimal weight: 7.9990 chunk 351 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 GLN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.100328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.078704 restraints weight = 861613.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.074931 restraints weight = 716635.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.074616 restraints weight = 694344.289| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37602 Z= 0.219 Angle : 0.602 9.827 51553 Z= 0.332 Chirality : 0.041 0.229 5871 Planarity : 0.004 0.070 6078 Dihedral : 19.724 172.556 6597 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.01 % Favored : 90.95 % Rotamer: Outliers : 0.86 % Allowed : 7.84 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 4164 helix: 0.49 (0.13), residues: 1656 sheet: -2.08 (0.23), residues: 454 loop : -2.05 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 85 HIS 0.006 0.001 HIS D 80 PHE 0.035 0.001 PHE C 972 TYR 0.011 0.001 TYR F 430 ARG 0.012 0.000 ARG D1290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9727.45 seconds wall clock time: 169 minutes 24.20 seconds (10164.20 seconds total)