Starting phenix.real_space_refine on Wed Jun 25 15:03:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yqz_39511/06_2025/8yqz_39511.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yqz_39511/06_2025/8yqz_39511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yqz_39511/06_2025/8yqz_39511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yqz_39511/06_2025/8yqz_39511.map" model { file = "/net/cci-nas-00/data/ceres_data/8yqz_39511/06_2025/8yqz_39511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yqz_39511/06_2025/8yqz_39511.cif" } resolution = 2.78 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 15 5.49 5 Mg 1 5.21 5 S 164 5.16 5 C 19040 2.51 5 N 5150 2.21 5 O 5569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29943 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 10954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1375, 10954 Classifications: {'peptide': 1375} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1310} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 9459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1196, 9459 Classifications: {'peptide': 1196} Link IDs: {'PTRANS': 52, 'TRANS': 1143} Chain breaks: 4 Chain: "C" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2897 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 19, 'TRANS': 337} Chain: "D" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1668 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 829 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "F" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2727 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 13, 'TRANS': 325} Chain: "G" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 468 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain: "H" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 630 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 5, 'TRANS': 74} Chain: "X" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 165 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "Y" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 442 SG CYS A 59 97.760 76.828 68.044 1.00 32.48 S ATOM 463 SG CYS A 62 95.521 75.645 65.304 1.00 33.87 S ATOM 523 SG CYS A 69 94.518 78.698 67.286 1.00 32.53 S ATOM 19933 SG CYS B1180 86.966 61.757 67.725 1.00 33.91 S ATOM 19958 SG CYS B1183 86.610 62.939 71.395 1.00 25.47 S ATOM 20074 SG CYS B1198 89.824 63.315 70.200 1.00 44.08 S ATOM 20096 SG CYS B1201 88.360 59.734 71.025 1.00 45.14 S ATOM 28754 SG CYS G 73 24.760 135.955 108.636 1.00 48.07 S ATOM 28775 SG CYS G 76 26.722 139.481 109.483 1.00 46.66 S ATOM 28932 SG CYS G 96 28.566 136.520 108.444 1.00 42.46 S ATOM 28949 SG CYS G 98 27.476 136.683 111.852 1.00 44.75 S ATOM 29053 SG CYS H 7 62.620 137.679 46.497 1.00 5.23 S ATOM 29077 SG CYS H 10 61.621 137.936 42.805 1.00 6.51 S ATOM 29496 SG CYS H 65 58.949 137.598 45.696 1.00 4.69 S ATOM 29502 SG CYS H 66 60.991 140.745 44.802 1.00 9.67 S Time building chain proxies: 19.31, per 1000 atoms: 0.64 Number of scatterers: 29943 At special positions: 0 Unit cell: (138.976, 172.912, 147.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 164 16.00 P 15 15.00 Mg 1 11.99 O 5569 8.00 N 5150 7.00 C 19040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1502 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 59 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1183 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1180 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1201 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1198 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 98 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 96 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 76 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 73 " pdb=" ZN H 101 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 10 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 7 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 65 " Number of angles added : 21 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7026 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 45 sheets defined 42.7% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.24 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 removed outlier: 3.586A pdb=" N HIS A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 87 through 96 removed outlier: 3.757A pdb=" N ARG A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.694A pdb=" N TYR A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.485A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ILE A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.698A pdb=" N HIS A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 225 through 239 removed outlier: 3.693A pdb=" N VAL A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 273 removed outlier: 3.633A pdb=" N LEU A 271 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.627A pdb=" N ARG A 302 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 303 " --> pdb=" O MET A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 303' Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 358 through 369 Proline residue: A 364 - end of helix Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 455 removed outlier: 4.209A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.688A pdb=" N PHE A 487 " --> pdb=" O ARG A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 524 through 530 Processing helix chain 'A' and resid 552 through 561 removed outlier: 3.879A pdb=" N LEU A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.543A pdb=" N MET A 582 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.821A pdb=" N ILE A 589 " --> pdb=" O LYS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 625 through 648 removed outlier: 4.064A pdb=" N ASN A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.809A pdb=" N LEU A 657 " --> pdb=" O ALA A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 686 removed outlier: 3.599A pdb=" N GLN A 664 " --> pdb=" O PRO A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 715 through 721 removed outlier: 3.876A pdb=" N ILE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 781 through 785 Processing helix chain 'A' and resid 797 through 834 removed outlier: 3.573A pdb=" N SER A 818 " --> pdb=" O ASN A 814 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 822 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 823 " --> pdb=" O THR A 819 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 861 through 865 removed outlier: 4.258A pdb=" N LEU A 865 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 885 removed outlier: 3.631A pdb=" N LYS A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 918 removed outlier: 3.702A pdb=" N PHE A 898 " --> pdb=" O PHE A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 944 removed outlier: 3.540A pdb=" N ILE A 941 " --> pdb=" O ILE A 937 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A 944 " --> pdb=" O ASN A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 970 Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 988 through 993 Processing helix chain 'A' and resid 995 through 1006 Processing helix chain 'A' and resid 1015 through 1032 removed outlier: 3.579A pdb=" N ALA A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1051 removed outlier: 3.515A pdb=" N GLU A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1083 removed outlier: 3.756A pdb=" N GLN A1078 " --> pdb=" O ILE A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1089 Processing helix chain 'A' and resid 1106 through 1117 Processing helix chain 'A' and resid 1148 through 1159 removed outlier: 3.909A pdb=" N LEU A1159 " --> pdb=" O MET A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1189 removed outlier: 4.333A pdb=" N MET A1185 " --> pdb=" O ASN A1181 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A1186 " --> pdb=" O LYS A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1200 removed outlier: 3.596A pdb=" N ARG A1200 " --> pdb=" O ILE A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1232 Processing helix chain 'A' and resid 1242 through 1256 removed outlier: 3.832A pdb=" N ILE A1246 " --> pdb=" O THR A1242 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A1256 " --> pdb=" O ASP A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1318 through 1327 Processing helix chain 'A' and resid 1327 through 1344 removed outlier: 3.560A pdb=" N VAL A1342 " --> pdb=" O GLU A1338 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A1344 " --> pdb=" O ARG A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 4.035A pdb=" N LEU A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A1356 " --> pdb=" O HIS A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1378 Processing helix chain 'A' and resid 1381 through 1389 removed outlier: 3.820A pdb=" N SER A1389 " --> pdb=" O ARG A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1402 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1422 through 1426 Processing helix chain 'A' and resid 1432 through 1440 removed outlier: 4.084A pdb=" N GLU A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 16 removed outlier: 3.890A pdb=" N VAL B 16 " --> pdb=" O ILE B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.929A pdb=" N ILE B 30 " --> pdb=" O MET B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 53 removed outlier: 3.588A pdb=" N PHE B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.965A pdb=" N GLN B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.515A pdb=" N PHE B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.773A pdb=" N VAL B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 313 Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 354 through 372 Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 382 through 402 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 420 through 437 removed outlier: 3.680A pdb=" N PHE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 471 through 489 removed outlier: 3.543A pdb=" N ALA B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 521 removed outlier: 3.524A pdb=" N LEU B 521 " --> pdb=" O THR B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.627A pdb=" N LEU B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 removed outlier: 3.520A pdb=" N VAL B 602 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 610 Processing helix chain 'B' and resid 627 through 642 removed outlier: 3.851A pdb=" N GLU B 641 " --> pdb=" O MET B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 697 Processing helix chain 'B' and resid 700 through 705 removed outlier: 3.558A pdb=" N LYS B 703 " --> pdb=" O ASP B 700 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B 704 " --> pdb=" O TRP B 701 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS B 705 " --> pdb=" O GLU B 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 705' Processing helix chain 'B' and resid 715 through 724 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.510A pdb=" N GLU B 747 " --> pdb=" O GLU B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 774 through 779 Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 805 removed outlier: 3.638A pdb=" N VAL B 797 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG B 805 " --> pdb=" O THR B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 818 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 869 through 874 Processing helix chain 'B' and resid 1011 through 1015 Processing helix chain 'B' and resid 1030 through 1033 Processing helix chain 'B' and resid 1038 through 1055 removed outlier: 4.051A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1078 removed outlier: 3.534A pdb=" N LEU B1075 " --> pdb=" O LEU B1071 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B1076 " --> pdb=" O SER B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1119 Processing helix chain 'B' and resid 1148 through 1159 Processing helix chain 'B' and resid 1160 through 1169 removed outlier: 3.580A pdb=" N ILE B1164 " --> pdb=" O ALA B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1214 through 1226 removed outlier: 3.562A pdb=" N ALA B1226 " --> pdb=" O GLU B1222 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 89 through 99 removed outlier: 3.787A pdb=" N PHE C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 230 through 258 removed outlier: 3.615A pdb=" N ILE C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 302 Processing helix chain 'C' and resid 328 through 358 Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.505A pdb=" N THR D 8 " --> pdb=" O GLN D 4 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TYR D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 39 Processing helix chain 'D' and resid 62 through 67 removed outlier: 3.684A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.840A pdb=" N MET D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 98 Processing helix chain 'D' and resid 99 through 113 removed outlier: 3.897A pdb=" N LEU D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 127 removed outlier: 3.637A pdb=" N CYS D 127 " --> pdb=" O HIS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 157 through 161 removed outlier: 3.606A pdb=" N LEU D 161 " --> pdb=" O PRO D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'E' and resid 44 through 49 removed outlier: 4.058A pdb=" N GLY E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.811A pdb=" N ARG E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 90 Processing helix chain 'E' and resid 101 through 112 Processing helix chain 'E' and resid 137 through 141 removed outlier: 3.577A pdb=" N MET E 141 " --> pdb=" O PRO E 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 171 through 195 removed outlier: 4.510A pdb=" N LYS F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS F 195 " --> pdb=" O SER F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 208 removed outlier: 3.557A pdb=" N ILE F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 248 removed outlier: 3.857A pdb=" N LYS F 248 " --> pdb=" O TYR F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 314 removed outlier: 3.611A pdb=" N MET F 292 " --> pdb=" O SER F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 323 removed outlier: 3.775A pdb=" N ILE F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 332 removed outlier: 3.667A pdb=" N TRP F 327 " --> pdb=" O HIS F 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'H' and resid 13 through 16 removed outlier: 3.694A pdb=" N THR H 16 " --> pdb=" O PRO H 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 13 through 16' Processing helix chain 'H' and resid 17 through 34 Processing helix chain 'H' and resid 42 through 48 removed outlier: 3.517A pdb=" N SER H 46 " --> pdb=" O PRO H 42 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN H 48 " --> pdb=" O ASP H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 59 removed outlier: 3.581A pdb=" N GLY H 59 " --> pdb=" O ILE H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.709A pdb=" N THR H 73 " --> pdb=" O HIS H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 79 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.262A pdb=" N GLY A 4 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ASP B1211 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1404 through 1406 removed outlier: 6.682A pdb=" N VAL B1233 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL A 11 " --> pdb=" O THR B1231 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR B1231 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 13 " --> pdb=" O ASN B1229 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASN B1229 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 83 removed outlier: 6.527A pdb=" N LYS A 199 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 10.958A pdb=" N ALA A 80 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N VAL A 197 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 146 Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA6, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 6.053A pdb=" N VAL A 338 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 436 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR A 340 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE A 444 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR A 326 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N MET A 446 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N CYS A 328 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 353 removed outlier: 3.900A pdb=" N ARG A 378 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP A 408 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N CYS A 376 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 386 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AA9, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AB1, first strand: chain 'A' and resid 566 through 569 removed outlier: 6.684A pdb=" N GLN A 592 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 753 through 754 Processing sheet with id=AB3, first strand: chain 'A' and resid 837 through 838 removed outlier: 6.535A pdb=" N VAL A 844 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 866 through 869 Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1095 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.620A pdb=" N ARG A1260 " --> pdb=" O ILE A1120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1126 through 1129 removed outlier: 4.397A pdb=" N GLN A1128 " --> pdb=" O GLU A1179 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A1179 " --> pdb=" O GLN A1128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1267 through 1278 removed outlier: 6.371A pdb=" N ASN A1267 " --> pdb=" O THR A1295 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR A1295 " --> pdb=" O ASN A1267 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN A1269 " --> pdb=" O ILE A1293 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE A1293 " --> pdb=" O ASN A1269 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A1271 " --> pdb=" O TYR A1291 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR A1291 " --> pdb=" O VAL A1271 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A1273 " --> pdb=" O ASN A1289 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN A1289 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1428 through 1431 removed outlier: 6.851A pdb=" N ILE E 132 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL E 125 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLN E 130 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR E 56 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL E 133 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL E 58 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE E 135 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE B1239 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N ILE E 59 " --> pdb=" O PHE B1239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 65 through 70 removed outlier: 3.544A pdb=" N VAL B 65 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL B 85 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N HIS B 139 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE B 87 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR B 137 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE B 89 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 135 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N PHE B 91 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU B 133 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP B 93 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY B 126 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER B 158 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 128 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLN B 156 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 130 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B 132 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC3, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC4, first strand: chain 'B' and resid 416 through 418 removed outlier: 6.557A pdb=" N LEU B 204 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 213 through 216 removed outlier: 3.757A pdb=" N ILE B 228 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 250 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AC7, first strand: chain 'B' and resid 710 through 712 removed outlier: 3.603A pdb=" N LEU B 674 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 596 through 597 removed outlier: 5.581A pdb=" N TRP B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE B 617 " --> pdb=" O TRP B 621 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 623 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 823 through 826 removed outlier: 3.598A pdb=" N ARG B 823 " --> pdb=" O TYR B 882 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU B 981 " --> pdb=" O VAL B 968 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL B 968 " --> pdb=" O LEU B 981 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG B 983 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AD2, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 6.216A pdb=" N VAL B 865 " --> pdb=" O ALA B1006 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B1008 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 894 through 896 Processing sheet with id=AD4, first strand: chain 'B' and resid 932 through 934 removed outlier: 7.160A pdb=" N VAL B 955 " --> pdb=" O ILE B 933 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AD6, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AD7, first strand: chain 'C' and resid 5 through 12 removed outlier: 5.069A pdb=" N PHE C 5 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS C 48 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN C 7 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP C 46 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N CYS C 222 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS C 181 " --> pdb=" O CYS C 222 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 68 through 73 removed outlier: 3.685A pdb=" N ASP C 162 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE C 111 " --> pdb=" O ASP C 162 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 110 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 123 through 126 removed outlier: 3.613A pdb=" N GLY C 150 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 267 through 271 Processing sheet with id=AE2, first strand: chain 'D' and resid 20 through 21 removed outlier: 6.728A pdb=" N ILE D 52 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ILE D 89 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER D 54 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE D 91 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE D 56 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 138 through 142 removed outlier: 3.519A pdb=" N LYS D 138 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE D 181 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 188 " --> pdb=" O MET D 192 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET D 162 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR D 201 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE D 164 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 2 through 13 removed outlier: 6.409A pdb=" N SER F 75 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL F 51 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL F 77 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR F 49 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N SER F 79 " --> pdb=" O ASN F 47 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ASN F 47 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 2 through 13 Processing sheet with id=AE6, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AE7, first strand: chain 'F' and resid 91 through 95 removed outlier: 5.803A pdb=" N ILE F 92 " --> pdb=" O GLU F 103 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU F 103 " --> pdb=" O ILE F 92 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 237 through 238 removed outlier: 3.525A pdb=" N TYR F 164 " --> pdb=" O TRP F 257 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 68 through 70 1263 hydrogen bonds defined for protein. 3459 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.03 Time building geometry restraints manager: 7.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8864 1.33 - 1.45: 4838 1.45 - 1.57: 16559 1.57 - 1.70: 29 1.70 - 1.82: 270 Bond restraints: 30560 Sorted by residual: bond pdb=" CG PRO A1101 " pdb=" CD PRO A1101 " ideal model delta sigma weight residual 1.503 1.339 0.164 3.40e-02 8.65e+02 2.32e+01 bond pdb=" C ARG A 569 " pdb=" N ALA A 570 " ideal model delta sigma weight residual 1.331 1.257 0.074 2.07e-02 2.33e+03 1.27e+01 bond pdb=" CB ARG A 512 " pdb=" CG ARG A 512 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.11e+00 bond pdb=" CB ARG B1119 " pdb=" CG ARG B1119 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.82e+00 bond pdb=" CG PRO B 971 " pdb=" CD PRO B 971 " ideal model delta sigma weight residual 1.503 1.423 0.080 3.40e-02 8.65e+02 5.51e+00 ... (remaining 30555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 40914 2.65 - 5.31: 441 5.31 - 7.96: 49 7.96 - 10.61: 13 10.61 - 13.27: 2 Bond angle restraints: 41419 Sorted by residual: angle pdb=" N PRO A1101 " pdb=" CD PRO A1101 " pdb=" CG PRO A1101 " ideal model delta sigma weight residual 103.20 91.07 12.13 1.50e+00 4.44e-01 6.54e+01 angle pdb=" N VAL B 323 " pdb=" CA VAL B 323 " pdb=" C VAL B 323 " ideal model delta sigma weight residual 113.10 107.25 5.85 9.70e-01 1.06e+00 3.64e+01 angle pdb=" CA PRO A1101 " pdb=" N PRO A1101 " pdb=" CD PRO A1101 " ideal model delta sigma weight residual 112.00 104.31 7.69 1.40e+00 5.10e-01 3.01e+01 angle pdb=" N PRO B 971 " pdb=" CD PRO B 971 " pdb=" CG PRO B 971 " ideal model delta sigma weight residual 103.20 95.11 8.09 1.50e+00 4.44e-01 2.91e+01 angle pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" CD PRO B 236 " ideal model delta sigma weight residual 112.00 104.59 7.41 1.40e+00 5.10e-01 2.80e+01 ... (remaining 41414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16290 17.96 - 35.93: 1634 35.93 - 53.89: 506 53.89 - 71.85: 107 71.85 - 89.81: 41 Dihedral angle restraints: 18578 sinusoidal: 7712 harmonic: 10866 Sorted by residual: dihedral pdb=" CA TYR A1207 " pdb=" C TYR A1207 " pdb=" N ILE A1208 " pdb=" CA ILE A1208 " ideal model delta harmonic sigma weight residual 180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA VAL A 500 " pdb=" C VAL A 500 " pdb=" N GLN A 501 " pdb=" CA GLN A 501 " ideal model delta harmonic sigma weight residual 180.00 155.21 24.79 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA LEU A 303 " pdb=" C LEU A 303 " pdb=" N PRO A 304 " pdb=" CA PRO A 304 " ideal model delta harmonic sigma weight residual 180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 18575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3292 0.053 - 0.106: 1157 0.106 - 0.159: 238 0.159 - 0.211: 12 0.211 - 0.264: 3 Chirality restraints: 4702 Sorted by residual: chirality pdb=" CG LEU F 106 " pdb=" CB LEU F 106 " pdb=" CD1 LEU F 106 " pdb=" CD2 LEU F 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA PRO A 304 " pdb=" N PRO A 304 " pdb=" C PRO A 304 " pdb=" CB PRO A 304 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB ILE A1422 " pdb=" CA ILE A1422 " pdb=" CG1 ILE A1422 " pdb=" CG2 ILE A1422 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 4699 not shown) Planarity restraints: 5277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B1193 " 0.074 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO B1194 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO B1194 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B1194 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 26 " -0.071 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO D 27 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO D 27 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO D 27 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 235 " 0.071 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 236 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.055 5.00e-02 4.00e+02 ... (remaining 5274 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 204 2.57 - 3.15: 22902 3.15 - 3.73: 44899 3.73 - 4.32: 67692 4.32 - 4.90: 110341 Nonbonded interactions: 246038 Sorted by model distance: nonbonded pdb=" OG1 THR B 807 " pdb=" ND2 ASN B 845 " model vdw 1.986 3.120 nonbonded pdb=" OD1 ASP A 459 " pdb="MG MG A1501 " model vdw 2.022 2.170 nonbonded pdb=" O ILE B 486 " pdb=" OG1 THR B 506 " model vdw 2.136 3.040 nonbonded pdb=" OG1 THR E 67 " pdb=" OE1 GLU E 134 " model vdw 2.137 3.040 nonbonded pdb=" O ARG A 49 " pdb=" OG1 THR A 61 " model vdw 2.138 3.040 ... (remaining 246033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.330 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 76.380 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0516 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 : 0.009 0.392 30576 Z= 0.338 Angle : 0.789 21.691 41440 Z= 0.421 Chirality : 0.053 0.264 4702 Planarity : 0.006 0.110 5277 Dihedral : 16.643 89.814 11552 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.52 % Allowed : 18.06 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.05 (0.13), residues: 3683 helix: -0.47 (0.13), residues: 1338 sheet: -0.43 (0.22), residues: 546 loop : -0.85 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 466 HIS 0.011 0.002 HIS A1210 PHE 0.037 0.003 PHE C 5 TYR 0.023 0.002 TYR B 413 ARG 0.014 0.001 ARG B1213 Details of bonding type rmsd hydrogen bonds : bond 0.22246 ( 1251) hydrogen bonds : angle 7.52828 ( 3459) metal coordination : bond 0.14077 ( 16) metal coordination : angle 8.31223 ( 21) covalent geometry : bond 0.00790 (30560) covalent geometry : angle 0.76681 (41419) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 309 time to evaluate : 3.254 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: A 390 ILE cc_start: 0.0871 (tp) cc_final: 0.0534 (mt) REVERT: A 878 GLN cc_start: 0.3768 (tp-100) cc_final: 0.3221 (mm110) REVERT: A 943 LEU cc_start: 0.3180 (OUTLIER) cc_final: 0.1886 (pp) REVERT: A 1144 MET cc_start: 0.0962 (mmt) cc_final: 0.0511 (ttm) REVERT: A 1168 PRO cc_start: -0.0651 (Cg_endo) cc_final: -0.0873 (Cg_exo) REVERT: A 1200 ARG cc_start: 0.1558 (mtp-110) cc_final: 0.1172 (ttp-110) REVERT: A 1434 LYS cc_start: 0.3621 (tttp) cc_final: 0.2899 (tttt) REVERT: B 27 LEU cc_start: 0.3362 (mt) cc_final: 0.2148 (tm) REVERT: B 261 ASN cc_start: 0.3131 (m-40) cc_final: 0.1792 (t160) REVERT: B 336 LEU cc_start: 0.0451 (tp) cc_final: 0.0074 (tp) REVERT: B 402 MET cc_start: -0.1945 (OUTLIER) cc_final: -0.2176 (ttm) REVERT: D 65 VAL cc_start: 0.2649 (t) cc_final: 0.2437 (t) REVERT: F 231 MET cc_start: 0.2500 (ttm) cc_final: 0.1365 (pmm) REVERT: G 49 MET cc_start: 0.2065 (ttt) cc_final: 0.1739 (mtm) REVERT: G 83 GLN cc_start: 0.2897 (pp30) cc_final: 0.2348 (tt0) REVERT: G 100 TYR cc_start: 0.2226 (t80) cc_final: 0.0246 (t80) outliers start: 83 outliers final: 15 residues processed: 379 average time/residue: 1.2706 time to fit residues: 588.3899 Evaluate side-chains 237 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 4.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1358 ASP Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 23 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 4.9990 chunk 278 optimal weight: 0.2980 chunk 154 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 148 optimal weight: 9.9990 chunk 287 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 333 optimal weight: 0.0170 overall best weight: 1.0624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 68 GLN A 114 HIS ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 HIS A 228 ASN A 231 GLN A 264 GLN A 265 GLN A 334 HIS A 420 GLN A 455 ASN A 501 GLN A 514 ASN A 592 GLN A 728 ASN A 758 ASN A 834 GLN A 853 GLN A 919 ASN A1161 ASN A1256 ASN A1276 HIS A1289 ASN A1349 ASN A1393 GLN B 75 HIS B 173 HIS B 207 ASN B 216 HIS B 235 GLN B 314 HIS B 325 HIS B 361 ASN B 364 GLN B 419 HIS B 557 GLN B 598 GLN B 735 GLN B 845 ASN B 861 GLN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 HIS B1227 ASN C 24 ASN C 118 ASN C 345 GLN D 44 ASN D 80 ASN D 119 ASN F 4 GLN F 308 ASN F 332 GLN G 103 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.236471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.193689 restraints weight = 34235.324| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.53 r_work: 0.3681 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0057 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30576 Z= 0.150 Angle : 0.638 8.592 41440 Z= 0.336 Chirality : 0.046 0.301 4702 Planarity : 0.005 0.072 5277 Dihedral : 8.754 85.279 4213 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.12 % Rotamer: Outliers : 3.82 % Allowed : 17.73 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.45 (0.13), residues: 3683 helix: 0.22 (0.14), residues: 1368 sheet: -0.24 (0.22), residues: 550 loop : -0.62 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 701 HIS 0.013 0.001 HIS B 75 PHE 0.028 0.002 PHE A 531 TYR 0.026 0.002 TYR A 166 ARG 0.008 0.001 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 1251) hydrogen bonds : angle 5.30407 ( 3459) metal coordination : bond 0.00997 ( 16) metal coordination : angle 3.25528 ( 21) covalent geometry : bond 0.00320 (30560) covalent geometry : angle 0.63434 (41419) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 250 time to evaluate : 3.100 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: A 192 HIS cc_start: 0.2810 (OUTLIER) cc_final: 0.2148 (t-170) REVERT: A 300 MET cc_start: -0.0008 (OUTLIER) cc_final: -0.1687 (tpt) REVERT: A 390 ILE cc_start: 0.0723 (tp) cc_final: 0.0337 (mt) REVERT: A 472 MET cc_start: 0.1283 (OUTLIER) cc_final: 0.0657 (mmt) REVERT: A 558 MET cc_start: 0.0544 (OUTLIER) cc_final: 0.0233 (ppp) REVERT: A 669 ILE cc_start: -0.0160 (OUTLIER) cc_final: -0.1656 (pp) REVERT: A 874 MET cc_start: 0.4602 (mmm) cc_final: 0.3728 (ttm) REVERT: A 878 GLN cc_start: 0.4582 (tp-100) cc_final: 0.3828 (mm-40) REVERT: A 1094 MET cc_start: 0.0035 (tpp) cc_final: -0.1497 (pp-130) REVERT: A 1109 TYR cc_start: 0.2863 (t80) cc_final: 0.2566 (t80) REVERT: A 1118 GLU cc_start: 0.4655 (OUTLIER) cc_final: 0.3736 (tm-30) REVERT: A 1144 MET cc_start: 0.0780 (mmt) cc_final: 0.0147 (ttm) REVERT: A 1227 LEU cc_start: 0.1184 (OUTLIER) cc_final: 0.0387 (mp) REVERT: A 1434 LYS cc_start: 0.4092 (tttp) cc_final: 0.3779 (ttpt) REVERT: A 1438 GLU cc_start: 0.2698 (tt0) cc_final: 0.2412 (mm-30) REVERT: B 27 LEU cc_start: 0.3668 (mt) cc_final: 0.2291 (tm) REVERT: B 336 LEU cc_start: 0.0949 (tp) cc_final: 0.0679 (tp) REVERT: B 371 ILE cc_start: 0.2771 (OUTLIER) cc_final: 0.2385 (mt) REVERT: B 402 MET cc_start: -0.1762 (OUTLIER) cc_final: -0.1971 (ttm) REVERT: B 701 TRP cc_start: 0.0062 (OUTLIER) cc_final: -0.0668 (p-90) REVERT: C 88 MET cc_start: -0.0640 (OUTLIER) cc_final: -0.0868 (ptm) REVERT: C 210 MET cc_start: 0.0353 (mmt) cc_final: 0.0033 (mmt) REVERT: D 89 ILE cc_start: 0.2864 (mp) cc_final: 0.2628 (pp) REVERT: D 101 ASN cc_start: 0.3194 (OUTLIER) cc_final: 0.2312 (t0) REVERT: D 185 GLU cc_start: 0.1213 (OUTLIER) cc_final: 0.0761 (mt-10) REVERT: F 81 LEU cc_start: 0.3572 (OUTLIER) cc_final: 0.3331 (mm) REVERT: F 231 MET cc_start: 0.1906 (ttm) cc_final: 0.0647 (pmm) REVERT: F 272 GLN cc_start: 0.1418 (pt0) cc_final: 0.0562 (pp30) REVERT: F 324 GLU cc_start: 0.4243 (tm-30) cc_final: 0.3612 (tp30) REVERT: G 49 MET cc_start: 0.2340 (ttt) cc_final: 0.1642 (mtm) REVERT: G 100 TYR cc_start: 0.2822 (t80) cc_final: 0.0965 (t80) outliers start: 126 outliers final: 31 residues processed: 336 average time/residue: 1.2798 time to fit residues: 516.8667 Evaluate side-chains 251 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 GLN Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 908 TYR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1158 PHE Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1324 GLU Chi-restraints excluded: chain A residue 1371 LYS Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 701 TRP Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain F residue 4 GLN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain H residue 62 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 285 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 chunk 299 optimal weight: 4.9990 chunk 332 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 292 optimal weight: 0.9980 chunk 275 optimal weight: 0.1980 chunk 17 optimal weight: 10.0000 chunk 348 optimal weight: 20.0000 chunk 60 optimal weight: 0.6980 chunk 346 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 497 ASN A 592 GLN A 747 HIS ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 HIS ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 GLN B1158 GLN C 24 ASN C 230 HIS C 342 ASN D 33 GLN D 80 ASN D 157 GLN F 302 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.253303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.220021 restraints weight = 36320.526| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 2.11 r_work: 0.4031 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0837 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 30576 Z= 0.184 Angle : 0.711 16.841 41440 Z= 0.370 Chirality : 0.048 0.417 4702 Planarity : 0.006 0.073 5277 Dihedral : 8.647 84.965 4194 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 3.64 % Allowed : 18.39 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.50 (0.13), residues: 3683 helix: 0.24 (0.14), residues: 1373 sheet: -0.35 (0.22), residues: 544 loop : -0.70 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP F 327 HIS 0.012 0.002 HIS A 618 PHE 0.030 0.003 PHE B1089 TYR 0.039 0.002 TYR D 85 ARG 0.014 0.001 ARG E 121 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 1251) hydrogen bonds : angle 5.18747 ( 3459) metal coordination : bond 0.01007 ( 16) metal coordination : angle 3.59263 ( 21) covalent geometry : bond 0.00407 (30560) covalent geometry : angle 0.70667 (41419) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 229 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.2451 (OUTLIER) cc_final: 0.1930 (ttp) REVERT: A 300 MET cc_start: 0.0348 (OUTLIER) cc_final: -0.1365 (tpt) REVERT: A 425 ARG cc_start: 0.1889 (OUTLIER) cc_final: -0.0901 (ttt180) REVERT: A 446 MET cc_start: 0.1601 (OUTLIER) cc_final: 0.0343 (tmt) REVERT: A 472 MET cc_start: 0.1675 (OUTLIER) cc_final: 0.0438 (mmt) REVERT: A 476 GLU cc_start: -0.1135 (OUTLIER) cc_final: -0.1472 (tt0) REVERT: A 558 MET cc_start: 0.1382 (OUTLIER) cc_final: 0.1043 (ptt) REVERT: A 582 MET cc_start: 0.3237 (mtm) cc_final: 0.1138 (tmt) REVERT: A 669 ILE cc_start: 0.0651 (OUTLIER) cc_final: -0.1018 (pp) REVERT: A 1094 MET cc_start: 0.1688 (tpp) cc_final: 0.0345 (ppp) REVERT: A 1144 MET cc_start: 0.0597 (mmt) cc_final: 0.0012 (ttm) REVERT: A 1197 ASN cc_start: 0.3085 (OUTLIER) cc_final: 0.2270 (t0) REVERT: A 1275 ARG cc_start: 0.4844 (mmt-90) cc_final: 0.4633 (mtt-85) REVERT: A 1312 TYR cc_start: 0.1597 (m-10) cc_final: 0.1308 (m-10) REVERT: A 1349 ASN cc_start: 0.4034 (OUTLIER) cc_final: 0.1566 (m-40) REVERT: A 1362 ARG cc_start: 0.1331 (OUTLIER) cc_final: -0.0965 (ptm-80) REVERT: B 376 MET cc_start: 0.2680 (mpt) cc_final: 0.2417 (mmt) REVERT: B 610 LYS cc_start: 0.3845 (mtmt) cc_final: 0.3357 (tttp) REVERT: B 926 VAL cc_start: 0.2549 (OUTLIER) cc_final: 0.2024 (p) REVERT: C 88 MET cc_start: -0.0878 (ptm) cc_final: -0.1101 (ptm) REVERT: C 200 MET cc_start: -0.0254 (mtp) cc_final: -0.1107 (ppp) REVERT: C 210 MET cc_start: 0.0468 (mmt) cc_final: -0.0090 (mmt) REVERT: C 323 ILE cc_start: 0.3717 (mt) cc_final: 0.3378 (mt) REVERT: D 81 GLU cc_start: 0.3429 (pm20) cc_final: 0.2479 (tm-30) REVERT: D 185 GLU cc_start: 0.1758 (OUTLIER) cc_final: 0.1281 (mm-30) REVERT: F 128 GLN cc_start: 0.2756 (mt0) cc_final: 0.2054 (mt0) REVERT: F 201 CYS cc_start: 0.4016 (m) cc_final: 0.3441 (t) REVERT: F 204 GLU cc_start: 0.3165 (OUTLIER) cc_final: 0.2919 (mp0) REVERT: F 212 ILE cc_start: 0.1005 (OUTLIER) cc_final: 0.0307 (tt) REVERT: F 231 MET cc_start: 0.1743 (ttm) cc_final: 0.0456 (pmm) REVERT: F 324 GLU cc_start: 0.4236 (tm-30) cc_final: 0.3521 (tp30) REVERT: G 49 MET cc_start: 0.2532 (ttt) cc_final: 0.1767 (mtm) outliers start: 120 outliers final: 33 residues processed: 318 average time/residue: 1.2553 time to fit residues: 485.6296 Evaluate side-chains 244 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1197 ASN Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1362 ARG Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain H residue 62 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 13 optimal weight: 20.0000 chunk 185 optimal weight: 9.9990 chunk 129 optimal weight: 0.0060 chunk 347 optimal weight: 6.9990 chunk 163 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 331 optimal weight: 1.9990 chunk 360 optimal weight: 1.9990 chunk 328 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN A 382 GLN A 485 ASN A 501 GLN A 535 GLN A 628 GLN A 852 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN A1161 ASN B 314 HIS B 761 HIS ** B1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 144 ASN C 230 HIS ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN D 139 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.264479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.236285 restraints weight = 37826.419| |-----------------------------------------------------------------------------| r_work (start): 0.4461 rms_B_bonded: 1.76 r_work: 0.4211 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1244 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 30576 Z= 0.152 Angle : 0.635 12.441 41440 Z= 0.332 Chirality : 0.046 0.386 4702 Planarity : 0.005 0.075 5277 Dihedral : 8.461 85.258 4188 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 3.09 % Allowed : 20.45 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.33 (0.14), residues: 3683 helix: 0.43 (0.14), residues: 1383 sheet: -0.17 (0.22), residues: 534 loop : -0.67 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 469 HIS 0.025 0.001 HIS A 192 PHE 0.036 0.002 PHE A1158 TYR 0.022 0.002 TYR A 179 ARG 0.015 0.001 ARG A1385 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 1251) hydrogen bonds : angle 4.99205 ( 3459) metal coordination : bond 0.00682 ( 16) metal coordination : angle 2.78601 ( 21) covalent geometry : bond 0.00332 (30560) covalent geometry : angle 0.63233 (41419) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 233 time to evaluate : 5.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ILE cc_start: 0.1709 (OUTLIER) cc_final: 0.0993 (tp) REVERT: A 212 ILE cc_start: 0.1559 (OUTLIER) cc_final: 0.0954 (mm) REVERT: A 300 MET cc_start: 0.0948 (OUTLIER) cc_final: -0.1647 (tpt) REVERT: A 446 MET cc_start: 0.1815 (OUTLIER) cc_final: 0.0595 (tmt) REVERT: A 472 MET cc_start: 0.1877 (OUTLIER) cc_final: 0.0848 (mmt) REVERT: A 558 MET cc_start: 0.1529 (OUTLIER) cc_final: 0.0196 (mmt) REVERT: A 582 MET cc_start: 0.3592 (mtm) cc_final: 0.1489 (tmt) REVERT: A 669 ILE cc_start: 0.0718 (OUTLIER) cc_final: -0.1016 (pp) REVERT: A 864 GLN cc_start: 0.5630 (mm-40) cc_final: 0.4924 (mm-40) REVERT: A 881 GLU cc_start: 0.5075 (tp30) cc_final: 0.4432 (mm-30) REVERT: A 1144 MET cc_start: 0.0766 (mmt) cc_final: 0.0088 (ttm) REVERT: A 1274 MET cc_start: 0.4392 (ttp) cc_final: 0.4062 (ttp) REVERT: A 1362 ARG cc_start: 0.1480 (OUTLIER) cc_final: -0.1093 (ptm-80) REVERT: A 1371 LYS cc_start: 0.1253 (OUTLIER) cc_final: 0.0725 (mmmt) REVERT: A 1431 MET cc_start: 0.5984 (tpt) cc_final: 0.5780 (tpt) REVERT: B 278 MET cc_start: -0.0545 (OUTLIER) cc_final: -0.0965 (ptm) REVERT: B 289 GLU cc_start: 0.1017 (OUTLIER) cc_final: 0.0795 (tt0) REVERT: B 336 LEU cc_start: 0.1335 (tp) cc_final: 0.1045 (tp) REVERT: B 376 MET cc_start: 0.2796 (mpt) cc_final: 0.2415 (mpt) REVERT: B 541 MET cc_start: 0.0488 (ptm) cc_final: 0.0274 (ptm) REVERT: B 831 MET cc_start: 0.2474 (pmt) cc_final: 0.2074 (pp-130) REVERT: B 926 VAL cc_start: 0.2869 (OUTLIER) cc_final: 0.2266 (p) REVERT: B 1209 MET cc_start: -0.1388 (mtp) cc_final: -0.1937 (pmt) REVERT: C 88 MET cc_start: -0.0702 (ptm) cc_final: -0.0953 (ptm) REVERT: C 200 MET cc_start: 0.0090 (mtp) cc_final: -0.0473 (ppp) REVERT: C 323 ILE cc_start: 0.4146 (mt) cc_final: 0.3816 (mt) REVERT: D 81 GLU cc_start: 0.3079 (pm20) cc_final: 0.2490 (tm-30) REVERT: F 78 VAL cc_start: 0.5091 (t) cc_final: 0.4691 (t) REVERT: F 128 GLN cc_start: 0.2537 (mt0) cc_final: 0.1981 (mt0) REVERT: F 173 GLU cc_start: 0.4054 (pm20) cc_final: 0.3186 (mm-30) REVERT: F 201 CYS cc_start: 0.3922 (m) cc_final: 0.3469 (t) REVERT: F 212 ILE cc_start: 0.1105 (OUTLIER) cc_final: 0.0373 (tt) REVERT: F 231 MET cc_start: 0.1960 (ttm) cc_final: 0.0411 (pmm) REVERT: F 272 GLN cc_start: 0.0940 (pt0) cc_final: -0.0084 (pp30) REVERT: F 324 GLU cc_start: 0.4331 (tm-30) cc_final: 0.3472 (tp30) REVERT: F 333 ARG cc_start: 0.2991 (ptm-80) cc_final: 0.1684 (tpt90) REVERT: G 49 MET cc_start: 0.2736 (ttt) cc_final: 0.2224 (mtm) outliers start: 102 outliers final: 28 residues processed: 306 average time/residue: 2.1744 time to fit residues: 799.3702 Evaluate side-chains 248 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 618 HIS Chi-restraints excluded: chain A residue 667 GLN Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 1000 MET Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1200 ARG Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1362 ARG Chi-restraints excluded: chain A residue 1371 LYS Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1161 MET Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain H residue 62 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 13 optimal weight: 0.4980 chunk 131 optimal weight: 0.8980 chunk 348 optimal weight: 6.9990 chunk 325 optimal weight: 0.0670 chunk 160 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 343 optimal weight: 0.7980 chunk 352 optimal weight: 10.0000 chunk 328 optimal weight: 6.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN A1281 GLN B 314 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 ASN ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1182 ASN C 230 HIS C 342 ASN D 33 GLN D 44 ASN D 77 ASN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.272008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.245123 restraints weight = 38364.100| |-----------------------------------------------------------------------------| r_work (start): 0.4531 rms_B_bonded: 1.45 r_work: 0.4318 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4234 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1546 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 30576 Z= 0.128 Angle : 0.600 11.163 41440 Z= 0.309 Chirality : 0.045 0.185 4702 Planarity : 0.004 0.063 5277 Dihedral : 8.343 87.206 4188 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 2.76 % Allowed : 20.88 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.19 (0.14), residues: 3683 helix: 0.64 (0.14), residues: 1377 sheet: -0.21 (0.23), residues: 530 loop : -0.63 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 469 HIS 0.007 0.001 HIS F 323 PHE 0.027 0.002 PHE A 918 TYR 0.019 0.001 TYR F 69 ARG 0.012 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 1251) hydrogen bonds : angle 4.77391 ( 3459) metal coordination : bond 0.00523 ( 16) metal coordination : angle 3.20833 ( 21) covalent geometry : bond 0.00280 (30560) covalent geometry : angle 0.59559 (41419) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 239 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ILE cc_start: 0.1804 (OUTLIER) cc_final: 0.1140 (tp) REVERT: A 300 MET cc_start: 0.0326 (OUTLIER) cc_final: -0.1185 (tpt) REVERT: A 425 ARG cc_start: 0.2732 (OUTLIER) cc_final: 0.1934 (ppp80) REVERT: A 472 MET cc_start: 0.1837 (ttm) cc_final: 0.0973 (mmt) REVERT: A 558 MET cc_start: 0.1708 (OUTLIER) cc_final: 0.1057 (mtt) REVERT: A 582 MET cc_start: 0.3568 (mtm) cc_final: 0.1891 (tmt) REVERT: A 656 MET cc_start: 0.0383 (tpt) cc_final: -0.2101 (mmt) REVERT: A 669 ILE cc_start: 0.0630 (OUTLIER) cc_final: -0.0992 (pp) REVERT: A 864 GLN cc_start: 0.6318 (mm-40) cc_final: 0.5882 (mm110) REVERT: A 963 MET cc_start: 0.5675 (mtt) cc_final: 0.5455 (mtt) REVERT: A 977 ASN cc_start: 0.5833 (p0) cc_final: 0.5339 (p0) REVERT: A 1144 MET cc_start: 0.0864 (mmt) cc_final: 0.0082 (ttm) REVERT: A 1185 MET cc_start: 0.2212 (OUTLIER) cc_final: 0.1628 (mtt) REVERT: A 1197 ASN cc_start: 0.3007 (OUTLIER) cc_final: 0.2173 (t0) REVERT: A 1281 GLN cc_start: 0.4130 (OUTLIER) cc_final: 0.3688 (tp40) REVERT: A 1312 TYR cc_start: 0.3591 (m-10) cc_final: 0.3081 (m-80) REVERT: A 1323 MET cc_start: 0.0429 (mmm) cc_final: 0.0091 (mmm) REVERT: A 1349 ASN cc_start: 0.4805 (OUTLIER) cc_final: 0.2859 (m-40) REVERT: B 26 MET cc_start: 0.0172 (OUTLIER) cc_final: -0.0434 (ppp) REVERT: B 376 MET cc_start: 0.2562 (mpt) cc_final: 0.2256 (mpt) REVERT: B 455 GLU cc_start: 0.2158 (OUTLIER) cc_final: 0.1285 (pt0) REVERT: B 637 MET cc_start: -0.0070 (tpt) cc_final: -0.0414 (tpt) REVERT: B 831 MET cc_start: 0.2479 (pmt) cc_final: 0.2079 (pp-130) REVERT: B 926 VAL cc_start: 0.2802 (OUTLIER) cc_final: 0.2172 (p) REVERT: B 1066 ILE cc_start: 0.0883 (OUTLIER) cc_final: 0.0533 (pp) REVERT: B 1209 MET cc_start: -0.1538 (mtp) cc_final: -0.1895 (pmt) REVERT: C 200 MET cc_start: -0.0009 (mtp) cc_final: -0.0406 (ppp) REVERT: C 323 ILE cc_start: 0.4522 (mt) cc_final: 0.4250 (mt) REVERT: D 81 GLU cc_start: 0.2840 (pm20) cc_final: 0.2600 (tt0) REVERT: E 121 ARG cc_start: 0.4312 (mtt180) cc_final: 0.2756 (mtt180) REVERT: F 78 VAL cc_start: 0.5009 (t) cc_final: 0.4607 (t) REVERT: F 128 GLN cc_start: 0.2706 (mt0) cc_final: 0.2225 (mt0) REVERT: F 173 GLU cc_start: 0.3979 (pm20) cc_final: 0.3103 (mm-30) REVERT: F 212 ILE cc_start: 0.1165 (OUTLIER) cc_final: 0.0550 (tt) REVERT: F 231 MET cc_start: 0.2028 (ttm) cc_final: 0.0422 (pmm) REVERT: F 243 LEU cc_start: 0.5338 (tp) cc_final: 0.4922 (mt) REVERT: F 324 GLU cc_start: 0.4486 (tm-30) cc_final: 0.3687 (tp30) REVERT: F 327 TRP cc_start: 0.2567 (m100) cc_final: 0.2266 (m100) REVERT: F 333 ARG cc_start: 0.3167 (ptm-80) cc_final: 0.1727 (tpt90) outliers start: 91 outliers final: 37 residues processed: 302 average time/residue: 1.3098 time to fit residues: 477.2399 Evaluate side-chains 257 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 206 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 618 HIS Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 1000 MET Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1197 ASN Chi-restraints excluded: chain A residue 1200 ARG Chi-restraints excluded: chain A residue 1281 GLN Chi-restraints excluded: chain A residue 1293 ILE Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain F residue 20 CYS Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 62 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 183 optimal weight: 20.0000 chunk 255 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 258 optimal weight: 0.9980 chunk 263 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 345 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 333 optimal weight: 30.0000 chunk 3 optimal weight: 0.4980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 355 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN A 980 GLN A1018 GLN B 214 HIS B 314 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 861 GLN B 912 ASN ** B1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1039 ASN B1108 HIS B1112 GLN B1134 GLN ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN C 144 ASN C 173 HIS ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN D 113 ASN F 71 HIS ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN G 103 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.299732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.279224 restraints weight = 41730.670| |-----------------------------------------------------------------------------| r_work (start): 0.4794 rms_B_bonded: 1.16 r_work: 0.4696 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.4634 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.4634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3607 moved from start: 0.9097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.212 30576 Z= 0.299 Angle : 0.976 26.100 41440 Z= 0.512 Chirality : 0.056 0.303 4702 Planarity : 0.008 0.104 5277 Dihedral : 9.286 86.535 4187 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.97 % Favored : 93.89 % Rotamer: Outliers : 4.18 % Allowed : 20.97 % Favored : 74.85 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.24 (0.13), residues: 3683 helix: -0.35 (0.13), residues: 1381 sheet: -0.66 (0.23), residues: 493 loop : -1.18 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 469 HIS 0.024 0.002 HIS A 56 PHE 0.046 0.004 PHE A 831 TYR 0.082 0.003 TYR A1326 ARG 0.019 0.001 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.05777 ( 1251) hydrogen bonds : angle 5.89050 ( 3459) metal coordination : bond 0.01166 ( 16) metal coordination : angle 6.14769 ( 21) covalent geometry : bond 0.00594 (30560) covalent geometry : angle 0.96604 (41419) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 267 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.0396 (tmt) cc_final: 0.0011 (tmt) REVERT: A 208 ILE cc_start: 0.2541 (OUTLIER) cc_final: 0.1527 (tp) REVERT: A 230 ILE cc_start: 0.0285 (OUTLIER) cc_final: 0.0015 (mp) REVERT: A 300 MET cc_start: 0.2379 (OUTLIER) cc_final: 0.1593 (mpt) REVERT: A 357 TYR cc_start: 0.3406 (OUTLIER) cc_final: 0.3204 (p90) REVERT: A 425 ARG cc_start: 0.5660 (OUTLIER) cc_final: 0.5232 (ttt180) REVERT: A 463 MET cc_start: 0.1736 (ttm) cc_final: 0.1467 (tmm) REVERT: A 572 THR cc_start: 0.7747 (m) cc_final: 0.7152 (m) REVERT: A 582 MET cc_start: 0.3609 (mtm) cc_final: 0.2645 (tmt) REVERT: A 881 GLU cc_start: 0.5811 (tp30) cc_final: 0.4625 (mm-30) REVERT: A 1144 MET cc_start: 0.0899 (mmt) cc_final: 0.0144 (ttm) REVERT: A 1197 ASN cc_start: 0.3066 (OUTLIER) cc_final: 0.2323 (t0) REVERT: A 1200 ARG cc_start: 0.1737 (OUTLIER) cc_final: 0.1093 (ttm-80) REVERT: A 1313 THR cc_start: 0.8663 (m) cc_final: 0.8072 (p) REVERT: A 1349 ASN cc_start: 0.6116 (OUTLIER) cc_final: 0.5870 (t0) REVERT: A 1371 LYS cc_start: 0.2091 (OUTLIER) cc_final: 0.1527 (mmmt) REVERT: A 1428 ASP cc_start: 0.5669 (m-30) cc_final: 0.5396 (m-30) REVERT: B 26 MET cc_start: 0.1016 (OUTLIER) cc_final: 0.0032 (ppp) REVERT: B 248 ILE cc_start: 0.3540 (OUTLIER) cc_final: 0.3006 (pt) REVERT: B 305 MET cc_start: -0.1012 (ttt) cc_final: -0.1237 (ppp) REVERT: B 376 MET cc_start: 0.2741 (mpt) cc_final: 0.2243 (mpt) REVERT: B 455 GLU cc_start: 0.2245 (OUTLIER) cc_final: 0.1266 (pt0) REVERT: B 610 LYS cc_start: 0.4179 (mtmt) cc_final: 0.3728 (tttp) REVERT: B 661 GLU cc_start: 0.2138 (mt-10) cc_final: 0.0114 (pm20) REVERT: B 720 LYS cc_start: 0.2442 (OUTLIER) cc_final: 0.2200 (tppt) REVERT: B 831 MET cc_start: 0.3120 (pmt) cc_final: 0.2740 (pp-130) REVERT: C 80 ILE cc_start: 0.3894 (OUTLIER) cc_final: 0.3138 (pp) REVERT: C 88 MET cc_start: -0.1092 (ptp) cc_final: -0.2091 (tpp) REVERT: C 169 ILE cc_start: 0.2668 (OUTLIER) cc_final: 0.1346 (pp) REVERT: C 298 ILE cc_start: 0.3224 (mt) cc_final: 0.2897 (mt) REVERT: D 36 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5611 (tm) REVERT: D 193 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6045 (p-80) REVERT: F 24 GLU cc_start: 0.2771 (OUTLIER) cc_final: 0.1724 (mp0) REVERT: F 69 TYR cc_start: 0.3128 (p90) cc_final: 0.2906 (p90) REVERT: F 128 GLN cc_start: 0.2845 (mt0) cc_final: 0.2351 (mt0) REVERT: F 231 MET cc_start: 0.1863 (ttm) cc_final: 0.0227 (pmm) REVERT: F 272 GLN cc_start: 0.0892 (pt0) cc_final: 0.0541 (pt0) outliers start: 138 outliers final: 43 residues processed: 366 average time/residue: 1.2764 time to fit residues: 561.7694 Evaluate side-chains 269 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 667 GLN Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1197 ASN Chi-restraints excluded: chain A residue 1200 ARG Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1371 LYS Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 720 LYS Chi-restraints excluded: chain B residue 757 GLU Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 996 MET Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 20 CYS Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 83 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 29 optimal weight: 0.8980 chunk 234 optimal weight: 0.7980 chunk 3 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 121 optimal weight: 0.0980 chunk 355 optimal weight: 0.5980 chunk 270 optimal weight: 3.9990 chunk 347 optimal weight: 0.0870 chunk 173 optimal weight: 7.9990 chunk 167 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 269 ASN A 445 GLN A 595 ASN A 642 ASN A 728 ASN A 852 GLN A 980 GLN B 314 HIS ** B1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS E 137 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.299350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.278490 restraints weight = 40958.884| |-----------------------------------------------------------------------------| r_work (start): 0.4795 rms_B_bonded: 1.26 r_work: 0.4682 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4614 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3557 moved from start: 0.9148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30576 Z= 0.130 Angle : 0.643 14.256 41440 Z= 0.329 Chirality : 0.046 0.291 4702 Planarity : 0.004 0.057 5277 Dihedral : 8.567 89.534 4187 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.69 % Rotamer: Outliers : 2.21 % Allowed : 23.64 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.58 (0.14), residues: 3683 helix: 0.36 (0.14), residues: 1394 sheet: -0.41 (0.23), residues: 527 loop : -0.92 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 469 HIS 0.009 0.001 HIS B1221 PHE 0.027 0.001 PHE A 918 TYR 0.030 0.001 TYR G 53 ARG 0.005 0.000 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 1251) hydrogen bonds : angle 5.05617 ( 3459) metal coordination : bond 0.00865 ( 16) metal coordination : angle 3.62620 ( 21) covalent geometry : bond 0.00268 (30560) covalent geometry : angle 0.63811 (41419) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 219 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.0048 (tmt) cc_final: -0.0180 (tmt) REVERT: A 208 ILE cc_start: 0.1836 (OUTLIER) cc_final: 0.1197 (tp) REVERT: A 300 MET cc_start: 0.1877 (OUTLIER) cc_final: 0.1114 (pmm) REVERT: A 472 MET cc_start: 0.3332 (ttm) cc_final: 0.2840 (mmt) REVERT: A 551 ASP cc_start: 0.8057 (p0) cc_final: 0.7753 (p0) REVERT: A 582 MET cc_start: 0.3618 (mtm) cc_final: 0.2922 (ttt) REVERT: A 883 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6799 (mtmt) REVERT: A 1144 MET cc_start: 0.1046 (mmt) cc_final: 0.0170 (ttm) REVERT: A 1185 MET cc_start: 0.2334 (OUTLIER) cc_final: 0.2023 (mtt) REVERT: A 1200 ARG cc_start: 0.1755 (OUTLIER) cc_final: 0.1275 (ttm-80) REVERT: A 1209 MET cc_start: 0.0911 (tpt) cc_final: -0.0490 (tmm) REVERT: A 1210 HIS cc_start: 0.3074 (OUTLIER) cc_final: 0.2800 (p90) REVERT: A 1349 ASN cc_start: 0.6080 (OUTLIER) cc_final: 0.5705 (t0) REVERT: A 1352 HIS cc_start: 0.6642 (m90) cc_final: 0.6427 (m-70) REVERT: A 1428 ASP cc_start: 0.6111 (m-30) cc_final: 0.5832 (m-30) REVERT: B 26 MET cc_start: 0.1250 (ptm) cc_final: 0.0556 (ppp) REVERT: B 251 MET cc_start: 0.2370 (OUTLIER) cc_final: 0.1310 (ptp) REVERT: B 321 GLN cc_start: 0.3683 (mt0) cc_final: 0.3433 (mp10) REVERT: B 376 MET cc_start: 0.2598 (mpt) cc_final: 0.2128 (mpt) REVERT: B 455 GLU cc_start: 0.2074 (OUTLIER) cc_final: 0.1439 (pt0) REVERT: B 610 LYS cc_start: 0.4194 (mtmt) cc_final: 0.3671 (tttp) REVERT: B 661 GLU cc_start: 0.1711 (mt-10) cc_final: 0.0148 (mt-10) REVERT: B 831 MET cc_start: 0.2775 (pmt) cc_final: 0.2425 (pp-130) REVERT: B 1209 MET cc_start: 0.0634 (pmt) cc_final: -0.0616 (mtp) REVERT: C 80 ILE cc_start: 0.3446 (OUTLIER) cc_final: 0.2769 (pp) REVERT: C 88 MET cc_start: -0.0833 (ptp) cc_final: -0.1995 (tpp) REVERT: D 192 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7840 (ttp) REVERT: E 94 MET cc_start: 0.5528 (tmm) cc_final: 0.4854 (ttm) REVERT: F 11 LEU cc_start: 0.4191 (mt) cc_final: 0.3955 (mp) REVERT: F 212 ILE cc_start: 0.1085 (OUTLIER) cc_final: 0.0489 (tt) REVERT: F 231 MET cc_start: 0.2202 (ttm) cc_final: 0.0383 (pmm) REVERT: F 243 LEU cc_start: 0.5505 (tp) cc_final: 0.5206 (mt) REVERT: F 272 GLN cc_start: 0.0889 (pt0) cc_final: 0.0557 (pt0) REVERT: F 324 GLU cc_start: 0.4369 (OUTLIER) cc_final: 0.3584 (tp30) REVERT: H 1 MET cc_start: 0.1912 (pp-130) cc_final: 0.1603 (pp-130) outliers start: 73 outliers final: 24 residues processed: 269 average time/residue: 1.4220 time to fit residues: 456.3981 Evaluate side-chains 230 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1200 ARG Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain F residue 20 CYS Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain G residue 83 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 219 optimal weight: 1.9990 chunk 269 optimal weight: 20.0000 chunk 284 optimal weight: 0.5980 chunk 151 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 255 optimal weight: 0.9980 chunk 229 optimal weight: 30.0000 chunk 182 optimal weight: 30.0000 chunk 204 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 933 ASN A 980 GLN A1018 GLN A1111 GLN ** B 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS B 461 ASN ** B1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 GLN ** B1169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN C 117 ASN F 249 ASN ** F 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.300132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.279826 restraints weight = 41322.246| |-----------------------------------------------------------------------------| r_work (start): 0.4801 rms_B_bonded: 1.28 r_work: 0.4656 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4580 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4178 moved from start: 0.9860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 30576 Z= 0.145 Angle : 0.680 13.658 41440 Z= 0.347 Chirality : 0.047 0.353 4702 Planarity : 0.005 0.170 5277 Dihedral : 8.504 88.264 4187 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.71 % Rotamer: Outliers : 2.18 % Allowed : 23.85 % Favored : 73.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.50 (0.14), residues: 3683 helix: 0.48 (0.14), residues: 1398 sheet: -0.49 (0.22), residues: 537 loop : -0.88 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 469 HIS 0.061 0.002 HIS B 314 PHE 0.024 0.002 PHE A 918 TYR 0.024 0.002 TYR B 828 ARG 0.014 0.001 ARG B 73 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 1251) hydrogen bonds : angle 4.99733 ( 3459) metal coordination : bond 0.00778 ( 16) metal coordination : angle 3.67978 ( 21) covalent geometry : bond 0.00314 (30560) covalent geometry : angle 0.67554 (41419) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 232 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ILE cc_start: 0.1724 (OUTLIER) cc_final: 0.1082 (mp) REVERT: A 300 MET cc_start: 0.2783 (OUTLIER) cc_final: 0.1807 (mpt) REVERT: A 582 MET cc_start: 0.3588 (mtm) cc_final: 0.3288 (ttt) REVERT: A 656 MET cc_start: 0.0406 (tpt) cc_final: -0.2264 (mmt) REVERT: A 874 MET cc_start: 0.7397 (mmm) cc_final: 0.7127 (mmm) REVERT: A 883 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7313 (mtmt) REVERT: A 1144 MET cc_start: 0.1163 (mmt) cc_final: 0.0254 (ttm) REVERT: A 1155 MET cc_start: 0.2876 (mmm) cc_final: 0.2638 (tpt) REVERT: A 1200 ARG cc_start: 0.1854 (OUTLIER) cc_final: 0.1326 (ttm-80) REVERT: A 1313 THR cc_start: 0.8495 (m) cc_final: 0.8127 (m) REVERT: A 1349 ASN cc_start: 0.6808 (OUTLIER) cc_final: 0.6536 (t0) REVERT: B 26 MET cc_start: 0.1747 (OUTLIER) cc_final: 0.1135 (ppp) REVERT: B 251 MET cc_start: 0.2644 (tpp) cc_final: 0.1499 (ptp) REVERT: B 321 GLN cc_start: 0.3692 (mt0) cc_final: 0.3489 (mp10) REVERT: B 376 MET cc_start: 0.2699 (mpt) cc_final: 0.2121 (mpt) REVERT: B 610 LYS cc_start: 0.4219 (mtmt) cc_final: 0.3639 (tttp) REVERT: B 661 GLU cc_start: 0.1868 (mt-10) cc_final: 0.0024 (mt-10) REVERT: B 821 MET cc_start: 0.1413 (OUTLIER) cc_final: 0.1091 (mpt) REVERT: B 831 MET cc_start: 0.2664 (pmt) cc_final: 0.2344 (pp-130) REVERT: B 1141 SER cc_start: -0.1783 (OUTLIER) cc_final: -0.2023 (p) REVERT: C 80 ILE cc_start: 0.3467 (OUTLIER) cc_final: 0.2757 (pp) REVERT: C 116 LEU cc_start: 0.3138 (OUTLIER) cc_final: 0.2656 (pt) REVERT: D 189 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: D 192 MET cc_start: 0.8236 (ttp) cc_final: 0.7990 (ttp) REVERT: E 94 MET cc_start: 0.5195 (tmm) cc_final: 0.4704 (ttm) REVERT: F 173 GLU cc_start: 0.4191 (pm20) cc_final: 0.3274 (mm-30) REVERT: F 212 ILE cc_start: 0.1145 (OUTLIER) cc_final: 0.0397 (tt) REVERT: F 231 MET cc_start: 0.2594 (ttm) cc_final: 0.0468 (pmm) REVERT: F 243 LEU cc_start: 0.5431 (tp) cc_final: 0.5208 (mt) REVERT: F 324 GLU cc_start: 0.4233 (tm-30) cc_final: 0.3460 (tp30) outliers start: 72 outliers final: 21 residues processed: 278 average time/residue: 1.2573 time to fit residues: 419.5797 Evaluate side-chains 236 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1200 ARG Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 821 MET Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain F residue 20 CYS Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 83 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 208 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 133 optimal weight: 0.0980 chunk 53 optimal weight: 0.4980 chunk 264 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 269 ASN A 520 ASN A 535 GLN A 642 ASN A 721 ASN A 980 GLN A1111 GLN ** B 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 989 ASN B1002 ASN B1169 HIS ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN F 64 ASN F 71 HIS ** F 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.301527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.281463 restraints weight = 41279.267| |-----------------------------------------------------------------------------| r_work (start): 0.4813 rms_B_bonded: 1.26 r_work: 0.4697 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4498 moved from start: 1.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 30576 Z= 0.196 Angle : 0.776 19.174 41440 Z= 0.396 Chirality : 0.050 0.415 4702 Planarity : 0.006 0.131 5277 Dihedral : 8.697 87.633 4187 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.44 % Rotamer: Outliers : 1.97 % Allowed : 24.67 % Favored : 73.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.54 (0.14), residues: 3683 helix: 0.35 (0.14), residues: 1375 sheet: -0.26 (0.22), residues: 546 loop : -0.90 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 469 HIS 0.013 0.002 HIS A 431 PHE 0.057 0.003 PHE A 541 TYR 0.025 0.002 TYR D 64 ARG 0.010 0.001 ARG A1233 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 1251) hydrogen bonds : angle 5.33396 ( 3459) metal coordination : bond 0.00733 ( 16) metal coordination : angle 4.49548 ( 21) covalent geometry : bond 0.00428 (30560) covalent geometry : angle 0.76932 (41419) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 254 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.2681 (ttp) cc_final: 0.2455 (ppp) REVERT: A 50 MET cc_start: -0.1240 (tmt) cc_final: -0.1961 (tmt) REVERT: A 300 MET cc_start: 0.3175 (OUTLIER) cc_final: 0.2595 (mpt) REVERT: A 543 ASN cc_start: 0.7127 (m-40) cc_final: 0.6897 (m110) REVERT: A 649 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.5128 (m-80) REVERT: A 881 GLU cc_start: 0.6305 (tp30) cc_final: 0.6033 (mm-30) REVERT: A 1144 MET cc_start: 0.1377 (mmt) cc_final: 0.0311 (ttm) REVERT: A 1155 MET cc_start: 0.3600 (mmm) cc_final: 0.3205 (tpt) REVERT: A 1200 ARG cc_start: 0.2330 (OUTLIER) cc_final: 0.1250 (mtt90) REVERT: A 1209 MET cc_start: 0.1535 (tpt) cc_final: 0.0587 (tmm) REVERT: A 1325 LEU cc_start: 0.8197 (tm) cc_final: 0.7965 (mm) REVERT: A 1360 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.7194 (pmm) REVERT: B 51 MET cc_start: 0.0715 (OUTLIER) cc_final: -0.0754 (mtt) REVERT: B 376 MET cc_start: 0.2238 (mpt) cc_final: 0.2001 (mpt) REVERT: B 661 GLU cc_start: 0.2423 (mt-10) cc_final: 0.1293 (pt0) REVERT: B 1002 ASN cc_start: 0.0381 (OUTLIER) cc_final: -0.0508 (t0) REVERT: B 1141 SER cc_start: -0.2278 (OUTLIER) cc_final: -0.2545 (p) REVERT: B 1209 MET cc_start: 0.4866 (OUTLIER) cc_final: 0.4415 (pmt) REVERT: C 80 ILE cc_start: 0.4120 (OUTLIER) cc_final: 0.3543 (pp) REVERT: C 181 LYS cc_start: 0.4526 (OUTLIER) cc_final: 0.3954 (mtmt) REVERT: D 189 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: F 48 ILE cc_start: 0.5902 (mm) cc_final: 0.5664 (tp) REVERT: F 70 MET cc_start: 0.8126 (ttt) cc_final: 0.7912 (ttt) REVERT: F 231 MET cc_start: 0.3249 (ttm) cc_final: 0.0782 (pmm) REVERT: F 324 GLU cc_start: 0.3271 (tm-30) cc_final: 0.2966 (tp30) outliers start: 65 outliers final: 17 residues processed: 289 average time/residue: 1.4768 time to fit residues: 507.8534 Evaluate side-chains 235 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 959 GLN Chi-restraints excluded: chain A residue 1200 ARG Chi-restraints excluded: chain A residue 1360 MET Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1002 ASN Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 189 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 79 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 256 optimal weight: 7.9990 chunk 301 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 0.0870 chunk 265 optimal weight: 0.6980 chunk 217 optimal weight: 8.9990 chunk 351 optimal weight: 3.9990 chunk 125 optimal weight: 0.0970 chunk 83 optimal weight: 0.8980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 GLN A 592 GLN A 933 ASN A 980 GLN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 GLN B 989 ASN B1002 ASN ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 HIS ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.302629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.282624 restraints weight = 41561.353| |-----------------------------------------------------------------------------| r_work (start): 0.4825 rms_B_bonded: 1.31 r_work: 0.4674 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4662 moved from start: 1.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30576 Z= 0.118 Angle : 0.662 17.235 41440 Z= 0.333 Chirality : 0.045 0.196 4702 Planarity : 0.004 0.066 5277 Dihedral : 8.396 86.691 4187 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 1.03 % Allowed : 26.00 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.30 (0.14), residues: 3683 helix: 0.63 (0.14), residues: 1379 sheet: -0.21 (0.23), residues: 521 loop : -0.80 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 469 HIS 0.005 0.001 HIS A1352 PHE 0.028 0.002 PHE A 918 TYR 0.025 0.001 TYR G 100 ARG 0.009 0.000 ARG C 218 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 1251) hydrogen bonds : angle 4.99667 ( 3459) metal coordination : bond 0.00458 ( 16) metal coordination : angle 3.13273 ( 21) covalent geometry : bond 0.00252 (30560) covalent geometry : angle 0.65825 (41419) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ILE cc_start: 0.1331 (OUTLIER) cc_final: 0.0709 (mp) REVERT: A 300 MET cc_start: 0.3210 (OUTLIER) cc_final: 0.2678 (mpt) REVERT: A 463 MET cc_start: 0.2021 (tpp) cc_final: 0.1772 (tpt) REVERT: A 543 ASN cc_start: 0.7132 (m-40) cc_final: 0.6900 (m-40) REVERT: A 649 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.4897 (m-80) REVERT: A 1144 MET cc_start: 0.1471 (mmt) cc_final: 0.0185 (ttm) REVERT: A 1155 MET cc_start: 0.3454 (mmm) cc_final: 0.3044 (tpt) REVERT: A 1200 ARG cc_start: 0.2295 (OUTLIER) cc_final: 0.1203 (mtt90) REVERT: A 1304 MET cc_start: 0.3172 (mmm) cc_final: 0.2908 (mtt) REVERT: B 26 MET cc_start: 0.1160 (ptm) cc_final: 0.0297 (ppp) REVERT: B 251 MET cc_start: 0.2795 (tpp) cc_final: 0.1772 (ptp) REVERT: B 376 MET cc_start: 0.2596 (mpt) cc_final: 0.2219 (mpt) REVERT: B 661 GLU cc_start: 0.1712 (mt-10) cc_final: 0.0105 (pm20) REVERT: B 831 MET cc_start: 0.2686 (pmm) cc_final: 0.2293 (pp-130) REVERT: C 80 ILE cc_start: 0.4146 (OUTLIER) cc_final: 0.3403 (pp) REVERT: C 181 LYS cc_start: 0.4834 (OUTLIER) cc_final: 0.4511 (ttmt) REVERT: D 34 MET cc_start: 0.5252 (ptm) cc_final: 0.5024 (ptp) REVERT: D 47 THR cc_start: 0.7564 (t) cc_final: 0.7349 (p) REVERT: F 128 GLN cc_start: 0.0854 (pt0) cc_final: -0.0982 (mt0) REVERT: F 173 GLU cc_start: 0.4298 (pm20) cc_final: 0.3347 (mm-30) REVERT: F 186 GLU cc_start: 0.2948 (tp30) cc_final: 0.1772 (tt0) REVERT: F 187 MET cc_start: 0.2484 (ppp) cc_final: 0.0167 (mpp) REVERT: F 200 ILE cc_start: 0.3516 (pt) cc_final: 0.3066 (mp) REVERT: F 231 MET cc_start: 0.3004 (ttm) cc_final: 0.0663 (pmm) REVERT: F 324 GLU cc_start: 0.3636 (tm-30) cc_final: 0.3153 (tp30) outliers start: 34 outliers final: 13 residues processed: 242 average time/residue: 1.3731 time to fit residues: 396.3030 Evaluate side-chains 223 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 1200 ARG Chi-restraints excluded: chain A residue 1408 TYR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain F residue 212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 239 optimal weight: 2.9990 chunk 285 optimal weight: 0.8980 chunk 297 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 46 optimal weight: 0.5980 chunk 284 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 92 optimal weight: 0.0170 chunk 52 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN A 721 ASN A 728 ASN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 GLN B 290 GLN B1002 ASN ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.302025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.281002 restraints weight = 41171.014| |-----------------------------------------------------------------------------| r_work (start): 0.4811 rms_B_bonded: 1.11 r_work: 0.4665 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work (final): 0.4665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4828 moved from start: 1.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30576 Z= 0.125 Angle : 0.662 13.641 41440 Z= 0.332 Chirality : 0.046 0.243 4702 Planarity : 0.004 0.053 5277 Dihedral : 8.302 85.849 4187 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 0.97 % Allowed : 26.21 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.27 (0.14), residues: 3683 helix: 0.58 (0.14), residues: 1385 sheet: -0.01 (0.23), residues: 540 loop : -0.79 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 469 HIS 0.011 0.001 HIS F 26 PHE 0.024 0.002 PHE A 918 TYR 0.025 0.001 TYR B1178 ARG 0.013 0.001 ARG C 218 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 1251) hydrogen bonds : angle 4.95585 ( 3459) metal coordination : bond 0.00462 ( 16) metal coordination : angle 2.86191 ( 21) covalent geometry : bond 0.00265 (30560) covalent geometry : angle 0.65901 (41419) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22186.47 seconds wall clock time: 386 minutes 27.24 seconds (23187.24 seconds total)