Starting phenix.real_space_refine on Wed Jun 25 15:00:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yqv_39507/06_2025/8yqv_39507.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yqv_39507/06_2025/8yqv_39507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yqv_39507/06_2025/8yqv_39507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yqv_39507/06_2025/8yqv_39507.map" model { file = "/net/cci-nas-00/data/ceres_data/8yqv_39507/06_2025/8yqv_39507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yqv_39507/06_2025/8yqv_39507.cif" } resolution = 2.67 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= 0.095 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 Mg 1 5.21 5 S 164 5.16 5 C 18896 2.51 5 N 5093 2.21 5 O 5479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29637 Number of models: 1 Model: "" Number of chains: 12 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: "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: "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: "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: "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: "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: "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: "H" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 442 SG CYS A 59 97.669 67.460 80.766 1.00 92.82 S ATOM 463 SG CYS A 62 94.556 65.360 80.403 1.00 89.13 S ATOM 523 SG CYS A 69 94.373 69.099 80.046 1.00 79.93 S ATOM 20762 SG CYS B1180 88.288 58.224 93.488 1.00 72.91 S ATOM 20787 SG CYS B1183 89.000 61.409 95.479 1.00 74.18 S ATOM 20903 SG CYS B1198 91.513 60.338 93.194 1.00 95.15 S ATOM 20925 SG CYS B1201 90.811 58.169 96.363 1.00106.04 S ATOM 25858 SG CYS H 7 55.558 106.371 36.393 1.00 52.91 S ATOM 25882 SG CYS H 10 53.302 104.459 33.945 1.00 65.10 S ATOM 26301 SG CYS H 65 51.821 106.542 36.879 1.00 48.64 S ATOM 26307 SG CYS H 66 53.343 107.905 33.570 1.00 55.87 S ATOM 26657 SG CYS G 73 42.630 151.453 91.063 1.00118.57 S ATOM 26678 SG CYS G 76 44.655 153.958 88.919 1.00123.31 S ATOM 26835 SG CYS G 96 45.909 150.514 89.339 1.00102.00 S ATOM 26852 SG CYS G 98 46.055 152.883 92.233 1.00111.79 S Time building chain proxies: 16.41, per 1000 atoms: 0.55 Number of scatterers: 29637 At special positions: 0 Unit cell: (143.016, 175.336, 155.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 164 16.00 Mg 1 11.99 O 5479 8.00 N 5093 7.00 C 18896 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: 7.02 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 69 " 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 B1198 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1180 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1201 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 76 " 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 73 " pdb=" ZN H 101 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 10 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 7 " 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: 152 helices and 44 sheets defined 42.2% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.495A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.903A pdb=" N ARG A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 184 Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 225 through 240 removed outlier: 3.513A pdb=" N VAL A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 273 removed outlier: 3.529A pdb=" N ASP A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.773A pdb=" N ARG A 302 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.765A 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 314 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 450 through 455 removed outlier: 4.127A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 552 through 561 removed outlier: 3.650A pdb=" N LEU A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.566A pdb=" N MET A 582 " --> pdb=" O ALA A 579 " (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: 4.058A pdb=" N ASN A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.712A pdb=" N LEU A 657 " --> pdb=" O ALA A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 686 removed outlier: 3.609A pdb=" N ILE A 680 " --> pdb=" O GLU A 676 " (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 723 removed outlier: 3.912A pdb=" N ILE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 723 " --> pdb=" O ILE A 719 " (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: 3.572A pdb=" N ASP A 811 " --> pdb=" O ASN A 807 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR A 822 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 861 through 865 removed outlier: 4.170A pdb=" N LEU A 865 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 891 through 918 removed outlier: 3.833A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 898 " --> pdb=" O PHE A 894 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 901 " --> pdb=" O GLU A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 944 removed outlier: 3.503A pdb=" N ILE A 941 " --> pdb=" O ILE A 937 " (cutoff:3.500A) removed outlier: 3.988A 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 995 removed outlier: 3.704A pdb=" N ALA A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1006 Processing helix chain 'A' and resid 1015 through 1032 Processing helix chain 'A' and resid 1040 through 1051 removed outlier: 3.501A pdb=" N GLU A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1081 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 1162 removed outlier: 3.607A pdb=" N LEU A1159 " --> pdb=" O MET A1155 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A1160 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS A1162 " --> pdb=" O PHE A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1188 removed outlier: 3.808A pdb=" N MET A1185 " --> pdb=" O ASN A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1200 Processing helix chain 'A' and resid 1229 through 1232 Processing helix chain 'A' and resid 1243 through 1256 Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1310 through 1314 removed outlier: 3.744A pdb=" N THR A1313 " --> pdb=" O ASP A1310 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE A1314 " --> pdb=" O PRO A1311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1310 through 1314' Processing helix chain 'A' and resid 1318 through 1327 Processing helix chain 'A' and resid 1327 through 1344 removed outlier: 3.662A pdb=" N VAL A1342 " --> pdb=" O GLU A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1361 removed outlier: 3.760A 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: 3.910A pdb=" N SER A1389 " --> pdb=" O ARG A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1401 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 1437 Processing helix chain 'E' and resid 44 through 49 removed outlier: 4.172A pdb=" N GLY E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.610A 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: 3.602A pdb=" N MET E 141 " --> pdb=" O PRO E 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 16 removed outlier: 3.560A pdb=" N THR B 15 " --> pdb=" O PRO B 12 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 16 " --> pdb=" O ILE B 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 12 through 16' Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.879A pdb=" N ILE B 30 " --> pdb=" O MET B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 53 removed outlier: 3.506A pdb=" N LYS B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.661A pdb=" N GLY B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 279 removed outlier: 3.898A pdb=" N PHE B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 289 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 removed outlier: 3.512A pdb=" N ASP B 353 " --> pdb=" O TYR B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 372 removed outlier: 3.668A pdb=" N GLN B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) 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 432 Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.502A pdb=" N VAL B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 458 through 470 Processing helix chain 'B' and resid 471 through 489 removed outlier: 3.525A pdb=" N ALA B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 521 removed outlier: 3.533A 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 561 through 565 removed outlier: 4.216A pdb=" N LYS B 564 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 565 " --> pdb=" O GLY B 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 561 through 565' Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.684A pdb=" N LEU B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 removed outlier: 3.721A 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: 3.572A 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: 3.623A pdb=" N LYS B 703 " --> pdb=" O ASP B 700 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 705 " --> pdb=" O GLU B 702 " (cutoff:3.500A) 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: 3.522A 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 removed outlier: 3.505A pdb=" N THR B 792 " --> pdb=" O ALA B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 805 removed outlier: 3.676A pdb=" N VAL B 797 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 4.329A 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: 4.110A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1078 removed outlier: 3.603A pdb=" N LEU B1075 " --> pdb=" O LEU B1071 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B1076 " --> pdb=" O SER B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1119 removed outlier: 3.536A pdb=" N ASP B1118 " --> pdb=" O PHE B1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1158 Processing helix chain 'B' and resid 1160 through 1169 removed outlier: 3.537A pdb=" N ILE B1164 " --> pdb=" O ALA B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1214 through 1225 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: 3.680A 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: 3.677A pdb=" N ILE C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU C 258 " --> pdb=" O GLN C 254 " (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: 3.656A pdb=" N THR D 8 " --> pdb=" O GLN D 4 " (cutoff:3.500A) removed outlier: 4.669A 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: 3.604A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.665A 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: 3.818A pdb=" N LEU D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 127 removed outlier: 3.650A 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: 3.644A 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 'H' and resid 14 through 16 No H-bonds generated for 'chain 'H' and resid 14 through 16' Processing helix chain 'H' and resid 17 through 34 Processing helix chain 'H' and resid 42 through 47 Processing helix chain 'H' and resid 51 through 58 Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.563A pdb=" N THR H 73 " --> pdb=" O HIS H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 79 Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' 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 193 removed outlier: 4.294A pdb=" N LYS F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 208 removed outlier: 3.563A pdb=" N ILE F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 248 removed outlier: 3.606A pdb=" N LYS F 248 " --> pdb=" O TYR F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 314 Processing helix chain 'F' and resid 316 through 323 removed outlier: 3.549A pdb=" N ILE F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 332 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.348A pdb=" N GLY A 4 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 7.981A 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: 6.685A pdb=" N VAL B1233 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 11 " --> pdb=" O THR B1231 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR B1231 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE A 13 " --> pdb=" O ASN B1229 " (cutoff:3.500A) removed outlier: 6.484A 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: 10.073A pdb=" N MET A 78 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLN A 202 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 10.534A pdb=" N ALA A 80 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA A 200 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.569A pdb=" N PHE A 154 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA6, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 7.320A pdb=" N PHE A 444 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR A 326 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N MET A 446 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N CYS A 328 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 353 removed outlier: 3.823A pdb=" N ARG A 378 " --> pdb=" O TYR A 406 " (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 522 Processing sheet with id=AB1, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.671A 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: 6.507A 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 1268 through 1278 removed outlier: 6.386A pdb=" N ASN A1269 " --> pdb=" O ILE A1293 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE A1293 " --> pdb=" O ASN A1269 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A1271 " --> pdb=" O TYR A1291 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR A1291 " --> pdb=" O VAL A1271 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A1273 " --> pdb=" O ASN A1289 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN A1289 " --> pdb=" O LEU A1273 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A1094 " --> pdb=" O THR A1295 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.520A pdb=" N ARG A1260 " --> pdb=" O ILE A1120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1126 through 1130 removed outlier: 3.737A pdb=" N GLN A1128 " --> pdb=" O GLU A1179 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1428 through 1431 removed outlier: 6.717A pdb=" N ILE E 132 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL E 125 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLN E 130 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR E 56 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL E 133 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL E 58 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE E 135 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 65 through 70 removed outlier: 3.782A pdb=" N SER B 84 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 88 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA B 131 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL B 94 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN B 129 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE B 96 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLY B 126 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR B 159 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 128 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ALA B 132 " --> pdb=" O PRO B 153 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 134 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N SER B 151 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU B 136 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ARG B 149 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 138 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL B 147 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TYR B 140 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLN B 145 " --> pdb=" O TYR B 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC2, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC3, first strand: chain 'B' and resid 416 through 418 removed outlier: 3.786A pdb=" N LEU B 204 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 213 through 216 removed outlier: 3.610A pdb=" N TYR B 250 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AC6, first strand: chain 'B' and resid 710 through 712 removed outlier: 3.569A pdb=" N LEU B 674 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 596 through 597 removed outlier: 5.658A pdb=" N TRP B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 617 " --> pdb=" O TRP B 621 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY B 623 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 823 through 826 removed outlier: 3.558A pdb=" N ALA B 967 " --> pdb=" O ARG B 983 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ARG B 985 " --> pdb=" O VAL B 965 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL B 965 " --> pdb=" O ARG B 985 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU B 987 " --> pdb=" O ALA B 963 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ALA B 963 " --> pdb=" O GLU B 987 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AD1, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 6.065A pdb=" N VAL B 865 " --> pdb=" O ALA B1006 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B1008 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 894 through 895 removed outlier: 3.703A pdb=" N ALA B 938 " --> pdb=" O ILE B 951 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 951 " --> pdb=" O ALA B 938 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 932 through 934 removed outlier: 6.978A pdb=" N VAL B 955 " --> pdb=" O ILE B 933 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AD5, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AD6, first strand: chain 'C' and resid 5 through 12 removed outlier: 4.851A pdb=" N PHE C 5 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS C 48 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASN C 7 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N CYS C 222 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LYS C 181 " --> pdb=" O CYS C 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 68 through 73 removed outlier: 5.014A pdb=" N ILE C 159 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N SER C 115 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLU C 161 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU C 113 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL C 110 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 123 through 126 Processing sheet with id=AD9, first strand: chain 'C' and resid 267 through 270 Processing sheet with id=AE1, first strand: chain 'D' and resid 20 through 21 removed outlier: 6.845A pdb=" N ILE D 52 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE D 89 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER D 54 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE D 91 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE D 56 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 117 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 138 through 142 removed outlier: 4.517A pdb=" N PHE D 181 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET D 162 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR D 201 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE D 164 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 67 through 69 removed outlier: 4.137A pdb=" N CYS G 67 " --> pdb=" O GLN G 83 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 3 through 13 removed outlier: 6.408A pdb=" N SER F 75 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL F 51 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL F 77 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR F 49 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 3 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 90 through 95 removed outlier: 6.732A pdb=" N LEU F 101 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN F 95 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE F 99 " --> pdb=" O ASN F 95 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL F 110 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR F 111 " --> pdb=" O ALA F 150 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 237 through 238 removed outlier: 6.826A pdb=" N VAL F 163 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N CYS F 287 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N HIS F 165 " --> pdb=" O CYS F 287 " (cutoff:3.500A) 1271 hydrogen bonds defined for protein. 3468 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: 14.59 Time building geometry restraints manager: 8.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4921 1.31 - 1.44: 7687 1.44 - 1.56: 17340 1.56 - 1.69: 1 1.69 - 1.81: 270 Bond restraints: 30219 Sorted by residual: bond pdb=" C ILE H 14 " pdb=" O ILE H 14 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.32e-02 5.74e+03 1.28e+01 bond pdb=" C PRO H 13 " pdb=" N ILE H 14 " ideal model delta sigma weight residual 1.335 1.307 0.028 1.15e-02 7.56e+03 5.88e+00 bond pdb=" C GLN A 501 " pdb=" N ASP A 502 " ideal model delta sigma weight residual 1.332 1.303 0.030 1.40e-02 5.10e+03 4.48e+00 bond pdb=" CG1 ILE D 105 " pdb=" CD1 ILE D 105 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.28e+00 bond pdb=" CA ASP A 502 " pdb=" C ASP A 502 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.34e-02 5.57e+03 3.47e+00 ... (remaining 30214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 40740 3.57 - 7.14: 150 7.14 - 10.72: 5 10.72 - 14.29: 2 14.29 - 17.86: 1 Bond angle restraints: 40898 Sorted by residual: angle pdb=" CA LEU A 185 " pdb=" CB LEU A 185 " pdb=" CG LEU A 185 " ideal model delta sigma weight residual 116.30 134.16 -17.86 3.50e+00 8.16e-02 2.60e+01 angle pdb=" CB LYS C 139 " pdb=" CG LYS C 139 " pdb=" CD LYS C 139 " ideal model delta sigma weight residual 111.30 121.66 -10.36 2.30e+00 1.89e-01 2.03e+01 angle pdb=" C ILE B 741 " pdb=" N THR B 742 " pdb=" CA THR B 742 " ideal model delta sigma weight residual 121.98 135.25 -13.27 3.11e+00 1.03e-01 1.82e+01 angle pdb=" C ILE A 846 " pdb=" N ASP A 847 " pdb=" CA ASP A 847 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C THR A 536 " pdb=" N ASP A 537 " pdb=" CA ASP A 537 " ideal model delta sigma weight residual 120.94 113.40 7.54 1.90e+00 2.77e-01 1.57e+01 ... (remaining 40893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16719 17.92 - 35.84: 1280 35.84 - 53.77: 343 53.77 - 71.69: 61 71.69 - 89.61: 23 Dihedral angle restraints: 18426 sinusoidal: 7560 harmonic: 10866 Sorted by residual: 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 -156.79 -23.21 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PRO A 304 " pdb=" C PRO A 304 " pdb=" N ARG A 305 " pdb=" CA ARG A 305 " ideal model delta harmonic sigma weight residual -180.00 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA SER A 767 " pdb=" C SER A 767 " pdb=" N PHE A 768 " pdb=" CA PHE A 768 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 18423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3607 0.056 - 0.113: 907 0.113 - 0.169: 126 0.169 - 0.226: 1 0.226 - 0.282: 1 Chirality restraints: 4642 Sorted by residual: chirality pdb=" CG LEU A 121 " pdb=" CB LEU A 121 " pdb=" CD1 LEU A 121 " pdb=" CD2 LEU A 121 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.99e+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 2.51 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB THR D 76 " pdb=" CA THR D 76 " pdb=" OG1 THR D 76 " pdb=" CG2 THR D 76 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.93e-01 ... (remaining 4639 not shown) Planarity restraints: 5262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 26 " -0.073 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO D 27 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO D 27 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO D 27 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 80 " -0.054 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO A 81 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 245 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C ILE C 245 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE C 245 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE C 246 " -0.012 2.00e-02 2.50e+03 ... (remaining 5259 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 166 2.50 - 3.10: 20867 3.10 - 3.70: 44795 3.70 - 4.30: 69213 4.30 - 4.90: 114401 Nonbonded interactions: 249442 Sorted by model distance: nonbonded pdb=" OD1 ASP A 459 " pdb="MG MG A1501 " model vdw 1.905 2.170 nonbonded pdb=" OD1 ASP A 461 " pdb="MG MG A1501 " model vdw 1.995 2.170 nonbonded pdb=" OD2 ASP A 54 " pdb=" ND1 HIS A 56 " model vdw 2.124 3.120 nonbonded pdb=" OD2 ASP A 332 " pdb=" OH TYR B 859 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR B 683 " pdb=" OD2 ASP G 79 " model vdw 2.130 3.040 ... (remaining 249437 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: 3.000 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: 1.210 Check model and map are aligned: 0.230 Set scattering table: 0.260 Process input model: 74.070 Find NCS groups from input model: 0.690 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:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 30235 Z= 0.263 Angle : 0.690 17.860 40919 Z= 0.371 Chirality : 0.049 0.282 4642 Planarity : 0.005 0.108 5262 Dihedral : 14.297 89.610 11400 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.36 % Allowed : 13.61 % Favored : 86.03 % 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: -1.25 (0.13), residues: 3683 helix: -0.70 (0.14), residues: 1344 sheet: -0.53 (0.22), residues: 529 loop : -0.90 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 466 HIS 0.013 0.002 HIS D 193 PHE 0.026 0.002 PHE A 918 TYR 0.027 0.002 TYR A1030 ARG 0.011 0.001 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.19881 ( 1259) hydrogen bonds : angle 7.68222 ( 3468) metal coordination : bond 0.01163 ( 16) metal coordination : angle 4.47538 ( 21) covalent geometry : bond 0.00633 (30219) covalent geometry : angle 0.68310 (40898) *********************** 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 355 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 343 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.6468 (mppt) cc_final: 0.6159 (mmtm) REVERT: A 678 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7087 (tm-30) REVERT: A 682 ASN cc_start: 0.7995 (t0) cc_final: 0.7610 (m-40) REVERT: A 1240 MET cc_start: 0.3451 (pmt) cc_final: 0.3203 (pmm) REVERT: B 542 MET cc_start: 0.6587 (ptm) cc_final: 0.6185 (pmm) REVERT: B 969 MET cc_start: 0.5630 (OUTLIER) cc_final: 0.5108 (mtt) REVERT: G 58 LYS cc_start: 0.7493 (ttpp) cc_final: 0.7014 (ptmm) outliers start: 12 outliers final: 10 residues processed: 351 average time/residue: 1.6674 time to fit residues: 681.8341 Evaluate side-chains 330 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 319 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain F residue 62 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 148 optimal weight: 0.1980 chunk 287 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 333 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 224 HIS A 264 GLN A 265 GLN A 420 GLN A 592 GLN A 721 ASN A 765 GLN A 826 ASN A 834 GLN A 910 GLN A 919 ASN A1161 ASN A1349 ASN A1350 HIS A1439 ASN E 63 ASN E 90 ASN B 75 HIS B 173 HIS B 235 GLN B 314 HIS B 325 HIS B 364 GLN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 ASN B 845 ASN B 861 GLN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1162 GLN B1227 ASN B1229 ASN C 315 HIS C 317 GLN C 345 GLN D 66 HIS D 119 ASN D 193 HIS F 4 GLN F 272 GLN F 308 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.188321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120897 restraints weight = 32703.532| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.37 r_work: 0.3219 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30235 Z= 0.222 Angle : 0.627 12.521 40919 Z= 0.327 Chirality : 0.048 0.200 4642 Planarity : 0.005 0.070 5262 Dihedral : 5.427 62.127 4052 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.88 % Allowed : 12.33 % Favored : 84.79 % 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: -0.73 (0.13), residues: 3683 helix: 0.03 (0.14), residues: 1372 sheet: -0.49 (0.22), residues: 526 loop : -0.79 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 466 HIS 0.012 0.001 HIS D 193 PHE 0.030 0.002 PHE A 918 TYR 0.016 0.002 TYR A1030 ARG 0.008 0.001 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.05167 ( 1259) hydrogen bonds : angle 5.49727 ( 3468) metal coordination : bond 0.00984 ( 16) metal coordination : angle 4.25793 ( 21) covalent geometry : bond 0.00538 (30219) covalent geometry : angle 0.61949 (40898) *********************** 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 450 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 355 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8566 (mp-120) cc_final: 0.8303 (mp-120) REVERT: A 119 LYS cc_start: 0.7585 (mtpt) cc_final: 0.6664 (tmtm) REVERT: A 138 LYS cc_start: 0.6423 (mppt) cc_final: 0.6086 (mmtm) REVERT: A 168 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: A 400 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: A 661 GLU cc_start: 0.7504 (tt0) cc_final: 0.7287 (mp0) REVERT: A 664 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: A 690 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7131 (mpp) REVERT: A 1286 ARG cc_start: 0.8202 (ttp-170) cc_final: 0.7972 (ttp80) REVERT: A 1355 MET cc_start: 0.9159 (tpt) cc_final: 0.8896 (mmm) REVERT: B 542 MET cc_start: 0.6766 (ptm) cc_final: 0.6167 (pmm) REVERT: B 731 ASP cc_start: 0.7628 (t0) cc_final: 0.6888 (m-30) REVERT: B 845 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8430 (p0) REVERT: B 957 TYR cc_start: 0.5391 (t80) cc_final: 0.5094 (t80) REVERT: B 969 MET cc_start: 0.5285 (mtp) cc_final: 0.4985 (mtp) REVERT: C 34 GLU cc_start: 0.7567 (pm20) cc_final: 0.7351 (pm20) REVERT: C 355 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7475 (m-30) REVERT: D 63 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6439 (pttt) REVERT: H 32 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7894 (mmtp) REVERT: G 68 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: G 79 ASP cc_start: 0.7886 (t0) cc_final: 0.7558 (t0) outliers start: 95 outliers final: 30 residues processed: 409 average time/residue: 1.4615 time to fit residues: 701.1624 Evaluate side-chains 371 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 332 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 586 LYS Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 633 GLN Chi-restraints excluded: chain B residue 845 ASN Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 CYS Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 263 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 291 optimal weight: 0.0980 chunk 281 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 245 optimal weight: 0.6980 chunk 314 optimal weight: 0.9980 chunk 240 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 266 optimal weight: 4.9990 chunk 364 optimal weight: 7.9990 chunk 292 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 GLN A 721 ASN B 235 GLN B 419 HIS ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1162 GLN C 317 GLN F 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.190779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127213 restraints weight = 32524.422| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.53 r_work: 0.3240 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30235 Z= 0.135 Angle : 0.545 11.113 40919 Z= 0.284 Chirality : 0.045 0.175 4642 Planarity : 0.004 0.059 5262 Dihedral : 5.017 56.884 4042 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.39 % Allowed : 13.39 % Favored : 84.21 % 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: -0.36 (0.14), residues: 3683 helix: 0.47 (0.14), residues: 1382 sheet: -0.50 (0.22), residues: 532 loop : -0.63 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 466 HIS 0.004 0.001 HIS C 216 PHE 0.025 0.001 PHE A 918 TYR 0.010 0.001 TYR A 908 ARG 0.006 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 1259) hydrogen bonds : angle 5.10411 ( 3468) metal coordination : bond 0.00724 ( 16) metal coordination : angle 3.73160 ( 21) covalent geometry : bond 0.00316 (30219) covalent geometry : angle 0.53828 (40898) *********************** 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 452 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 373 time to evaluate : 4.308 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8550 (mp-120) cc_final: 0.8278 (mp-120) REVERT: A 119 LYS cc_start: 0.7489 (mtpt) cc_final: 0.6591 (tmtm) REVERT: A 138 LYS cc_start: 0.6404 (mppt) cc_final: 0.6059 (mmtm) REVERT: A 272 LEU cc_start: 0.8464 (mt) cc_final: 0.8249 (mt) REVERT: A 400 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: A 520 ASN cc_start: 0.9218 (t0) cc_final: 0.8914 (t0) REVERT: A 562 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7612 (mm-40) REVERT: A 664 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7641 (mp10) REVERT: A 676 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: A 690 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7075 (mpp) REVERT: A 900 ARG cc_start: 0.7463 (mtp85) cc_final: 0.6811 (tpt90) REVERT: A 903 LYS cc_start: 0.7583 (mtmt) cc_final: 0.7130 (mttp) REVERT: A 1209 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.5767 (ttt) REVERT: A 1260 ARG cc_start: 0.7193 (ttp-170) cc_final: 0.6913 (ttp-170) REVERT: A 1286 ARG cc_start: 0.8111 (ttp-170) cc_final: 0.7890 (ttp80) REVERT: A 1355 MET cc_start: 0.9098 (tpt) cc_final: 0.8821 (mmm) REVERT: A 1393 GLN cc_start: 0.6850 (tp40) cc_final: 0.5976 (mp10) REVERT: B 542 MET cc_start: 0.6490 (ptm) cc_final: 0.5699 (pmm) REVERT: B 544 ARG cc_start: 0.6945 (tpp80) cc_final: 0.6683 (tpp80) REVERT: B 731 ASP cc_start: 0.7473 (t0) cc_final: 0.6767 (m-30) REVERT: B 969 MET cc_start: 0.5163 (mtp) cc_final: 0.4892 (mtp) REVERT: B 1177 SER cc_start: 0.8591 (t) cc_final: 0.8351 (p) REVERT: C 34 GLU cc_start: 0.7549 (pm20) cc_final: 0.7286 (pm20) REVERT: C 210 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7846 (mmt) REVERT: C 355 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: D 1 MET cc_start: 0.5276 (OUTLIER) cc_final: 0.5001 (ttm) REVERT: D 63 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6275 (pttt) REVERT: D 86 GLU cc_start: 0.7415 (tt0) cc_final: 0.7141 (mt-10) REVERT: G 58 LYS cc_start: 0.7509 (ttpp) cc_final: 0.6974 (ptmm) REVERT: G 68 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: G 79 ASP cc_start: 0.7927 (t0) cc_final: 0.7511 (t0) outliers start: 79 outliers final: 29 residues processed: 413 average time/residue: 2.2897 time to fit residues: 1108.7531 Evaluate side-chains 384 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 344 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 586 LYS Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 633 GLN Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 CYS Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 336 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 172 optimal weight: 0.0370 chunk 276 optimal weight: 0.0060 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 293 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 282 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 overall best weight: 1.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 721 ASN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS C 317 GLN F 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.190592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126472 restraints weight = 32483.331| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.41 r_work: 0.3229 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30235 Z= 0.142 Angle : 0.539 11.216 40919 Z= 0.279 Chirality : 0.045 0.176 4642 Planarity : 0.004 0.056 5262 Dihedral : 4.908 54.323 4042 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.82 % Allowed : 13.55 % Favored : 83.64 % 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: -0.17 (0.14), residues: 3683 helix: 0.70 (0.14), residues: 1378 sheet: -0.52 (0.22), residues: 515 loop : -0.54 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 466 HIS 0.004 0.001 HIS B1031 PHE 0.025 0.001 PHE A 918 TYR 0.011 0.001 TYR A 908 ARG 0.007 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 1259) hydrogen bonds : angle 4.95034 ( 3468) metal coordination : bond 0.00660 ( 16) metal coordination : angle 3.65402 ( 21) covalent geometry : bond 0.00339 (30219) covalent geometry : angle 0.53273 (40898) *********************** 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 447 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 354 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8526 (mp-120) cc_final: 0.8258 (mp-120) REVERT: A 119 LYS cc_start: 0.7491 (mtpt) cc_final: 0.6588 (tmtm) REVERT: A 171 ARG cc_start: 0.6909 (ttm110) cc_final: 0.6535 (ttm110) REVERT: A 400 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: A 520 ASN cc_start: 0.9225 (t0) cc_final: 0.8923 (t0) REVERT: A 664 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7604 (mp10) REVERT: A 676 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: A 690 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7054 (mpp) REVERT: A 900 ARG cc_start: 0.7328 (mtp85) cc_final: 0.6690 (tpt90) REVERT: A 903 LYS cc_start: 0.7532 (mtmt) cc_final: 0.7089 (mttp) REVERT: A 1260 ARG cc_start: 0.7118 (ttp-170) cc_final: 0.6748 (ttp-170) REVERT: A 1286 ARG cc_start: 0.8051 (ttp-170) cc_final: 0.7800 (ttp80) REVERT: A 1355 MET cc_start: 0.9074 (tpt) cc_final: 0.8792 (mmm) REVERT: A 1393 GLN cc_start: 0.6828 (tp40) cc_final: 0.6000 (mp10) REVERT: B 116 LYS cc_start: 0.5650 (tptt) cc_final: 0.5380 (tptt) REVERT: B 542 MET cc_start: 0.6477 (ptm) cc_final: 0.5591 (pmm) REVERT: B 544 ARG cc_start: 0.6910 (tpp80) cc_final: 0.6236 (mpt180) REVERT: B 731 ASP cc_start: 0.7439 (t0) cc_final: 0.6743 (m-30) REVERT: B 1177 SER cc_start: 0.8552 (t) cc_final: 0.8307 (p) REVERT: B 1203 VAL cc_start: 0.6996 (m) cc_final: 0.6649 (t) REVERT: C 34 GLU cc_start: 0.7498 (pm20) cc_final: 0.7295 (pm20) REVERT: C 82 ASP cc_start: 0.6085 (OUTLIER) cc_final: 0.5831 (m-30) REVERT: C 355 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7277 (m-30) REVERT: D 63 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6292 (pttt) REVERT: D 86 GLU cc_start: 0.7407 (tt0) cc_final: 0.7127 (mt-10) REVERT: G 58 LYS cc_start: 0.7511 (ttpp) cc_final: 0.6951 (ptmm) REVERT: G 68 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7220 (mt0) REVERT: G 79 ASP cc_start: 0.7903 (t0) cc_final: 0.7442 (t0) REVERT: F 2 ILE cc_start: 0.6065 (OUTLIER) cc_final: 0.5681 (mp) outliers start: 93 outliers final: 39 residues processed: 402 average time/residue: 1.5605 time to fit residues: 753.6099 Evaluate side-chains 385 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 337 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 586 LYS Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 633 GLN Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 CYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 149 SER Chi-restraints excluded: chain F residue 263 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 208 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 chunk 321 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 341 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.0060 chunk 88 optimal weight: 4.9990 chunk 103 optimal weight: 0.0670 chunk 209 optimal weight: 2.9990 overall best weight: 0.9936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 420 GLN A 721 ASN B 235 GLN B 290 GLN B 334 GLN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN D 157 GLN F 4 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.192493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128736 restraints weight = 32538.136| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.57 r_work: 0.3250 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30235 Z= 0.111 Angle : 0.505 10.776 40919 Z= 0.261 Chirality : 0.044 0.189 4642 Planarity : 0.004 0.054 5262 Dihedral : 4.660 52.978 4042 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.70 % Allowed : 14.09 % Favored : 83.21 % 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: 0.09 (0.14), residues: 3683 helix: 0.97 (0.14), residues: 1376 sheet: -0.39 (0.22), residues: 514 loop : -0.43 (0.15), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 466 HIS 0.004 0.001 HIS C 315 PHE 0.024 0.001 PHE A 918 TYR 0.009 0.001 TYR A 567 ARG 0.008 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 1259) hydrogen bonds : angle 4.72697 ( 3468) metal coordination : bond 0.00550 ( 16) metal coordination : angle 3.25147 ( 21) covalent geometry : bond 0.00254 (30219) covalent geometry : angle 0.49943 (40898) *********************** 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 451 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 362 time to evaluate : 3.179 Fit side-chains revert: symmetry clash REVERT: A 119 LYS cc_start: 0.7462 (mtpt) cc_final: 0.6547 (tmtm) REVERT: A 171 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6500 (ttm110) REVERT: A 400 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: A 676 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: A 690 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.6982 (mpp) REVERT: A 900 ARG cc_start: 0.7352 (mtp85) cc_final: 0.6857 (tpt90) REVERT: A 903 LYS cc_start: 0.7595 (mtmt) cc_final: 0.7371 (mtpm) REVERT: A 1260 ARG cc_start: 0.7098 (ttp-170) cc_final: 0.6721 (ttp-170) REVERT: A 1324 GLU cc_start: 0.8012 (tt0) cc_final: 0.6896 (mp0) REVERT: A 1355 MET cc_start: 0.9084 (tpt) cc_final: 0.8800 (mmm) REVERT: A 1393 GLN cc_start: 0.6882 (tp40) cc_final: 0.5983 (mp10) REVERT: B 116 LYS cc_start: 0.5861 (tptt) cc_final: 0.5495 (tptt) REVERT: B 268 LEU cc_start: 0.4351 (OUTLIER) cc_final: 0.3827 (tp) REVERT: B 281 MET cc_start: 0.5348 (mtm) cc_final: 0.4846 (ptm) REVERT: B 542 MET cc_start: 0.6345 (ptm) cc_final: 0.5448 (pmm) REVERT: B 544 ARG cc_start: 0.6750 (tpp80) cc_final: 0.6263 (mpt180) REVERT: B 731 ASP cc_start: 0.7404 (t0) cc_final: 0.6731 (m-30) REVERT: B 987 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7478 (mm-30) REVERT: B 1177 SER cc_start: 0.8566 (t) cc_final: 0.8338 (p) REVERT: B 1203 VAL cc_start: 0.7016 (m) cc_final: 0.6744 (t) REVERT: C 34 GLU cc_start: 0.7580 (pm20) cc_final: 0.7338 (pm20) REVERT: C 210 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7825 (mmt) REVERT: C 355 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: D 3 MET cc_start: 0.6952 (tpp) cc_final: 0.6679 (tpp) REVERT: D 63 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6341 (pttt) REVERT: D 81 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: G 58 LYS cc_start: 0.7505 (ttpp) cc_final: 0.6988 (ptmm) REVERT: G 79 ASP cc_start: 0.7986 (t0) cc_final: 0.7510 (t0) REVERT: F 2 ILE cc_start: 0.6107 (OUTLIER) cc_final: 0.5722 (mp) outliers start: 89 outliers final: 27 residues processed: 412 average time/residue: 1.4493 time to fit residues: 702.5456 Evaluate side-chains 377 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 340 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 586 LYS Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 633 GLN Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 149 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 226 optimal weight: 0.6980 chunk 142 optimal weight: 0.0020 chunk 110 optimal weight: 9.9990 chunk 160 optimal weight: 30.0000 chunk 255 optimal weight: 6.9990 chunk 224 optimal weight: 0.9990 chunk 310 optimal weight: 4.9990 chunk 281 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 292 optimal weight: 0.9990 chunk 269 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 420 GLN A 642 ASN A1276 HIS B 525 ASN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN F 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.193374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128953 restraints weight = 32535.999| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.49 r_work: 0.3277 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 30235 Z= 0.102 Angle : 0.500 13.443 40919 Z= 0.258 Chirality : 0.044 0.236 4642 Planarity : 0.004 0.052 5262 Dihedral : 4.396 44.269 4039 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.03 % Allowed : 15.39 % Favored : 82.58 % 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: 0.26 (0.14), residues: 3683 helix: 1.10 (0.14), residues: 1378 sheet: -0.35 (0.22), residues: 525 loop : -0.31 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 466 HIS 0.004 0.001 HIS C 315 PHE 0.023 0.001 PHE A 918 TYR 0.010 0.001 TYR A 567 ARG 0.009 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 1259) hydrogen bonds : angle 4.62665 ( 3468) metal coordination : bond 0.00500 ( 16) metal coordination : angle 3.06667 ( 21) covalent geometry : bond 0.00230 (30219) covalent geometry : angle 0.49553 (40898) *********************** 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 421 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 354 time to evaluate : 3.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.7537 (mtpt) cc_final: 0.6951 (ptpt) REVERT: A 171 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6434 (ttm170) REVERT: A 307 GLU cc_start: 0.7499 (pm20) cc_final: 0.6251 (tm-30) REVERT: A 639 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8493 (mp) REVERT: A 676 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: A 716 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8021 (tp) REVERT: A 900 ARG cc_start: 0.7430 (mtp85) cc_final: 0.7012 (tpt90) REVERT: A 903 LYS cc_start: 0.7637 (mtmt) cc_final: 0.7421 (mtpm) REVERT: A 941 ILE cc_start: 0.8261 (tt) cc_final: 0.7997 (tt) REVERT: A 1324 GLU cc_start: 0.8085 (tt0) cc_final: 0.6977 (mp0) REVERT: A 1355 MET cc_start: 0.9105 (tpt) cc_final: 0.8828 (mmm) REVERT: A 1393 GLN cc_start: 0.6948 (tp40) cc_final: 0.6115 (mp10) REVERT: B 116 LYS cc_start: 0.6043 (tptt) cc_final: 0.5704 (tptt) REVERT: B 268 LEU cc_start: 0.4451 (OUTLIER) cc_final: 0.3921 (tp) REVERT: B 405 PHE cc_start: 0.7914 (m-80) cc_final: 0.7581 (m-80) REVERT: B 542 MET cc_start: 0.6393 (ptm) cc_final: 0.5487 (pmm) REVERT: B 731 ASP cc_start: 0.7461 (t0) cc_final: 0.6784 (m-30) REVERT: B 845 ASN cc_start: 0.8640 (p0) cc_final: 0.8407 (p0) REVERT: B 969 MET cc_start: 0.5370 (mtp) cc_final: 0.4983 (mtt) REVERT: B 987 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7499 (mm-30) REVERT: B 1012 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8242 (t) REVERT: B 1177 SER cc_start: 0.8597 (t) cc_final: 0.8389 (p) REVERT: B 1203 VAL cc_start: 0.6989 (m) cc_final: 0.6774 (t) REVERT: C 5 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.5202 (p90) REVERT: C 28 LYS cc_start: 0.8423 (ptpt) cc_final: 0.7837 (ptmt) REVERT: C 34 GLU cc_start: 0.7576 (pm20) cc_final: 0.7346 (pm20) REVERT: C 82 ASP cc_start: 0.6247 (OUTLIER) cc_final: 0.5883 (m-30) REVERT: C 355 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7160 (m-30) REVERT: D 3 MET cc_start: 0.7100 (tpp) cc_final: 0.6840 (tpp) REVERT: D 63 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6374 (pttt) REVERT: D 81 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: G 58 LYS cc_start: 0.7484 (ttpp) cc_final: 0.6929 (ptmm) REVERT: G 79 ASP cc_start: 0.7951 (t0) cc_final: 0.7520 (t0) REVERT: F 2 ILE cc_start: 0.6065 (OUTLIER) cc_final: 0.5694 (mp) outliers start: 67 outliers final: 22 residues processed: 391 average time/residue: 1.4458 time to fit residues: 667.7629 Evaluate side-chains 376 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 342 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 633 GLN Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 263 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 118 optimal weight: 9.9990 chunk 327 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 212 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 304 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 287 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 721 ASN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 ASN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN F 4 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.191757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127510 restraints weight = 32382.258| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.58 r_work: 0.3238 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30235 Z= 0.138 Angle : 0.522 11.336 40919 Z= 0.269 Chirality : 0.045 0.207 4642 Planarity : 0.004 0.056 5262 Dihedral : 4.367 34.437 4035 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.21 % Allowed : 15.30 % Favored : 82.48 % 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: 0.25 (0.14), residues: 3683 helix: 1.07 (0.14), residues: 1377 sheet: -0.32 (0.22), residues: 524 loop : -0.31 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 466 HIS 0.004 0.001 HIS B 839 PHE 0.024 0.001 PHE A 918 TYR 0.013 0.001 TYR A 908 ARG 0.011 0.000 ARG B 544 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 1259) hydrogen bonds : angle 4.67342 ( 3468) metal coordination : bond 0.00611 ( 16) metal coordination : angle 3.39118 ( 21) covalent geometry : bond 0.00331 (30219) covalent geometry : angle 0.51652 (40898) *********************** 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 417 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 344 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.7441 (mtpt) cc_final: 0.6838 (ptpt) REVERT: A 171 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6427 (ttm110) REVERT: A 520 ASN cc_start: 0.9238 (t0) cc_final: 0.8929 (t0) REVERT: A 639 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8475 (mp) REVERT: A 676 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: A 690 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.6951 (mpp) REVERT: A 903 LYS cc_start: 0.7617 (mtmt) cc_final: 0.7370 (mtpm) REVERT: A 941 ILE cc_start: 0.8198 (tt) cc_final: 0.7920 (tt) REVERT: A 1324 GLU cc_start: 0.8013 (tt0) cc_final: 0.6870 (mp0) REVERT: A 1355 MET cc_start: 0.9071 (tpt) cc_final: 0.8766 (mmm) REVERT: A 1393 GLN cc_start: 0.6843 (tp40) cc_final: 0.5902 (mp10) REVERT: E 96 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7700 (mptt) REVERT: B 116 LYS cc_start: 0.5901 (tptt) cc_final: 0.5576 (tptt) REVERT: B 268 LEU cc_start: 0.4368 (OUTLIER) cc_final: 0.3837 (tp) REVERT: B 542 MET cc_start: 0.6342 (ptm) cc_final: 0.5435 (pmm) REVERT: B 544 ARG cc_start: 0.6961 (tpp80) cc_final: 0.6172 (mpt180) REVERT: B 987 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7475 (mm-30) REVERT: B 1203 VAL cc_start: 0.6914 (m) cc_final: 0.6665 (t) REVERT: C 5 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.5172 (p90) REVERT: C 28 LYS cc_start: 0.8371 (ptpt) cc_final: 0.7734 (ptmt) REVERT: C 34 GLU cc_start: 0.7557 (pm20) cc_final: 0.7300 (pm20) REVERT: C 82 ASP cc_start: 0.6126 (OUTLIER) cc_final: 0.5773 (m-30) REVERT: C 355 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: D 63 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6345 (pttt) REVERT: D 81 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: G 58 LYS cc_start: 0.7466 (ttpp) cc_final: 0.6900 (ptmm) REVERT: G 79 ASP cc_start: 0.7987 (t0) cc_final: 0.7552 (t0) REVERT: F 2 ILE cc_start: 0.6015 (OUTLIER) cc_final: 0.5650 (mp) outliers start: 73 outliers final: 36 residues processed: 387 average time/residue: 1.4168 time to fit residues: 646.6352 Evaluate side-chains 384 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 336 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 633 GLN Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 120 CYS Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 149 SER Chi-restraints excluded: chain F residue 263 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.3359 > 50: distance: 127 - 135: 33.880 distance: 135 - 136: 49.065 distance: 136 - 137: 42.697 distance: 136 - 139: 63.297 distance: 137 - 138: 23.216 distance: 137 - 144: 52.840 distance: 139 - 140: 40.783 distance: 140 - 141: 3.643 distance: 141 - 142: 25.834 distance: 142 - 143: 25.295 distance: 144 - 145: 38.899 distance: 145 - 146: 56.437 distance: 145 - 148: 51.659 distance: 146 - 147: 45.185 distance: 146 - 154: 51.824 distance: 147 - 164: 44.522 distance: 148 - 149: 55.529 distance: 149 - 150: 48.932 distance: 149 - 151: 56.064 distance: 150 - 152: 57.191 distance: 151 - 153: 61.098 distance: 152 - 153: 48.238 distance: 154 - 155: 7.189 distance: 155 - 156: 56.573 distance: 155 - 158: 61.162 distance: 156 - 157: 39.609 distance: 156 - 159: 46.300 distance: 157 - 175: 37.870 distance: 159 - 160: 46.301 distance: 160 - 161: 15.419 distance: 160 - 163: 57.572 distance: 161 - 162: 44.788 distance: 161 - 164: 30.299 distance: 164 - 165: 34.104 distance: 165 - 166: 21.234 distance: 165 - 168: 38.357 distance: 166 - 167: 54.394 distance: 166 - 175: 56.371 distance: 168 - 169: 9.611 distance: 169 - 170: 43.530 distance: 169 - 171: 43.830 distance: 170 - 172: 23.582 distance: 171 - 173: 54.204 distance: 172 - 174: 42.789 distance: 173 - 174: 8.703 distance: 175 - 176: 45.560 distance: 176 - 177: 18.143 distance: 176 - 179: 10.341 distance: 177 - 178: 49.553 distance: 177 - 183: 47.624 distance: 179 - 180: 11.166 distance: 180 - 181: 39.396 distance: 180 - 182: 45.386 distance: 183 - 184: 53.736 distance: 184 - 187: 56.047 distance: 185 - 186: 15.786 distance: 185 - 191: 57.982 distance: 187 - 188: 20.750 distance: 188 - 189: 42.637 distance: 188 - 190: 40.964 distance: 192 - 193: 24.931 distance: 192 - 195: 48.499 distance: 193 - 194: 11.987 distance: 193 - 196: 51.367 distance: 196 - 197: 35.224 distance: 197 - 198: 34.663 distance: 197 - 200: 30.331 distance: 198 - 199: 36.666 distance: 198 - 203: 32.923 distance: 200 - 201: 42.284 distance: 200 - 202: 16.201 distance: 203 - 204: 9.010 distance: 204 - 205: 22.696 distance: 204 - 207: 56.947 distance: 205 - 206: 49.649 distance: 205 - 212: 34.458 distance: 207 - 208: 60.984 distance: 208 - 209: 43.176 distance: 209 - 210: 39.645 distance: 210 - 211: 28.120