Starting phenix.real_space_refine on Tue May 27 15:02:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yqv_39507/05_2025/8yqv_39507.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yqv_39507/05_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_39507/05_2025/8yqv_39507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yqv_39507/05_2025/8yqv_39507.map" model { file = "/net/cci-nas-00/data/ceres_data/8yqv_39507/05_2025/8yqv_39507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yqv_39507/05_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 16.88, per 1000 atoms: 0.57 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: 7.17 Conformation dependent library (CDL) restraints added in 3.7 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: 4.16 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: 13.27 Time building geometry restraints manager: 8.22 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.120 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 71.270 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.100 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:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.230 ------------------------------------------------------------------------------- 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 : 3.318 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: 1.4823 time to fit residues: 606.5913 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 : 3.079 ------------------------------------------------------------------------------- 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 = 0.188320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120893 restraints weight = 32703.431| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.37 r_work: 0.3208 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 62.128 4052 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.38 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 5.49730 ( 3468) metal coordination : bond 0.00984 ( 16) metal coordination : angle 4.25791 ( 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 : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8524 (mp-120) cc_final: 0.8259 (mp-120) REVERT: A 119 LYS cc_start: 0.7553 (mtpt) cc_final: 0.6635 (tmtm) REVERT: A 138 LYS cc_start: 0.6413 (mppt) cc_final: 0.6078 (mmtm) REVERT: A 168 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: A 400 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: A 661 GLU cc_start: 0.7448 (tt0) cc_final: 0.7218 (mp0) REVERT: A 664 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: A 690 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7106 (mpp) REVERT: A 1286 ARG cc_start: 0.8175 (ttp-170) cc_final: 0.7943 (ttp80) REVERT: A 1355 MET cc_start: 0.9132 (tpt) cc_final: 0.8860 (mmm) REVERT: B 542 MET cc_start: 0.6743 (ptm) cc_final: 0.6143 (pmm) REVERT: B 731 ASP cc_start: 0.7581 (t0) cc_final: 0.6830 (m-30) REVERT: B 845 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8407 (p0) REVERT: B 957 TYR cc_start: 0.5340 (t80) cc_final: 0.5038 (t80) REVERT: B 969 MET cc_start: 0.5256 (mtp) cc_final: 0.4960 (mtp) REVERT: C 34 GLU cc_start: 0.7541 (pm20) cc_final: 0.7318 (pm20) REVERT: C 355 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: D 63 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6428 (pttt) REVERT: H 32 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7851 (mmtp) REVERT: G 68 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: G 79 ASP cc_start: 0.7865 (t0) cc_final: 0.7535 (t0) outliers start: 95 outliers final: 30 residues processed: 409 average time/residue: 1.3649 time to fit residues: 657.4745 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 : 3.261 ------------------------------------------------------------------------------- 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: 0.2980 chunk 281 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 245 optimal weight: 0.6980 chunk 314 optimal weight: 0.5980 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: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN B 419 HIS ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 ASN ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS C 317 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 = 0.4126 r_free = 0.4126 target = 0.189344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125861 restraints weight = 32537.298| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.50 r_work: 0.3220 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30235 Z= 0.175 Angle : 0.577 12.083 40919 Z= 0.300 Chirality : 0.046 0.195 4642 Planarity : 0.005 0.060 5262 Dihedral : 5.156 56.412 4042 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.76 % Allowed : 13.15 % Favored : 84.09 % 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: -0.47 (0.14), residues: 3683 helix: 0.35 (0.14), residues: 1381 sheet: -0.51 (0.22), residues: 526 loop : -0.69 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 466 HIS 0.005 0.001 HIS B1221 PHE 0.027 0.002 PHE A 918 TYR 0.012 0.001 TYR A 908 ARG 0.006 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.04543 ( 1259) hydrogen bonds : angle 5.20200 ( 3468) metal coordination : bond 0.00852 ( 16) metal coordination : angle 4.02642 ( 21) covalent geometry : bond 0.00422 (30219) covalent geometry : angle 0.56993 (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 446 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 355 time to evaluate : 3.099 Fit side-chains revert: symmetry clash REVERT: A 119 LYS cc_start: 0.7557 (mtpt) cc_final: 0.6663 (tmtm) REVERT: A 138 LYS cc_start: 0.6434 (mppt) cc_final: 0.6089 (mmtm) REVERT: A 400 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: A 520 ASN cc_start: 0.9246 (t0) cc_final: 0.8962 (t0) REVERT: A 562 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7646 (mm-40) REVERT: A 664 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7615 (mp10) REVERT: A 676 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: A 690 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7128 (mpp) REVERT: A 900 ARG cc_start: 0.7461 (mtp85) cc_final: 0.6929 (tpt90) REVERT: A 923 LEU cc_start: 0.8377 (mt) cc_final: 0.8145 (mp) REVERT: A 1209 MET cc_start: 0.6006 (OUTLIER) cc_final: 0.5696 (ttt) REVERT: A 1260 ARG cc_start: 0.7199 (ttp-170) cc_final: 0.6865 (ttp-170) REVERT: A 1286 ARG cc_start: 0.8139 (ttp-170) cc_final: 0.7897 (ttp80) REVERT: A 1355 MET cc_start: 0.9117 (tpt) cc_final: 0.8815 (mmm) REVERT: A 1393 GLN cc_start: 0.6849 (tp40) cc_final: 0.5992 (mp10) REVERT: B 541 MET cc_start: 0.4914 (tpp) cc_final: 0.4636 (mmm) REVERT: B 542 MET cc_start: 0.6538 (ptm) cc_final: 0.5705 (pmm) REVERT: B 544 ARG cc_start: 0.6982 (tpp80) cc_final: 0.6761 (tpp80) REVERT: B 731 ASP cc_start: 0.7510 (t0) cc_final: 0.6776 (m-30) REVERT: B 969 MET cc_start: 0.5188 (mtp) cc_final: 0.4918 (mtp) REVERT: B 1177 SER cc_start: 0.8607 (t) cc_final: 0.8340 (p) REVERT: C 34 GLU cc_start: 0.7553 (pm20) cc_final: 0.7291 (pm20) REVERT: C 355 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7422 (m-30) REVERT: D 63 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6333 (pttt) REVERT: D 86 GLU cc_start: 0.7422 (tt0) cc_final: 0.7131 (mt-10) REVERT: G 58 LYS cc_start: 0.7519 (ttpp) cc_final: 0.6985 (ptmm) REVERT: G 68 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7272 (mp10) REVERT: G 79 ASP cc_start: 0.7962 (t0) cc_final: 0.7582 (t0) outliers start: 91 outliers final: 36 residues processed: 402 average time/residue: 1.3873 time to fit residues: 655.7779 Evaluate side-chains 382 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 337 time to evaluate : 3.006 ------------------------------------------------------------------------------- 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 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 1295 THR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 633 GLN Chi-restraints excluded: chain B residue 807 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 80 ILE 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 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 70 MET Chi-restraints excluded: chain F residue 149 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 336 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 244 optimal weight: 0.1980 chunk 282 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 845 ASN ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1162 GLN C 317 GLN D 157 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 = 0.4147 r_free = 0.4147 target = 0.191564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128328 restraints weight = 32516.881| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.55 r_work: 0.3272 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 30235 Z= 0.117 Angle : 0.520 10.490 40919 Z= 0.270 Chirality : 0.044 0.170 4642 Planarity : 0.004 0.055 5262 Dihedral : 4.841 53.317 4042 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.55 % Allowed : 13.76 % Favored : 83.70 % 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: -0.14 (0.14), residues: 3683 helix: 0.73 (0.14), residues: 1378 sheet: -0.52 (0.22), residues: 515 loop : -0.53 (0.15), residues: 1790 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 B 811 ARG 0.007 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 1259) hydrogen bonds : angle 4.90432 ( 3468) metal coordination : bond 0.00601 ( 16) metal coordination : angle 3.49138 ( 21) covalent geometry : bond 0.00271 (30219) covalent geometry : angle 0.51417 (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 453 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 369 time to evaluate : 3.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8600 (mt-10) REVERT: A 119 LYS cc_start: 0.7564 (mtpt) cc_final: 0.6649 (tmtm) REVERT: A 171 ARG cc_start: 0.7009 (ttm110) cc_final: 0.6632 (ttm110) REVERT: A 307 GLU cc_start: 0.7561 (pm20) cc_final: 0.6278 (tm-30) REVERT: A 400 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: A 664 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7736 (mp10) REVERT: A 676 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: A 690 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7112 (mpp) REVERT: A 900 ARG cc_start: 0.7480 (mtp85) cc_final: 0.7001 (tpt90) REVERT: A 903 LYS cc_start: 0.7649 (mtmt) cc_final: 0.7364 (mtpm) REVERT: A 956 SER cc_start: 0.7368 (t) cc_final: 0.7145 (p) REVERT: A 1260 ARG cc_start: 0.7222 (ttp-170) cc_final: 0.6864 (ttp-170) REVERT: A 1286 ARG cc_start: 0.8125 (ttp-170) cc_final: 0.7906 (ttp80) REVERT: A 1355 MET cc_start: 0.9123 (tpt) cc_final: 0.8851 (mmm) REVERT: A 1393 GLN cc_start: 0.7005 (tp40) cc_final: 0.6142 (mp10) REVERT: B 116 LYS cc_start: 0.5840 (tptt) cc_final: 0.5547 (tptt) REVERT: B 542 MET cc_start: 0.6509 (ptm) cc_final: 0.5609 (pmm) REVERT: B 731 ASP cc_start: 0.7541 (t0) cc_final: 0.6869 (m-30) REVERT: B 1203 VAL cc_start: 0.7051 (m) cc_final: 0.6734 (t) REVERT: C 82 ASP cc_start: 0.6212 (OUTLIER) cc_final: 0.5911 (m-30) REVERT: C 210 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.7885 (mmt) REVERT: C 355 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: D 63 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6321 (pttt) REVERT: G 58 LYS cc_start: 0.7530 (ttpp) cc_final: 0.7041 (ptmm) REVERT: G 79 ASP cc_start: 0.7930 (t0) cc_final: 0.7466 (t0) REVERT: F 2 ILE cc_start: 0.6122 (OUTLIER) cc_final: 0.5724 (mp) outliers start: 84 outliers final: 28 residues processed: 412 average time/residue: 1.4126 time to fit residues: 687.7652 Evaluate side-chains 375 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 338 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LYS 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 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 1105 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 1012 THR Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 116 LEU 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 125 LEU 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 263 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 208 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 321 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 341 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 21 optimal weight: 0.0060 chunk 88 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- 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 A 765 GLN B 235 GLN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 ASN ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 ASN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1162 GLN C 317 GLN F 4 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.188374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123944 restraints weight = 32509.511| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.37 r_work: 0.3231 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30235 Z= 0.222 Angle : 0.602 12.849 40919 Z= 0.311 Chirality : 0.048 0.213 4642 Planarity : 0.005 0.057 5262 Dihedral : 5.095 57.636 4042 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.06 % Allowed : 13.88 % Favored : 83.06 % 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: 0.58 (0.14), residues: 1383 sheet: -0.53 (0.22), residues: 515 loop : -0.58 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 466 HIS 0.007 0.001 HIS B1221 PHE 0.027 0.002 PHE A 918 TYR 0.014 0.002 TYR A 908 ARG 0.008 0.001 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 1259) hydrogen bonds : angle 5.05269 ( 3468) metal coordination : bond 0.00869 ( 16) metal coordination : angle 4.12639 ( 21) covalent geometry : bond 0.00546 (30219) covalent geometry : angle 0.59459 (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 445 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 344 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.7679 (mtpt) cc_final: 0.6750 (tmtm) REVERT: A 168 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: A 171 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6640 (ttm110) REVERT: A 400 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: A 639 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8507 (mp) REVERT: A 664 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7706 (mp10) REVERT: A 676 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: A 690 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7115 (mpp) REVERT: A 900 ARG cc_start: 0.7481 (mtp85) cc_final: 0.6840 (tpt90) REVERT: A 1393 GLN cc_start: 0.6998 (tp40) cc_final: 0.6163 (mp10) REVERT: E 96 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7736 (mptt) REVERT: B 268 LEU cc_start: 0.4383 (OUTLIER) cc_final: 0.3893 (tp) REVERT: B 542 MET cc_start: 0.6590 (ptm) cc_final: 0.5593 (pmm) REVERT: B 544 ARG cc_start: 0.7035 (tpp80) cc_final: 0.6332 (mpt180) REVERT: B 731 ASP cc_start: 0.7542 (t0) cc_final: 0.6808 (m-30) REVERT: C 5 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.5281 (p90) REVERT: C 351 GLU cc_start: 0.7759 (tt0) cc_final: 0.7520 (tt0) REVERT: C 355 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: D 63 LYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6384 (pttt) REVERT: D 81 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: G 58 LYS cc_start: 0.7572 (ttpp) cc_final: 0.7068 (ptmm) REVERT: G 79 ASP cc_start: 0.8068 (t0) cc_final: 0.7621 (t0) outliers start: 101 outliers final: 47 residues processed: 408 average time/residue: 1.3865 time to fit residues: 668.4032 Evaluate side-chains 394 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 334 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 GLN 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 528 MET Chi-restraints excluded: chain A residue 586 LYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 664 GLN 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 54 SER Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 268 LEU 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 965 VAL Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 11 LYS 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 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 115 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 182 VAL 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 95 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 149 SER Chi-restraints excluded: chain F residue 263 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 226 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 160 optimal weight: 20.0000 chunk 255 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 281 optimal weight: 3.9990 chunk 273 optimal weight: 0.7980 chunk 292 optimal weight: 4.9990 chunk 269 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A1276 HIS ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.190751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127577 restraints weight = 32477.811| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.51 r_work: 0.3239 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30235 Z= 0.130 Angle : 0.533 13.094 40919 Z= 0.276 Chirality : 0.045 0.213 4642 Planarity : 0.004 0.055 5262 Dihedral : 4.852 56.303 4042 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.61 % Allowed : 14.88 % Favored : 82.52 % 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: -0.03 (0.14), residues: 3683 helix: 0.83 (0.14), residues: 1381 sheet: -0.46 (0.22), residues: 514 loop : -0.47 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 466 HIS 0.005 0.001 HIS C 315 PHE 0.024 0.001 PHE A 918 TYR 0.010 0.001 TYR D 123 ARG 0.008 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 1259) hydrogen bonds : angle 4.86438 ( 3468) metal coordination : bond 0.00635 ( 16) metal coordination : angle 3.54012 ( 21) covalent geometry : bond 0.00306 (30219) covalent geometry : angle 0.52754 (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 433 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 347 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.7540 (mtpt) cc_final: 0.6621 (tmtm) REVERT: A 171 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6472 (ttm110) REVERT: A 307 GLU cc_start: 0.7482 (pm20) cc_final: 0.6236 (tm-30) REVERT: A 400 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: A 520 ASN cc_start: 0.9245 (t0) cc_final: 0.8943 (t0) REVERT: A 664 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7685 (mp10) REVERT: A 676 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: A 690 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7079 (mpp) REVERT: A 900 ARG cc_start: 0.7442 (mtp85) cc_final: 0.6767 (tpt90) REVERT: A 903 LYS cc_start: 0.7595 (mtmt) cc_final: 0.7139 (mttp) REVERT: A 1355 MET cc_start: 0.9051 (tpt) cc_final: 0.8767 (mmm) REVERT: A 1393 GLN cc_start: 0.6871 (tp40) cc_final: 0.5993 (mp10) REVERT: E 96 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7674 (mptt) REVERT: B 116 LYS cc_start: 0.5818 (tptt) cc_final: 0.5531 (tptt) REVERT: B 268 LEU cc_start: 0.4354 (OUTLIER) cc_final: 0.3883 (tp) REVERT: B 542 MET cc_start: 0.6355 (ptm) cc_final: 0.5447 (pmm) REVERT: B 544 ARG cc_start: 0.6903 (tpp80) cc_final: 0.6382 (mpt180) REVERT: B 731 ASP cc_start: 0.7470 (t0) cc_final: 0.6750 (m-30) REVERT: B 957 TYR cc_start: 0.5401 (t80) cc_final: 0.5031 (t80) REVERT: B 1203 VAL cc_start: 0.7005 (m) cc_final: 0.6662 (t) REVERT: C 5 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.5235 (p90) REVERT: C 82 ASP cc_start: 0.6251 (OUTLIER) cc_final: 0.5873 (m-30) REVERT: C 210 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7879 (mmt) REVERT: C 355 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7256 (m-30) REVERT: D 63 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6335 (pttt) REVERT: D 81 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: H 32 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7979 (mmtp) REVERT: G 58 LYS cc_start: 0.7511 (ttpp) cc_final: 0.6985 (ptmm) REVERT: G 79 ASP cc_start: 0.8036 (t0) cc_final: 0.7587 (t0) REVERT: F 2 ILE cc_start: 0.6040 (OUTLIER) cc_final: 0.5668 (mp) outliers start: 86 outliers final: 42 residues processed: 394 average time/residue: 1.3817 time to fit residues: 647.6065 Evaluate side-chains 395 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 338 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 122 ILE 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 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 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 1342 VAL Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 96 LYS 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 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 1012 THR Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 107 GLU 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 127 SER 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 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 32 LYS 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 111 THR 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: 10.0000 chunk 327 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 287 optimal weight: 7.9990 chunk 266 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 B 235 GLN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 ASN ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN G 103 ASN F 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.189372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125980 restraints weight = 32410.301| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.50 r_work: 0.3208 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30235 Z= 0.175 Angle : 0.566 14.537 40919 Z= 0.291 Chirality : 0.046 0.213 4642 Planarity : 0.004 0.056 5262 Dihedral : 4.925 58.223 4042 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.79 % Allowed : 15.03 % Favored : 82.18 % 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: -0.04 (0.14), residues: 3683 helix: 0.81 (0.14), residues: 1378 sheet: -0.50 (0.22), residues: 527 loop : -0.46 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 466 HIS 0.005 0.001 HIS B1221 PHE 0.026 0.002 PHE A 918 TYR 0.013 0.001 TYR A 908 ARG 0.009 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 1259) hydrogen bonds : angle 4.89983 ( 3468) metal coordination : bond 0.00720 ( 16) metal coordination : angle 3.80328 ( 21) covalent geometry : bond 0.00424 (30219) covalent geometry : angle 0.55921 (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 435 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 343 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.7541 (mtpt) cc_final: 0.6621 (tmtm) REVERT: A 171 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6532 (ttm110) REVERT: A 400 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: A 664 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: A 676 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: A 678 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6647 (tm-30) REVERT: A 690 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7055 (mpp) REVERT: A 871 GLU cc_start: 0.8337 (pt0) cc_final: 0.7965 (pt0) REVERT: A 903 LYS cc_start: 0.7635 (mtmt) cc_final: 0.7226 (mttp) REVERT: A 941 ILE cc_start: 0.8234 (tt) cc_final: 0.7941 (tt) REVERT: A 1355 MET cc_start: 0.9068 (tpt) cc_final: 0.8784 (mmm) REVERT: A 1393 GLN cc_start: 0.6887 (tp40) cc_final: 0.5996 (mp10) REVERT: E 96 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7619 (mptt) REVERT: B 116 LYS cc_start: 0.5805 (tptt) cc_final: 0.5500 (tptt) REVERT: B 268 LEU cc_start: 0.4320 (OUTLIER) cc_final: 0.3847 (tp) REVERT: B 542 MET cc_start: 0.6482 (ptm) cc_final: 0.5527 (pmm) REVERT: B 544 ARG cc_start: 0.6902 (tpp80) cc_final: 0.6395 (mpt180) REVERT: B 731 ASP cc_start: 0.7497 (t0) cc_final: 0.6751 (m-30) REVERT: B 969 MET cc_start: 0.5190 (mtp) cc_final: 0.4775 (mtt) REVERT: B 1203 VAL cc_start: 0.7011 (m) cc_final: 0.6660 (t) REVERT: C 5 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.5233 (p90) REVERT: C 82 ASP cc_start: 0.6245 (OUTLIER) cc_final: 0.5867 (m-30) REVERT: C 351 GLU cc_start: 0.7650 (tt0) cc_final: 0.7429 (tt0) REVERT: C 355 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7266 (m-30) REVERT: D 63 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6358 (pttt) REVERT: D 81 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: H 32 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7960 (mmtp) REVERT: G 58 LYS cc_start: 0.7497 (ttpp) cc_final: 0.6929 (ptmm) REVERT: G 79 ASP cc_start: 0.8088 (t0) cc_final: 0.7648 (t0) REVERT: F 2 ILE cc_start: 0.6035 (OUTLIER) cc_final: 0.5659 (mp) outliers start: 92 outliers final: 42 residues processed: 399 average time/residue: 1.3733 time to fit residues: 646.1249 Evaluate side-chains 390 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 333 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 122 ILE 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 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 664 GLN Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 678 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 54 SER Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain B residue 268 LEU 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 1012 THR Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 ILE 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 121 GLU Chi-restraints excluded: chain C residue 127 SER 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 115 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 263 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 344 optimal weight: 2.9990 chunk 283 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 359 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 ASN ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.189433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126151 restraints weight = 32550.028| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.51 r_work: 0.3219 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30235 Z= 0.174 Angle : 0.566 12.764 40919 Z= 0.292 Chirality : 0.046 0.213 4642 Planarity : 0.004 0.057 5262 Dihedral : 4.924 58.215 4042 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.61 % Allowed : 15.39 % Favored : 82.00 % 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: -0.02 (0.14), residues: 3683 helix: 0.83 (0.14), residues: 1377 sheet: -0.49 (0.22), residues: 527 loop : -0.45 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 466 HIS 0.005 0.001 HIS B1031 PHE 0.026 0.002 PHE A 918 TYR 0.012 0.001 TYR A 908 ARG 0.010 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 1259) hydrogen bonds : angle 4.89379 ( 3468) metal coordination : bond 0.00725 ( 16) metal coordination : angle 3.74295 ( 21) covalent geometry : bond 0.00424 (30219) covalent geometry : angle 0.56007 (40898) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 340 time to evaluate : 3.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.7584 (mtpt) cc_final: 0.6642 (tmtm) REVERT: A 171 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6559 (ttm110) REVERT: A 664 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7669 (mp10) REVERT: A 676 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: A 678 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6638 (tm-30) REVERT: A 690 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7065 (mpp) REVERT: A 871 GLU cc_start: 0.8341 (pt0) cc_final: 0.7984 (pt0) REVERT: A 900 ARG cc_start: 0.7514 (mmp80) cc_final: 0.6899 (tpt90) REVERT: A 903 LYS cc_start: 0.7602 (mtmt) cc_final: 0.7129 (mttp) REVERT: A 941 ILE cc_start: 0.8256 (tt) cc_final: 0.7956 (tt) REVERT: A 1240 MET cc_start: 0.2144 (pmm) cc_final: 0.0456 (ptp) REVERT: A 1355 MET cc_start: 0.9064 (tpt) cc_final: 0.8795 (mmm) REVERT: A 1393 GLN cc_start: 0.6914 (tp40) cc_final: 0.6017 (mp10) REVERT: E 96 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7626 (mptt) REVERT: B 116 LYS cc_start: 0.5768 (tptt) cc_final: 0.5345 (tptt) REVERT: B 268 LEU cc_start: 0.4344 (OUTLIER) cc_final: 0.3862 (tp) REVERT: B 542 MET cc_start: 0.6413 (ptm) cc_final: 0.5479 (pmm) REVERT: B 544 ARG cc_start: 0.6952 (tpp80) cc_final: 0.6440 (mpt180) REVERT: B 731 ASP cc_start: 0.7507 (t0) cc_final: 0.6767 (m-30) REVERT: B 969 MET cc_start: 0.5234 (mtp) cc_final: 0.4828 (mtt) REVERT: B 1203 VAL cc_start: 0.7004 (m) cc_final: 0.6643 (t) REVERT: C 5 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.5263 (p90) REVERT: C 82 ASP cc_start: 0.6214 (OUTLIER) cc_final: 0.5850 (m-30) REVERT: C 351 GLU cc_start: 0.7667 (tt0) cc_final: 0.7459 (tt0) REVERT: C 355 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: D 63 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6398 (pttt) REVERT: D 81 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: H 32 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7954 (mmtp) REVERT: G 58 LYS cc_start: 0.7526 (ttpp) cc_final: 0.6934 (ptmm) REVERT: G 79 ASP cc_start: 0.8080 (t0) cc_final: 0.7653 (t0) REVERT: F 2 ILE cc_start: 0.6032 (OUTLIER) cc_final: 0.5655 (mp) outliers start: 86 outliers final: 48 residues processed: 395 average time/residue: 1.3899 time to fit residues: 651.2662 Evaluate side-chains 396 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 334 time to evaluate : 3.208 ------------------------------------------------------------------------------- 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 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 528 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 678 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 1152 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 54 SER Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 PHE 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 1012 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 ILE 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 121 GLU Chi-restraints excluded: chain C residue 127 SER 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 115 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 91 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 336 optimal weight: 7.9990 chunk 285 optimal weight: 0.7980 chunk 219 optimal weight: 3.9990 chunk 348 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 344 optimal weight: 0.2980 chunk 85 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 330 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 226 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 765 GLN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 ASN ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.190265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123890 restraints weight = 32238.426| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.39 r_work: 0.3259 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30235 Z= 0.155 Angle : 0.551 12.047 40919 Z= 0.284 Chirality : 0.045 0.198 4642 Planarity : 0.004 0.057 5262 Dihedral : 4.757 58.364 4039 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.33 % Allowed : 15.79 % Favored : 81.88 % 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: 0.04 (0.14), residues: 3683 helix: 0.89 (0.14), residues: 1378 sheet: -0.49 (0.22), residues: 531 loop : -0.40 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 466 HIS 0.005 0.001 HIS C 315 PHE 0.026 0.001 PHE A 918 TYR 0.011 0.001 TYR A 908 ARG 0.011 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 1259) hydrogen bonds : angle 4.83865 ( 3468) metal coordination : bond 0.00675 ( 16) metal coordination : angle 3.61873 ( 21) covalent geometry : bond 0.00373 (30219) covalent geometry : angle 0.54540 (40898) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 349 time to evaluate : 3.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8632 (mt-10) REVERT: A 119 LYS cc_start: 0.7596 (mtpt) cc_final: 0.6988 (ptpt) REVERT: A 171 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6561 (ttm110) REVERT: A 664 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: A 676 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: A 678 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6657 (tm-30) REVERT: A 690 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7036 (mpp) REVERT: A 871 GLU cc_start: 0.8337 (pt0) cc_final: 0.7981 (pt0) REVERT: A 900 ARG cc_start: 0.7472 (mmp80) cc_final: 0.6876 (tpt90) REVERT: A 903 LYS cc_start: 0.7601 (mtmt) cc_final: 0.7121 (mttp) REVERT: A 941 ILE cc_start: 0.8265 (tt) cc_final: 0.7962 (tt) REVERT: A 1240 MET cc_start: 0.2156 (pmm) cc_final: 0.0720 (ptt) REVERT: A 1355 MET cc_start: 0.9062 (tpt) cc_final: 0.8779 (mmm) REVERT: A 1393 GLN cc_start: 0.6926 (tp40) cc_final: 0.6030 (mp10) REVERT: E 96 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7622 (mptt) REVERT: B 116 LYS cc_start: 0.5817 (tptt) cc_final: 0.5432 (tptt) REVERT: B 241 GLU cc_start: 0.5410 (OUTLIER) cc_final: 0.4818 (mm-30) REVERT: B 268 LEU cc_start: 0.4325 (OUTLIER) cc_final: 0.3855 (tp) REVERT: B 542 MET cc_start: 0.6366 (ptm) cc_final: 0.5466 (pmm) REVERT: B 544 ARG cc_start: 0.6883 (tpp80) cc_final: 0.6415 (mpt180) REVERT: B 731 ASP cc_start: 0.7536 (t0) cc_final: 0.6787 (m-30) REVERT: B 969 MET cc_start: 0.5205 (mtp) cc_final: 0.4805 (mtt) REVERT: B 1203 VAL cc_start: 0.7015 (m) cc_final: 0.6680 (t) REVERT: C 5 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.5329 (p90) REVERT: C 28 LYS cc_start: 0.8419 (ptpt) cc_final: 0.7747 (ptmt) REVERT: C 82 ASP cc_start: 0.6211 (OUTLIER) cc_final: 0.5854 (m-30) REVERT: C 355 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7284 (m-30) REVERT: D 63 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6351 (pttt) REVERT: D 81 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: H 32 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7965 (mmtp) REVERT: G 58 LYS cc_start: 0.7536 (ttpp) cc_final: 0.6948 (ptmm) REVERT: G 79 ASP cc_start: 0.8110 (t0) cc_final: 0.7720 (t0) REVERT: F 2 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5623 (mp) outliers start: 77 outliers final: 44 residues processed: 397 average time/residue: 1.4050 time to fit residues: 656.8926 Evaluate side-chains 398 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 339 time to evaluate : 3.180 ------------------------------------------------------------------------------- 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 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 528 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 678 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 974 VAL Chi-restraints excluded: chain A residue 1152 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 54 SER Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 268 LEU 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 1012 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 82 ASP 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 121 GLU Chi-restraints excluded: chain C residue 127 SER 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 115 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 LYS 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 111 THR Chi-restraints excluded: chain F residue 149 SER Chi-restraints excluded: chain F residue 263 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 86 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 191 optimal weight: 0.0030 chunk 206 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 263 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 525 ASN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 ASN ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.192166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124422 restraints weight = 32593.911| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.41 r_work: 0.3326 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 30235 Z= 0.098 Angle : 0.501 11.727 40919 Z= 0.259 Chirality : 0.044 0.180 4642 Planarity : 0.004 0.053 5262 Dihedral : 4.424 55.461 4039 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.67 % Allowed : 16.61 % Favored : 81.73 % 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: 0.32 (0.14), residues: 3683 helix: 1.16 (0.14), residues: 1376 sheet: -0.35 (0.22), residues: 535 loop : -0.27 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 466 HIS 0.005 0.001 HIS C 315 PHE 0.025 0.001 PHE A 918 TYR 0.011 0.001 TYR A 567 ARG 0.011 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 1259) hydrogen bonds : angle 4.62040 ( 3468) metal coordination : bond 0.00506 ( 16) metal coordination : angle 2.95407 ( 21) covalent geometry : bond 0.00221 (30219) covalent geometry : angle 0.49682 (40898) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7366 Ramachandran restraints generated. 3683 Oldfield, 0 Emsley, 3683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 362 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8603 (mt-10) REVERT: A 119 LYS cc_start: 0.7395 (mtpt) cc_final: 0.6907 (ptpt) REVERT: A 171 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6461 (ttm110) REVERT: A 185 LEU cc_start: 0.7434 (tt) cc_final: 0.7130 (tt) REVERT: A 517 MET cc_start: 0.8478 (mmp) cc_final: 0.7920 (mmp) REVERT: A 676 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: A 716 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7965 (tp) REVERT: A 900 ARG cc_start: 0.7450 (mmp80) cc_final: 0.7038 (tpt90) REVERT: A 903 LYS cc_start: 0.7599 (mtmt) cc_final: 0.7373 (mtpm) REVERT: A 1078 GLN cc_start: 0.7692 (mt0) cc_final: 0.7384 (mm-40) REVERT: A 1240 MET cc_start: 0.1940 (pmm) cc_final: 0.0390 (ptp) REVERT: A 1324 GLU cc_start: 0.7965 (tt0) cc_final: 0.6872 (mp0) REVERT: A 1355 MET cc_start: 0.9068 (tpt) cc_final: 0.8794 (mmm) REVERT: A 1393 GLN cc_start: 0.6935 (tp40) cc_final: 0.6068 (mp10) REVERT: E 96 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7665 (mptt) REVERT: B 116 LYS cc_start: 0.5950 (tptt) cc_final: 0.5592 (tptt) REVERT: B 241 GLU cc_start: 0.5352 (OUTLIER) cc_final: 0.4738 (mm-30) REVERT: B 268 LEU cc_start: 0.4383 (OUTLIER) cc_final: 0.3860 (tp) REVERT: B 542 MET cc_start: 0.6335 (ptm) cc_final: 0.5513 (pmm) REVERT: B 544 ARG cc_start: 0.6683 (tpp80) cc_final: 0.6291 (mpt180) REVERT: B 731 ASP cc_start: 0.7432 (t0) cc_final: 0.6752 (m-30) REVERT: B 957 TYR cc_start: 0.5365 (t80) cc_final: 0.5128 (t80) REVERT: B 969 MET cc_start: 0.5182 (mtp) cc_final: 0.4793 (mtt) REVERT: B 987 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7525 (mm-30) REVERT: B 1012 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8215 (t) REVERT: B 1203 VAL cc_start: 0.7023 (m) cc_final: 0.6818 (t) REVERT: C 5 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.5197 (p90) REVERT: C 28 LYS cc_start: 0.8394 (ptpt) cc_final: 0.7827 (ptmt) REVERT: C 355 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7031 (m-30) REVERT: D 63 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6277 (pttt) REVERT: D 81 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: G 58 LYS cc_start: 0.7471 (ttpp) cc_final: 0.6900 (ptmm) REVERT: G 79 ASP cc_start: 0.8130 (t0) cc_final: 0.7764 (t0) REVERT: F 2 ILE cc_start: 0.5985 (OUTLIER) cc_final: 0.5627 (mp) outliers start: 55 outliers final: 24 residues processed: 398 average time/residue: 1.3690 time to fit residues: 647.3830 Evaluate side-chains 380 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 344 time to evaluate : 3.204 ------------------------------------------------------------------------------- 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 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 1152 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain B residue 241 GLU 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 1012 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain C residue 5 PHE 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 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 111 THR Chi-restraints excluded: chain F residue 149 SER Chi-restraints excluded: chain F residue 263 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 11 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 271 optimal weight: 0.7980 chunk 297 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 347 optimal weight: 4.9990 chunk 250 optimal weight: 0.0470 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 642 ASN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.192772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128193 restraints weight = 32670.030| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.44 r_work: 0.3270 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30235 Z= 0.110 Angle : 0.513 10.970 40919 Z= 0.264 Chirality : 0.044 0.179 4642 Planarity : 0.004 0.055 5262 Dihedral : 4.222 26.091 4034 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.39 % Allowed : 17.00 % Favored : 81.61 % 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: 0.38 (0.14), residues: 3683 helix: 1.18 (0.14), residues: 1381 sheet: -0.25 (0.22), residues: 527 loop : -0.25 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 466 HIS 0.005 0.001 HIS C 315 PHE 0.024 0.001 PHE A 918 TYR 0.011 0.001 TYR A 908 ARG 0.006 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 1259) hydrogen bonds : angle 4.59521 ( 3468) metal coordination : bond 0.00460 ( 16) metal coordination : angle 3.13092 ( 21) covalent geometry : bond 0.00256 (30219) covalent geometry : angle 0.50816 (40898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28796.82 seconds wall clock time: 495 minutes 30.82 seconds (29730.82 seconds total)