Starting phenix.real_space_refine on Fri Jun 20 21:36:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8him_34821/06_2025/8him_34821.cif Found real_map, /net/cci-nas-00/data/ceres_data/8him_34821/06_2025/8him_34821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8him_34821/06_2025/8him_34821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8him_34821/06_2025/8him_34821.map" model { file = "/net/cci-nas-00/data/ceres_data/8him_34821/06_2025/8him_34821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8him_34821/06_2025/8him_34821.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 63 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 14907 2.51 5 N 4189 2.21 5 O 4641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23948 Number of models: 1 Model: "" Number of chains: 18 Chain: "T" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 529 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "N" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 539 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "P" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 239 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 6640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6640 Classifications: {'peptide': 848} Link IDs: {'PTRANS': 27, 'TRANS': 820} Chain breaks: 3 Chain: "C" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 1 Chain: "F" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 507 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "K" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 890 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "H" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "I" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 787 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "E" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1706 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain: "B" Number of atoms: 7694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7694 Classifications: {'peptide': 971} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 36, 'TRANS': 934} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6411 SG CYS A 989 128.830 61.009 74.922 1.00131.65 S ATOM 6518 SG CYS A1004 127.128 61.695 78.578 1.00125.74 S ATOM 8652 SG CYS C 90 9.537 90.446 48.460 1.00 74.39 S ATOM 8671 SG CYS C 93 9.634 86.372 50.269 1.00 97.12 S ATOM 8710 SG CYS C 99 8.020 86.719 46.406 1.00 65.02 S ATOM 8736 SG CYS C 102 11.425 87.508 47.370 1.00 60.53 S ATOM 10918 SG CYS J 7 42.506 83.503 38.934 1.00 19.02 S ATOM 10942 SG CYS J 10 40.716 86.503 37.027 1.00 20.13 S ATOM 11208 SG CYS J 44 45.023 86.205 37.500 1.00 22.75 S ATOM 11214 SG CYS J 45 42.706 84.312 34.980 1.00 22.24 S ATOM 12306 SG CYS L 12 29.095 43.429 56.574 1.00 65.81 S ATOM 12324 SG CYS L 15 27.588 41.693 53.802 1.00 71.88 S ATOM 12426 SG CYS L 29 26.637 40.525 57.600 1.00 74.02 S ATOM 12452 SG CYS L 32 30.155 39.384 54.574 1.00 75.69 S ATOM 13795 SG CYS I 7 120.429 30.427 74.025 1.00112.85 S ATOM 13980 SG CYS I 29 118.227 30.994 78.250 1.00122.56 S ATOM 14005 SG CYS I 32 120.449 28.349 77.137 1.00125.28 S Time building chain proxies: 12.90, per 1000 atoms: 0.54 Number of scatterers: 23948 At special positions: 0 Unit cell: (146.73, 158.775, 137.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 141 16.00 P 63 15.00 Mg 1 11.99 O 4641 8.00 N 4189 7.00 C 14907 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: 5.43 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A 938 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 940 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 989 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1004 " pdb=" ZN C 400 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 102 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 99 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 93 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 90 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " Number of angles added : 20 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5364 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 34 sheets defined 35.3% alpha, 19.1% beta 20 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 7.65 Creating SS restraints... Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 359 through 369 removed outlier: 3.566A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 442 through 447 removed outlier: 3.569A pdb=" N LEU A 446 " --> pdb=" O MET A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 Processing helix chain 'A' and resid 492 through 505 removed outlier: 3.665A pdb=" N GLN A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 576 through 591 Processing helix chain 'A' and resid 595 through 613 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 620 through 624 Processing helix chain 'A' and resid 627 through 650 removed outlier: 5.466A pdb=" N SER A 643 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Proline residue: A 644 - end of helix removed outlier: 3.614A pdb=" N SER A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 675 removed outlier: 3.611A pdb=" N ASN A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 683 removed outlier: 3.579A pdb=" N ARG A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN A 682 " --> pdb=" O TYR A 678 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 683' Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.944A pdb=" N LYS A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 729 removed outlier: 4.039A pdb=" N VAL A 718 " --> pdb=" O THR A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 771 removed outlier: 3.534A pdb=" N ALA A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 787 removed outlier: 3.561A pdb=" N LYS A 780 " --> pdb=" O GLY A 776 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 847 Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 863 removed outlier: 3.658A pdb=" N TRP A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 874 No H-bonds generated for 'chain 'A' and resid 872 through 874' Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 891 through 904 removed outlier: 3.586A pdb=" N SER A 895 " --> pdb=" O CYS A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 942 through 949 removed outlier: 3.939A pdb=" N LEU A 946 " --> pdb=" O ASN A 942 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 947 " --> pdb=" O LYS A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 970 removed outlier: 3.606A pdb=" N ILE A 956 " --> pdb=" O SER A 952 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA A 963 " --> pdb=" O ARG A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 979 removed outlier: 4.129A pdb=" N PHE A 978 " --> pdb=" O ALA A 975 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 979 " --> pdb=" O GLU A 976 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 975 through 979' Processing helix chain 'A' and resid 1017 through 1027 Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 3.536A pdb=" N VAL A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A1033 " --> pdb=" O TYR A1029 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A1034 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 removed outlier: 3.916A pdb=" N ARG A1089 " --> pdb=" O GLY A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1120 through 1140 removed outlier: 3.664A pdb=" N ALA A1134 " --> pdb=" O GLN A1130 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A1139 " --> pdb=" O SER A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1156 removed outlier: 4.086A pdb=" N ILE A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1176 removed outlier: 3.579A pdb=" N ALA A1171 " --> pdb=" O GLY A1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.721A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 276 through 294 removed outlier: 3.948A pdb=" N VAL C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 83 removed outlier: 3.520A pdb=" N ARG F 72 " --> pdb=" O TYR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 37 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.723A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.658A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.728A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'E' and resid 31 through 51 Processing helix chain 'E' and resid 63 through 71 Processing helix chain 'E' and resid 104 through 119 removed outlier: 4.077A pdb=" N ILE E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU E 119 " --> pdb=" O ILE E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 139 removed outlier: 4.347A pdb=" N LYS E 138 " --> pdb=" O ASP E 134 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 184 removed outlier: 3.832A pdb=" N GLN E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 204 removed outlier: 3.523A pdb=" N ARG E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.558A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 removed outlier: 3.882A pdb=" N SER B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 300 through 315 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 360 through 380 Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 398 through 428 removed outlier: 3.586A pdb=" N ARG B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B 421 " --> pdb=" O THR B 417 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N HIS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 4.124A pdb=" N TYR B 438 " --> pdb=" O PRO B 434 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 434 through 439' Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.682A pdb=" N THR B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 486 removed outlier: 3.633A pdb=" N SER B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.679A pdb=" N TRP B 510 " --> pdb=" O PRO B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 removed outlier: 4.075A pdb=" N PHE B 549 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP B 550 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 removed outlier: 3.611A pdb=" N PHE B 586 " --> pdb=" O ASP B 582 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ALA B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 removed outlier: 4.852A pdb=" N HIS B 634 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 635 " --> pdb=" O ASN B 632 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 636 " --> pdb=" O LEU B 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 631 through 636' Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.748A pdb=" N GLU B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 660 through 664' Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.519A pdb=" N LEU B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 702 through 706 removed outlier: 4.024A pdb=" N ASP B 706 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 717 Processing helix chain 'B' and resid 729 through 733 removed outlier: 3.561A pdb=" N ILE B 732 " --> pdb=" O ASN B 729 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 733 " --> pdb=" O PRO B 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 729 through 733' Processing helix chain 'B' and resid 751 through 758 Processing helix chain 'B' and resid 788 through 793 Processing helix chain 'B' and resid 925 through 929 Processing helix chain 'B' and resid 943 through 945 No H-bonds generated for 'chain 'B' and resid 943 through 945' Processing helix chain 'B' and resid 946 through 951 removed outlier: 3.637A pdb=" N ARG B 950 " --> pdb=" O ALA B 946 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN B 951 " --> pdb=" O PHE B 947 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 946 through 951' Processing helix chain 'B' and resid 953 through 967 removed outlier: 3.640A pdb=" N GLY B 964 " --> pdb=" O ALA B 960 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS B 967 " --> pdb=" O LYS B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1004 Processing helix chain 'B' and resid 1040 through 1044 Processing sheet with id=AA1, first strand: chain 'B' and resid 1046 through 1048 removed outlier: 3.675A pdb=" N SER A 323 " --> pdb=" O ARG B1048 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 322 " --> pdb=" O TYR A 459 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 354 removed outlier: 6.361A pdb=" N ARG A 403 " --> pdb=" O CYS A 372 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N CYS A 372 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 531 removed outlier: 5.820A pdb=" N VAL A 529 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS H 94 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS A 531 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 529 through 531 removed outlier: 5.820A pdb=" N VAL A 529 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS H 94 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS A 531 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR H 33 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL H 14 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR H 59 " --> pdb=" O ARG H 144 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG H 144 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 554 through 556 removed outlier: 6.640A pdb=" N GLY A 563 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 703 through 704 Processing sheet with id=AA8, first strand: chain 'A' and resid 789 through 791 removed outlier: 6.277A pdb=" N ASN A 799 " --> pdb=" O ILE A 805 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE A 805 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1043 through 1049 removed outlier: 3.844A pdb=" N ASN A1047 " --> pdb=" O ASP A1073 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 906 through 907 removed outlier: 7.325A pdb=" N VAL A 906 " --> pdb=" O ILE A1037 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 982 through 986 removed outlier: 4.098A pdb=" N GLU A 914 " --> pdb=" O HIS A 940 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 915 " --> pdb=" O ASN I 46 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR I 44 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N TYR A 919 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS I 42 " --> pdb=" O TYR A 919 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1229 through 1230 Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 18 removed outlier: 5.577A pdb=" N VAL C 12 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG C 27 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE C 14 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU C 25 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 270 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR C 184 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 18 removed outlier: 5.577A pdb=" N VAL C 12 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG C 27 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE C 14 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU C 25 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU C 190 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.470A pdb=" N GLU C 161 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN C 58 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS C 163 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG C 169 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE C 50 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY C 171 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL C 48 " --> pdb=" O GLY C 171 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AB8, first strand: chain 'C' and resid 220 through 223 Processing sheet with id=AB9, first strand: chain 'K' and resid 19 through 20 Processing sheet with id=AC1, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.330A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N GLY B 877 " --> pdb=" O VAL B 901 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N VAL B 901 " --> pdb=" O GLY B 877 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL B 879 " --> pdb=" O ARG B 899 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG B 899 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 881 " --> pdb=" O SER B 897 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.330A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 14 through 16 Processing sheet with id=AC4, first strand: chain 'I' and resid 84 through 89 Processing sheet with id=AC5, first strand: chain 'E' and resid 94 through 96 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.612A pdb=" N ARG E 169 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS E 212 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR E 223 " --> pdb=" O TYR E 215 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 68 through 70 removed outlier: 5.476A pdb=" N VAL B 89 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLU B 133 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE B 91 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP B 131 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU B 93 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 129 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG B 125 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ALA B 124 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG B 169 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET B 126 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC9, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AD1, first strand: chain 'B' and resid 394 through 397 removed outlier: 6.639A pdb=" N ALA B 215 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 225 through 226 removed outlier: 3.639A pdb=" N ILE B 245 " --> pdb=" O TYR B 267 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AD4, first strand: chain 'B' and resid 535 through 536 removed outlier: 3.518A pdb=" N CYS B 685 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 575 through 580 removed outlier: 5.543A pdb=" N TRP B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 572 " --> pdb=" O TRP B 576 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 578 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS B 569 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE B 616 " --> pdb=" O LYS B 569 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU B 571 " --> pdb=" O ILE B 616 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1011 through 1012 removed outlier: 7.080A pdb=" N ILE B 784 " --> pdb=" O GLY B 921 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE B 923 " --> pdb=" O ILE B 784 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET B 786 " --> pdb=" O ILE B 923 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ILE B 940 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE B 769 " --> pdb=" O ILE B 940 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE B 942 " --> pdb=" O ILE B 769 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA B 771 " --> pdb=" O ILE B 942 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE B1028 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 855 through 857 removed outlier: 3.580A pdb=" N ILE B 857 " --> pdb=" O VAL B 869 " (cutoff:3.500A) 878 hydrogen bonds defined for protein. 2436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 10.04 Time building geometry restraints manager: 6.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4701 1.32 - 1.45: 5971 1.45 - 1.57: 13493 1.57 - 1.69: 123 1.69 - 1.82: 217 Bond restraints: 24505 Sorted by residual: bond pdb=" N PRO A1053 " pdb=" CD PRO A1053 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.94e+01 bond pdb=" C SER B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.333 1.363 -0.029 7.80e-03 1.64e+04 1.42e+01 bond pdb=" C PHE B 110 " pdb=" N LEU B 111 " ideal model delta sigma weight residual 1.327 1.267 0.060 1.71e-02 3.42e+03 1.22e+01 bond pdb=" N VAL B1014 " pdb=" CA VAL B1014 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N VAL A1023 " pdb=" CA VAL A1023 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.57e+00 ... (remaining 24500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 32084 2.31 - 4.62: 1098 4.62 - 6.93: 106 6.93 - 9.24: 34 9.24 - 11.55: 6 Bond angle restraints: 33328 Sorted by residual: angle pdb=" N THR B 427 " pdb=" CA THR B 427 " pdb=" C THR B 427 " ideal model delta sigma weight residual 111.71 101.80 9.91 1.15e+00 7.56e-01 7.43e+01 angle pdb=" N VAL A 574 " pdb=" CA VAL A 574 " pdb=" C VAL A 574 " ideal model delta sigma weight residual 113.71 105.89 7.82 9.50e-01 1.11e+00 6.78e+01 angle pdb=" N ARG B 490 " pdb=" CA ARG B 490 " pdb=" C ARG B 490 " ideal model delta sigma weight residual 108.76 120.31 -11.55 1.69e+00 3.50e-01 4.67e+01 angle pdb=" N CYS A 886 " pdb=" CA CYS A 886 " pdb=" CB CYS A 886 " ideal model delta sigma weight residual 112.28 102.63 9.65 1.49e+00 4.50e-01 4.19e+01 angle pdb=" N THR A 898 " pdb=" CA THR A 898 " pdb=" C THR A 898 " ideal model delta sigma weight residual 111.14 104.34 6.80 1.08e+00 8.57e-01 3.96e+01 ... (remaining 33323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 14200 35.81 - 71.63: 542 71.63 - 107.44: 31 107.44 - 143.25: 0 143.25 - 179.06: 3 Dihedral angle restraints: 14776 sinusoidal: 6493 harmonic: 8283 Sorted by residual: dihedral pdb=" CA GLU E 57 " pdb=" C GLU E 57 " pdb=" N ASP E 58 " pdb=" CA ASP E 58 " ideal model delta harmonic sigma weight residual 180.00 150.68 29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" C CYS A 884 " pdb=" N CYS A 884 " pdb=" CA CYS A 884 " pdb=" CB CYS A 884 " ideal model delta harmonic sigma weight residual -122.60 -137.15 14.55 0 2.50e+00 1.60e-01 3.39e+01 dihedral pdb=" CA GLY H 105 " pdb=" C GLY H 105 " pdb=" N GLN H 106 " pdb=" CA GLN H 106 " ideal model delta harmonic sigma weight residual -180.00 -151.95 -28.05 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 14773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 3529 0.117 - 0.234: 209 0.234 - 0.351: 11 0.351 - 0.467: 1 0.467 - 0.584: 2 Chirality restraints: 3752 Sorted by residual: chirality pdb=" CA CYS A 884 " pdb=" N CYS A 884 " pdb=" C CYS A 884 " pdb=" CB CYS A 884 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.54e+00 chirality pdb=" P DT T 12 " pdb=" OP1 DT T 12 " pdb=" OP2 DT T 12 " pdb=" O5' DT T 12 " both_signs ideal model delta sigma weight residual True 2.35 -2.82 -0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CB ILE H 100 " pdb=" CA ILE H 100 " pdb=" CG1 ILE H 100 " pdb=" CG2 ILE H 100 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 3749 not shown) Planarity restraints: 4062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 295 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C VAL C 295 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL C 295 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG C 296 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 478 " -0.051 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO B 479 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 848 " -0.048 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO A 849 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 849 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 849 " -0.040 5.00e-02 4.00e+02 ... (remaining 4059 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1365 2.72 - 3.26: 21617 3.26 - 3.81: 38332 3.81 - 4.35: 48012 4.35 - 4.90: 79958 Nonbonded interactions: 189284 Sorted by model distance: nonbonded pdb=" OD1 ASP A 449 " pdb="MG MG A3000 " model vdw 2.173 2.170 nonbonded pdb=" OD1 ASP A 451 " pdb="MG MG A3000 " model vdw 2.185 2.170 nonbonded pdb=" N GLY I 82 " pdb="ZN ZN I 201 " model vdw 2.223 2.310 nonbonded pdb=" O GLY B 430 " pdb=" N LEU B 432 " model vdw 2.291 3.120 nonbonded pdb=" O THR A1056 " pdb=" OG1 THR A1057 " model vdw 2.295 3.040 ... (remaining 189279 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 61.060 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 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:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.010 0.488 24524 Z= 0.413 Angle : 1.079 51.092 33348 Z= 0.591 Chirality : 0.062 0.584 3752 Planarity : 0.007 0.077 4062 Dihedral : 17.535 179.063 9412 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.66 % Favored : 94.23 % Rotamer: Outliers : 0.60 % Allowed : 6.99 % Favored : 92.42 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % 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: -3.49 (0.13), residues: 2809 helix: -2.44 (0.13), residues: 876 sheet: -1.51 (0.21), residues: 524 loop : -2.53 (0.13), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP F 126 HIS 0.010 0.002 HIS H 42 PHE 0.040 0.003 PHE B 213 TYR 0.018 0.003 TYR K 87 ARG 0.009 0.001 ARG C 157 Details of bonding type rmsd hydrogen bonds : bond 0.17965 ( 907) hydrogen bonds : angle 7.57562 ( 2530) metal coordination : bond 0.23383 ( 19) metal coordination : angle 17.21836 ( 20) covalent geometry : bond 0.00793 (24505) covalent geometry : angle 0.99382 (33328) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 347 time to evaluate : 2.573 Fit side-chains revert: symmetry clash REVERT: A 961 GLU cc_start: 0.7949 (tp30) cc_final: 0.7649 (tp30) REVERT: A 981 MET cc_start: 0.6954 (ptm) cc_final: 0.6680 (ptm) REVERT: A 1066 ARG cc_start: 0.4407 (mtt90) cc_final: 0.4076 (mpp80) REVERT: F 103 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7901 (mtpt) REVERT: F 106 ARG cc_start: 0.7337 (tpp-160) cc_final: 0.7000 (tpp-160) REVERT: F 130 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8202 (mt-10) REVERT: H 31 GLU cc_start: 0.6735 (mm-30) cc_final: 0.6412 (tp30) REVERT: H 39 MET cc_start: 0.4220 (mmt) cc_final: 0.3919 (mtt) REVERT: H 111 GLU cc_start: 0.5863 (pt0) cc_final: 0.5316 (pt0) REVERT: I 17 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7201 (ttpp) REVERT: I 100 PHE cc_start: 0.5066 (m-10) cc_final: 0.4520 (t80) REVERT: E 42 ASN cc_start: 0.8055 (t0) cc_final: 0.7378 (t0) REVERT: E 44 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7560 (mt) REVERT: E 130 ASN cc_start: 0.6516 (p0) cc_final: 0.6237 (p0) REVERT: B 243 ARG cc_start: 0.6948 (mtt180) cc_final: 0.6711 (mtm180) REVERT: B 603 MET cc_start: 0.8611 (ttp) cc_final: 0.8272 (ttp) REVERT: B 686 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7568 (mm-30) REVERT: B 752 MET cc_start: 0.8725 (tpt) cc_final: 0.8456 (tpp) REVERT: B 834 ARG cc_start: 0.6685 (ttt90) cc_final: 0.6217 (ttp80) REVERT: B 950 ARG cc_start: 0.7715 (mmt90) cc_final: 0.7229 (mmt90) outliers start: 15 outliers final: 2 residues processed: 357 average time/residue: 1.7849 time to fit residues: 712.1788 Evaluate side-chains 241 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 237 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 686 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 223 optimal weight: 0.0570 chunk 86 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS A 401 HIS A 421 HIS A 424 GLN A 431 HIS A 611 HIS A 693 ASN A 781 ASN A 942 ASN A1011 ASN A1114 GLN K 29 ASN H 46 ASN H 94 HIS I 31 ASN E 84 HIS B 59 GLN B 163 GLN B 216 GLN B 323 HIS B 506 HIS B 596 GLN B 684 HIS B 705 HIS B 714 GLN B 721 GLN B 745 GLN B 758 GLN B 764 ASN B 767 ASN B 780 GLN B 824 GLN B 892 ASN B 970 GLN B1000 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.138801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.089323 restraints weight = 38649.690| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.37 r_work: 0.3039 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24524 Z= 0.147 Angle : 0.645 16.654 33348 Z= 0.338 Chirality : 0.043 0.219 3752 Planarity : 0.005 0.056 4062 Dihedral : 16.629 178.713 3833 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 2.46 % Allowed : 11.91 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.15 (0.14), residues: 2809 helix: -0.57 (0.17), residues: 887 sheet: -1.16 (0.22), residues: 511 loop : -2.11 (0.14), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 113 HIS 0.006 0.001 HIS H 42 PHE 0.027 0.002 PHE A 411 TYR 0.014 0.001 TYR B 235 ARG 0.007 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.05350 ( 907) hydrogen bonds : angle 5.12099 ( 2530) metal coordination : bond 0.01156 ( 19) metal coordination : angle 7.16206 ( 20) covalent geometry : bond 0.00333 (24505) covalent geometry : angle 0.62083 (33328) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 262 time to evaluate : 2.447 Fit side-chains revert: symmetry clash REVERT: A 592 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5775 (mmmt) REVERT: A 961 GLU cc_start: 0.8226 (tp30) cc_final: 0.7881 (tp30) REVERT: C 149 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.5801 (mpt180) REVERT: F 59 ARG cc_start: 0.5887 (mtm-85) cc_final: 0.4958 (pmt170) REVERT: F 99 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7622 (mm-30) REVERT: F 103 LYS cc_start: 0.8365 (mmmt) cc_final: 0.8040 (mtpt) REVERT: F 115 ARG cc_start: 0.7597 (mtt90) cc_final: 0.7334 (ttm-80) REVERT: K 22 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7947 (tm-30) REVERT: K 23 ARG cc_start: 0.8055 (tmm-80) cc_final: 0.7654 (ttp80) REVERT: H 31 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6211 (tp30) REVERT: H 39 MET cc_start: 0.4387 (mmt) cc_final: 0.3451 (mtt) REVERT: H 111 GLU cc_start: 0.5834 (pt0) cc_final: 0.5551 (pt0) REVERT: H 112 MET cc_start: 0.5660 (ttp) cc_final: 0.5438 (ttm) REVERT: H 113 TYR cc_start: 0.7175 (m-80) cc_final: 0.6830 (m-80) REVERT: I 100 PHE cc_start: 0.4740 (m-10) cc_final: 0.4154 (t80) REVERT: E 42 ASN cc_start: 0.7921 (t0) cc_final: 0.7291 (t0) REVERT: E 44 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7513 (mt) REVERT: E 130 ASN cc_start: 0.6550 (p0) cc_final: 0.6324 (p0) REVERT: B 71 GLU cc_start: 0.5509 (mm-30) cc_final: 0.5228 (mm-30) REVERT: B 88 THR cc_start: 0.7259 (t) cc_final: 0.7044 (m) REVERT: B 163 GLN cc_start: 0.6950 (tp40) cc_final: 0.6685 (tp40) REVERT: B 227 SER cc_start: 0.8364 (m) cc_final: 0.8008 (p) REVERT: B 243 ARG cc_start: 0.7698 (mtt180) cc_final: 0.7339 (mtm180) REVERT: B 333 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: B 418 MET cc_start: 0.7845 (ttm) cc_final: 0.7080 (tpt) REVERT: B 603 MET cc_start: 0.8964 (ttp) cc_final: 0.8622 (ttp) REVERT: B 686 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: B 752 MET cc_start: 0.9126 (tpt) cc_final: 0.8908 (tpp) REVERT: B 834 ARG cc_start: 0.6705 (ttt90) cc_final: 0.5949 (ttp80) outliers start: 62 outliers final: 22 residues processed: 299 average time/residue: 1.5233 time to fit residues: 516.9373 Evaluate side-chains 250 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 TRP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 333 GLN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 867 HIS Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 158 optimal weight: 5.9990 chunk 183 optimal weight: 0.5980 chunk 283 optimal weight: 4.9990 chunk 199 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 125 optimal weight: 0.4980 chunk 267 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1147 HIS H 46 ASN H 129 HIS I 34 HIS E 34 HIS B 824 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.138190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088583 restraints weight = 38307.170| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.04 r_work: 0.3058 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24524 Z= 0.154 Angle : 0.619 14.381 33348 Z= 0.323 Chirality : 0.043 0.208 3752 Planarity : 0.005 0.082 4062 Dihedral : 16.419 178.866 3831 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.62 % Allowed : 14.25 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.15), residues: 2809 helix: 0.18 (0.18), residues: 892 sheet: -0.93 (0.23), residues: 503 loop : -1.80 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 113 HIS 0.006 0.001 HIS H 42 PHE 0.028 0.002 PHE A 411 TYR 0.015 0.001 TYR K 87 ARG 0.008 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.04998 ( 907) hydrogen bonds : angle 4.80527 ( 2530) metal coordination : bond 0.01086 ( 19) metal coordination : angle 6.71702 ( 20) covalent geometry : bond 0.00361 (24505) covalent geometry : angle 0.59678 (33328) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 249 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7782 (p90) REVERT: A 941 LEU cc_start: 0.7625 (mm) cc_final: 0.7336 (mm) REVERT: A 961 GLU cc_start: 0.8203 (tp30) cc_final: 0.7822 (tp30) REVERT: A 1066 ARG cc_start: 0.4550 (mtt90) cc_final: 0.3993 (mpp80) REVERT: F 59 ARG cc_start: 0.6027 (mtm-85) cc_final: 0.4944 (pmt170) REVERT: F 99 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7643 (mm-30) REVERT: F 103 LYS cc_start: 0.8343 (mmmt) cc_final: 0.8112 (mmmm) REVERT: F 104 GLU cc_start: 0.7229 (mt-10) cc_final: 0.7012 (mt-10) REVERT: F 115 ARG cc_start: 0.7606 (mtt90) cc_final: 0.7378 (ttm-80) REVERT: K 22 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7962 (tm-30) REVERT: K 23 ARG cc_start: 0.8068 (tmm-80) cc_final: 0.7842 (ttm170) REVERT: H 8 PHE cc_start: 0.7757 (t80) cc_final: 0.7313 (t80) REVERT: H 29 ARG cc_start: 0.6809 (ttm-80) cc_final: 0.6567 (ttm170) REVERT: H 31 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6241 (tp30) REVERT: H 39 MET cc_start: 0.4195 (mmt) cc_final: 0.3336 (mtt) REVERT: H 111 GLU cc_start: 0.5717 (pt0) cc_final: 0.5329 (pt0) REVERT: H 112 MET cc_start: 0.5520 (ttp) cc_final: 0.5277 (ttp) REVERT: H 113 TYR cc_start: 0.7134 (m-80) cc_final: 0.6721 (m-80) REVERT: I 17 LYS cc_start: 0.7459 (ttmt) cc_final: 0.6991 (tppt) REVERT: I 100 PHE cc_start: 0.4592 (m-80) cc_final: 0.4209 (t80) REVERT: E 42 ASN cc_start: 0.7921 (t0) cc_final: 0.7357 (t0) REVERT: B 71 GLU cc_start: 0.5487 (mm-30) cc_final: 0.5217 (mm-30) REVERT: B 88 THR cc_start: 0.7342 (t) cc_final: 0.7112 (m) REVERT: B 163 GLN cc_start: 0.6769 (tp40) cc_final: 0.6464 (tp40) REVERT: B 227 SER cc_start: 0.8326 (m) cc_final: 0.8053 (p) REVERT: B 603 MET cc_start: 0.8929 (ttp) cc_final: 0.8624 (ttp) REVERT: B 686 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: B 752 MET cc_start: 0.9167 (tpt) cc_final: 0.8936 (tpp) REVERT: B 834 ARG cc_start: 0.6607 (ttt90) cc_final: 0.5919 (ttp80) REVERT: B 860 CYS cc_start: 0.7518 (t) cc_final: 0.6937 (p) outliers start: 66 outliers final: 27 residues processed: 288 average time/residue: 1.5031 time to fit residues: 491.1342 Evaluate side-chains 251 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 TRP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 867 HIS Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.6838 > 50: distance: 36 - 75: 28.979 distance: 39 - 72: 19.369 distance: 56 - 63: 16.407 distance: 63 - 64: 16.289 distance: 64 - 65: 16.198 distance: 64 - 67: 16.928 distance: 65 - 66: 25.640 distance: 65 - 72: 20.268 distance: 67 - 68: 8.130 distance: 69 - 70: 10.230 distance: 69 - 71: 17.445 distance: 72 - 73: 13.340 distance: 73 - 74: 34.052 distance: 73 - 76: 13.836 distance: 74 - 75: 19.412 distance: 74 - 80: 27.417 distance: 76 - 77: 19.393 distance: 77 - 78: 11.575 distance: 77 - 79: 20.641 distance: 80 - 81: 29.874 distance: 81 - 82: 21.836 distance: 81 - 84: 10.107 distance: 82 - 83: 25.513 distance: 82 - 87: 19.931 distance: 84 - 85: 13.841 distance: 84 - 86: 15.644 distance: 87 - 88: 14.150 distance: 88 - 89: 39.030 distance: 88 - 91: 13.477 distance: 89 - 90: 5.758 distance: 89 - 98: 35.286 distance: 91 - 92: 20.589 distance: 92 - 93: 4.990 distance: 92 - 94: 13.994 distance: 93 - 95: 12.723 distance: 94 - 96: 13.502 distance: 95 - 97: 7.526 distance: 96 - 97: 7.133 distance: 98 - 99: 17.176 distance: 99 - 100: 20.869 distance: 99 - 102: 32.804 distance: 100 - 101: 4.758 distance: 100 - 106: 19.319 distance: 101 - 137: 47.170 distance: 102 - 103: 22.380 distance: 103 - 104: 29.517 distance: 103 - 105: 41.819 distance: 106 - 107: 10.304 distance: 106 - 112: 4.928 distance: 107 - 108: 11.377 distance: 107 - 110: 31.262 distance: 108 - 109: 13.336 distance: 108 - 113: 25.417 distance: 109 - 142: 34.106 distance: 111 - 112: 28.679 distance: 113 - 114: 14.535 distance: 114 - 115: 10.858 distance: 114 - 117: 13.168 distance: 115 - 116: 8.192 distance: 115 - 127: 20.345 distance: 116 - 153: 18.078 distance: 117 - 118: 12.809 distance: 118 - 119: 9.381 distance: 118 - 120: 4.994 distance: 119 - 121: 8.566 distance: 120 - 122: 11.619 distance: 120 - 123: 8.541 distance: 121 - 122: 9.676 distance: 122 - 124: 10.436 distance: 123 - 125: 11.490 distance: 124 - 126: 7.095 distance: 125 - 126: 11.305 distance: 127 - 128: 22.030 distance: 128 - 129: 15.045 distance: 128 - 131: 14.480 distance: 129 - 130: 7.333 distance: 129 - 137: 22.130 distance: 130 - 161: 32.865 distance: 131 - 132: 11.716 distance: 132 - 133: 18.434 distance: 132 - 134: 15.674 distance: 133 - 135: 12.570 distance: 134 - 136: 25.153 distance: 135 - 136: 19.693 distance: 137 - 138: 11.979 distance: 138 - 139: 27.525 distance: 138 - 141: 40.575 distance: 139 - 140: 5.239 distance: 139 - 142: 17.211 distance: 142 - 143: 19.735 distance: 143 - 146: 25.298 distance: 144 - 145: 12.347 distance: 144 - 153: 22.058 distance: 147 - 148: 16.841 distance: 148 - 149: 12.443 distance: 149 - 150: 7.012 distance: 150 - 151: 5.808 distance: 150 - 152: 8.174