Starting phenix.real_space_refine on Fri Jul 19 12:47:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eij_28158/07_2024/8eij_28158_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eij_28158/07_2024/8eij_28158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eij_28158/07_2024/8eij_28158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eij_28158/07_2024/8eij_28158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eij_28158/07_2024/8eij_28158_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eij_28158/07_2024/8eij_28158_neut.cif" } resolution = 3.34 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= 0.023 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: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 67 5.16 5 C 4981 2.51 5 N 1358 2.21 5 O 1401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 697": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7813 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3290 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3374 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1091 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 141} Chain breaks: 4 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 135 SG CYS A 435 26.424 27.415 32.413 1.00178.98 S ATOM 155 SG CYS A 438 25.215 31.209 31.853 1.00187.35 S ATOM 285 SG CYS A 455 28.546 30.007 30.785 1.00177.92 S ATOM 307 SG CYS A 458 27.548 30.039 34.660 1.00170.71 S ATOM 486 SG CYS A 478 22.876 28.790 44.559 1.00175.25 S ATOM 506 SG CYS A 481 22.882 30.984 41.410 1.00178.78 S ATOM 634 SG CYS A 500 20.007 31.376 43.847 1.00186.48 S ATOM 656 SG CYS A 503 20.370 28.301 41.694 1.00188.66 S ATOM 562 SG CYS A 490 22.405 22.242 56.090 1.00184.01 S ATOM 594 SG CYS A 495 26.004 21.481 55.050 1.00179.16 S ATOM 802 SG CYS A 524 23.099 20.593 52.676 1.00185.18 S ATOM 828 SG CYS A 527 23.780 18.623 55.673 1.00186.73 S ATOM 3452 SG CYS B 435 62.529 63.225 118.249 1.00149.11 S ATOM 3472 SG CYS B 438 60.666 66.486 118.207 1.00153.62 S ATOM 3599 SG CYS B 455 58.974 63.401 119.750 1.00139.43 S ATOM 3621 SG CYS B 458 59.431 63.631 116.053 1.00135.76 S ATOM 3803 SG CYS B 478 63.011 64.741 105.525 1.00146.43 S ATOM 3823 SG CYS B 481 61.056 66.889 107.659 1.00161.00 S ATOM 3961 SG CYS B 500 63.713 68.585 105.341 1.00161.15 S ATOM 3983 SG CYS B 503 64.726 66.837 108.382 1.00155.41 S ATOM 3888 SG CYS B 490 71.769 59.476 96.562 1.00153.98 S ATOM 3921 SG CYS B 495 70.391 56.345 98.327 1.00159.43 S ATOM 4122 SG CYS B 524 72.350 58.893 100.342 1.00153.71 S ATOM 4148 SG CYS B 527 74.107 56.682 98.006 1.00159.17 S Time building chain proxies: 4.95, per 1000 atoms: 0.63 Number of scatterers: 7813 At special positions: 0 Unit cell: (91.3, 84.7, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 67 16.00 O 1401 8.00 N 1358 7.00 C 4981 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 - 3.50 Amino acid : False - 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: 2.47 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 435 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 455 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 458 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 438 " pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 503 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 481 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 500 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 478 " pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 527 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 495 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 524 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 490 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 458 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 438 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 455 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 435 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 481 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 503 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 478 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 500 " pdb=" ZN B 904 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 524 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 527 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 495 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 490 " Number of angles added : 36 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1882 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 7 sheets defined 38.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.807A pdb=" N MET A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 removed outlier: 3.854A pdb=" N ASP A 433 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 466 removed outlier: 3.619A pdb=" N ASP A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE A 462 " --> pdb=" O CYS A 458 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 removed outlier: 4.486A pdb=" N GLU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 507 " --> pdb=" O CYS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 519 removed outlier: 3.667A pdb=" N ALA A 516 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 518 " --> pdb=" O ALA A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 removed outlier: 4.375A pdb=" N GLN A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.514A pdb=" N ILE A 611 " --> pdb=" O CYS A 607 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 617 " --> pdb=" O VAL A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 631 removed outlier: 3.506A pdb=" N ASN A 630 " --> pdb=" O ASP A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 640 removed outlier: 4.135A pdb=" N ILE A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 669 No H-bonds generated for 'chain 'A' and resid 667 through 669' Processing helix chain 'A' and resid 670 through 683 removed outlier: 3.817A pdb=" N GLU A 674 " --> pdb=" O ARG A 670 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.943A pdb=" N LYS A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG A 708 " --> pdb=" O VAL A 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 703 through 708' Processing helix chain 'A' and resid 708 through 714 Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 755 through 759 Processing helix chain 'A' and resid 801 through 809 removed outlier: 3.523A pdb=" N LEU A 805 " --> pdb=" O TRP A 801 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU A 806 " --> pdb=" O CYS A 802 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG A 807 " --> pdb=" O THR A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 829 removed outlier: 3.738A pdb=" N LYS A 828 " --> pdb=" O GLY A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 843 removed outlier: 3.540A pdb=" N HIS A 841 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 842 " --> pdb=" O VAL A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 849 removed outlier: 3.659A pdb=" N LYS A 847 " --> pdb=" O ALA A 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 426 removed outlier: 4.316A pdb=" N MET B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 removed outlier: 3.891A pdb=" N GLY B 434 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 460 removed outlier: 3.526A pdb=" N ARG B 459 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 455 through 460' Processing helix chain 'B' and resid 461 through 466 removed outlier: 3.746A pdb=" N LEU B 465 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 461 through 466' Processing helix chain 'B' and resid 500 through 509 removed outlier: 4.577A pdb=" N LEU B 507 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 519 removed outlier: 4.087A pdb=" N GLU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 550 removed outlier: 3.599A pdb=" N ARG B 545 " --> pdb=" O ASP B 541 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B 550 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 595 Processing helix chain 'B' and resid 607 through 618 removed outlier: 3.887A pdb=" N HIS B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 631 Processing helix chain 'B' and resid 632 through 640 removed outlier: 3.658A pdb=" N ILE B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 669 Processing helix chain 'B' and resid 670 through 683 removed outlier: 3.501A pdb=" N GLU B 674 " --> pdb=" O ARG B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 715 Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 755 through 760 removed outlier: 3.951A pdb=" N LEU B 760 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 809 removed outlier: 3.588A pdb=" N ARG B 807 " --> pdb=" O THR B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 832 removed outlier: 3.566A pdb=" N ARG B 826 " --> pdb=" O GLY B 822 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 832 " --> pdb=" O LYS B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 844 Processing helix chain 'B' and resid 845 through 849 removed outlier: 3.538A pdb=" N TYR B 849 " --> pdb=" O LEU B 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 594 removed outlier: 3.652A pdb=" N LEU D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 640 Processing helix chain 'D' and resid 667 through 683 removed outlier: 4.299A pdb=" N LEU D 671 " --> pdb=" O GLY D 667 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU D 674 " --> pdb=" O ARG D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 715 Processing helix chain 'D' and resid 836 through 843 Processing helix chain 'D' and resid 844 through 848 removed outlier: 3.860A pdb=" N LYS D 847 " --> pdb=" O ALA D 844 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP D 848 " --> pdb=" O PRO D 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 844 through 848' Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA2, first strand: chain 'A' and resid 600 through 601 removed outlier: 6.140A pdb=" N LYS A 600 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU A 644 " --> pdb=" O ARG A 576 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL A 645 " --> pdb=" O MET A 695 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N GLU A 697 " --> pdb=" O VAL A 645 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 696 " --> pdb=" O TRP A 736 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 733 " --> pdb=" O ILE A 721 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 721 " --> pdb=" O ARG A 733 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 719 " --> pdb=" O PHE A 735 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 764 through 766 removed outlier: 3.813A pdb=" N VAL A 791 " --> pdb=" O ASP A 798 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 623 through 625 removed outlier: 8.945A pdb=" N LYS B 623 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR B 601 " --> pdb=" O LYS B 623 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL B 625 " --> pdb=" O TYR B 601 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA B 603 " --> pdb=" O VAL B 625 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE B 575 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL B 602 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 577 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N SER B 604 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N SER B 579 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG B 576 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ILE B 646 " --> pdb=" O ARG B 576 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B 578 " --> pdb=" O ILE B 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 695 through 699 removed outlier: 4.073A pdb=" N PHE B 696 " --> pdb=" O TRP B 736 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B 698 " --> pdb=" O TYR B 734 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 765 through 766 removed outlier: 4.073A pdb=" N ILE B 765 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 792 " --> pdb=" O ILE B 765 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 791 " --> pdb=" O ASP B 798 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 697 through 699 removed outlier: 3.697A pdb=" N ILE D 721 " --> pdb=" O ARG D 733 " (cutoff:3.500A) 189 hydrogen bonds defined for protein. 513 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: 1.96 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2554 1.34 - 1.46: 1868 1.46 - 1.58: 3484 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 7995 Sorted by residual: bond pdb=" C2 SAH A 901 " pdb=" N3 SAH A 901 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" C2 SAH B 901 " pdb=" N3 SAH B 901 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.34e+00 bond pdb=" CA HIS D 677 " pdb=" C HIS D 677 " ideal model delta sigma weight residual 1.524 1.489 0.034 1.27e-02 6.20e+03 7.30e+00 bond pdb=" C8 SAH A 901 " pdb=" N7 SAH A 901 " ideal model delta sigma weight residual 1.299 1.353 -0.054 2.00e-02 2.50e+03 7.18e+00 bond pdb=" C8 SAH B 901 " pdb=" N7 SAH B 901 " ideal model delta sigma weight residual 1.299 1.352 -0.053 2.00e-02 2.50e+03 7.14e+00 ... (remaining 7990 not shown) Histogram of bond angle deviations from ideal: 89.83 - 98.66: 2 98.66 - 107.49: 321 107.49 - 116.32: 4932 116.32 - 125.15: 5450 125.15 - 133.98: 147 Bond angle restraints: 10852 Sorted by residual: angle pdb=" CA GLU B 715 " pdb=" CB GLU B 715 " pdb=" CG GLU B 715 " ideal model delta sigma weight residual 114.10 124.02 -9.92 2.00e+00 2.50e-01 2.46e+01 angle pdb=" N ASP D 706 " pdb=" CA ASP D 706 " pdb=" C ASP D 706 " ideal model delta sigma weight residual 111.07 105.97 5.10 1.07e+00 8.73e-01 2.28e+01 angle pdb=" C ASN B 442 " pdb=" N PRO B 443 " pdb=" CA PRO B 443 " ideal model delta sigma weight residual 119.84 125.15 -5.31 1.25e+00 6.40e-01 1.80e+01 angle pdb=" CG SAH B 901 " pdb=" SD SAH B 901 " pdb=" C5' SAH B 901 " ideal model delta sigma weight residual 101.77 89.83 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C GLU B 715 " pdb=" CA GLU B 715 " pdb=" CB GLU B 715 " ideal model delta sigma weight residual 112.27 119.13 -6.86 1.75e+00 3.27e-01 1.54e+01 ... (remaining 10847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4104 17.94 - 35.87: 486 35.87 - 53.80: 95 53.80 - 71.74: 9 71.74 - 89.67: 4 Dihedral angle restraints: 4698 sinusoidal: 1771 harmonic: 2927 Sorted by residual: dihedral pdb=" CA ASN D 626 " pdb=" C ASN D 626 " pdb=" N ASP D 627 " pdb=" CA ASP D 627 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" C GLU B 715 " pdb=" N GLU B 715 " pdb=" CA GLU B 715 " pdb=" CB GLU B 715 " ideal model delta harmonic sigma weight residual -122.60 -131.92 9.32 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" CA GLU A 464 " pdb=" C GLU A 464 " pdb=" N LEU A 465 " pdb=" CA LEU A 465 " ideal model delta harmonic sigma weight residual 180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 4695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1041 0.063 - 0.126: 137 0.126 - 0.188: 3 0.188 - 0.251: 1 0.251 - 0.314: 1 Chirality restraints: 1183 Sorted by residual: chirality pdb=" CA ASN B 442 " pdb=" N ASN B 442 " pdb=" C ASN B 442 " pdb=" CB ASN B 442 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA GLU B 715 " pdb=" N GLU B 715 " pdb=" C GLU B 715 " pdb=" CB GLU B 715 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.23e-01 chirality pdb=" CA ASP D 706 " pdb=" N ASP D 706 " pdb=" C ASP D 706 " pdb=" CB ASP D 706 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 1180 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 441 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C LYS B 441 " -0.049 2.00e-02 2.50e+03 pdb=" O LYS B 441 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 442 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 640 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO D 641 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 641 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 641 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 705 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C GLY D 705 " -0.029 2.00e-02 2.50e+03 pdb=" O GLY D 705 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP D 706 " 0.010 2.00e-02 2.50e+03 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 331 2.72 - 3.26: 7711 3.26 - 3.81: 11605 3.81 - 4.35: 14144 4.35 - 4.90: 23743 Nonbonded interactions: 57534 Sorted by model distance: nonbonded pdb=" O ASN B 738 " pdb=" ND2 ASN B 738 " model vdw 2.172 2.520 nonbonded pdb=" OG SER B 491 " pdb=" O TRP B 522 " model vdw 2.227 2.440 nonbonded pdb=" OD1 ASP A 709 " pdb=" NH2 ARG A 712 " model vdw 2.260 2.520 nonbonded pdb=" O SER D 649 " pdb=" OG SER D 649 " model vdw 2.297 2.440 nonbonded pdb=" OE2 GLU B 605 " pdb=" O2' SAH B 901 " model vdw 2.300 2.440 ... (remaining 57529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 415 through 441 or (resid 442 and (name N or name CA or na \ me C or name O or name CB )) or resid 443 through 504 or (resid 505 and (name N \ or name CA or name C or name O or name CB )) or resid 506 through 509 or (resid \ 510 and (name N or name CA or name C or name O or name CB )) or resid 511 throug \ h 518 or (resid 519 and (name N or name CA or name C or name O or name CB )) or \ resid 520 through 556 or (resid 557 and (name N or name CA or name C or name O o \ r name CB )) or resid 558 or (resid 559 through 560 and (name N or name CA or na \ me C or name O or name CB )) or resid 561 through 633 or (resid 634 and (name N \ or name CA or name C or name O or name CB )) or resid 635 through 724 or (resid \ 725 and (name N or name CA or name C or name O or name CB )) or resid 726 throug \ h 773 or resid 777 or resid 788 through 796 or (resid 797 and (name N or name CA \ or name C or name O or name CB )) or resid 798 through 853 or resid 901 or resi \ d 902 through 904)) selection = (chain 'B' and ((resid 415 and (name N or name CA or name C or name O or name CB \ )) or resid 416 through 426 or (resid 427 through 430 and (name N or name CA or \ name C or name O or name CB )) or resid 431 through 432 or (resid 433 and (name \ N or name CA or name C or name O or name CB )) or resid 434 through 471 or (res \ id 472 and (name N or name CA or name C or name O or name CB )) or resid 473 thr \ ough 484 or (resid 485 through 487 and (name N or name CA or name C or name O or \ name CB )) or resid 488 through 493 or (resid 494 and (name N or name CA or nam \ e C or name O or name CB )) or resid 495 through 517 or (resid 518 through 519 a \ nd (name N or name CA or name C or name O or name CB )) or resid 520 through 529 \ or (resid 530 through 531 and (name N or name CA or name C or name O or name CB \ )) or resid 532 through 536 or (resid 537 through 538 and (name N or name CA or \ name C or name O or name CB )) or resid 539 or (resid 540 through 541 and (name \ N or name CA or name C or name O or name CB )) or resid 542 through 572 or (res \ id 573 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE )) or resid 574 through 651 or (resid 652 and (name N or name CA o \ r name C or name O or name CB )) or resid 653 through 656 or (resid 657 through \ 658 and (name N or name CA or name C or name O or name CB )) or resid 659 throug \ h 660 or (resid 661 through 662 and (name N or name CA or name C or name O or na \ me CB )) or resid 663 through 665 or (resid 666 and (name N or name CA or name C \ or name O or name CB )) or resid 667 through 702 or (resid 703 and (name N or n \ ame CA or name C or name O or name CB )) or resid 704 through 766 or (resid 767 \ and (name N or name CA or name C or name O or name CB or name CG or name CD )) o \ r resid 768 through 773 or resid 785 or resid 788 through 795 or (resid 796 thro \ ugh 797 and (name N or name CA or name C or name O or name CB )) or resid 798 th \ rough 852 or (resid 853 and (name N or name CA or name C or name O or name CB )) \ or resid 901 or resid 902 through 904)) } 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: 4.030 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.290 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 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 : 0.003 0.062 7995 Z= 0.213 Angle : 0.731 11.942 10852 Z= 0.385 Chirality : 0.042 0.314 1183 Planarity : 0.004 0.043 1407 Dihedral : 15.166 89.671 2816 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.38 % Allowed : 13.17 % Favored : 86.45 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 10.20 % 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: -1.92 (0.27), residues: 997 helix: -0.43 (0.34), residues: 253 sheet: -2.92 (0.52), residues: 88 loop : -1.42 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 639 HIS 0.003 0.001 HIS D 677 PHE 0.018 0.001 PHE D 672 TYR 0.008 0.001 TYR B 588 ARG 0.004 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 497 ARG cc_start: 0.7028 (mtt90) cc_final: 0.6314 (mtm-85) REVERT: B 754 LEU cc_start: 0.7510 (tp) cc_final: 0.6982 (mp) REVERT: B 772 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6817 (pp30) REVERT: D 842 LEU cc_start: 0.8504 (mm) cc_final: 0.8139 (mm) outliers start: 3 outliers final: 1 residues processed: 94 average time/residue: 0.2332 time to fit residues: 28.9878 Evaluate side-chains 85 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 772 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.0970 chunk 30 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 772 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7995 Z= 0.175 Angle : 0.546 5.915 10852 Z= 0.280 Chirality : 0.040 0.136 1183 Planarity : 0.004 0.040 1407 Dihedral : 5.434 59.115 1117 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.17 % Allowed : 15.98 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: -1.63 (0.27), residues: 997 helix: -0.10 (0.32), residues: 276 sheet: -2.99 (0.50), residues: 97 loop : -1.23 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 639 HIS 0.003 0.001 HIS A 677 PHE 0.016 0.001 PHE D 675 TYR 0.008 0.001 TYR D 849 ARG 0.004 0.000 ARG D 629 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 497 ARG cc_start: 0.6934 (mtt90) cc_final: 0.6711 (mtm110) REVERT: B 754 LEU cc_start: 0.7538 (tp) cc_final: 0.6948 (mp) REVERT: B 772 GLN cc_start: 0.7085 (pp30) cc_final: 0.6841 (pp30) REVERT: D 842 LEU cc_start: 0.8418 (mm) cc_final: 0.8026 (mm) outliers start: 17 outliers final: 8 residues processed: 101 average time/residue: 0.2037 time to fit residues: 27.9691 Evaluate side-chains 89 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 711 SER Chi-restraints excluded: chain D residue 722 ASP Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.3583 > 50: distance: 46 - 72: 21.820 distance: 52 - 59: 18.910 distance: 53 - 80: 8.833 distance: 59 - 60: 18.287 distance: 60 - 61: 6.359 distance: 60 - 63: 11.874 distance: 61 - 62: 12.650 distance: 61 - 64: 18.273 distance: 62 - 89: 24.832 distance: 64 - 65: 31.132 distance: 65 - 66: 34.695 distance: 65 - 68: 25.422 distance: 66 - 67: 45.590 distance: 66 - 72: 45.058 distance: 67 - 94: 26.040 distance: 68 - 69: 13.275 distance: 69 - 70: 19.197 distance: 69 - 71: 17.287 distance: 72 - 73: 28.185 distance: 73 - 74: 15.814 distance: 73 - 76: 15.251 distance: 74 - 75: 22.380 distance: 74 - 80: 16.092 distance: 75 - 108: 25.206 distance: 76 - 77: 14.214 distance: 76 - 78: 28.904 distance: 77 - 79: 7.705 distance: 80 - 81: 23.108 distance: 81 - 82: 38.699 distance: 81 - 84: 24.928 distance: 82 - 83: 35.664 distance: 82 - 89: 38.621 distance: 84 - 85: 11.011 distance: 85 - 86: 9.909 distance: 86 - 87: 6.181 distance: 86 - 88: 7.199 distance: 89 - 90: 29.561 distance: 90 - 91: 61.358 distance: 90 - 93: 24.717 distance: 91 - 92: 45.897 distance: 91 - 94: 45.468 distance: 94 - 95: 25.678 distance: 95 - 96: 23.706 distance: 95 - 98: 25.822 distance: 96 - 97: 19.399 distance: 96 - 108: 34.206 distance: 98 - 99: 18.666 distance: 99 - 100: 3.283 distance: 99 - 101: 7.041 distance: 100 - 102: 6.838 distance: 101 - 103: 19.407 distance: 101 - 104: 12.032 distance: 102 - 103: 13.599 distance: 103 - 105: 11.689 distance: 104 - 106: 4.141 distance: 105 - 107: 8.342 distance: 106 - 107: 6.281 distance: 108 - 109: 25.144 distance: 109 - 110: 16.033 distance: 110 - 111: 23.609 distance: 110 - 112: 31.855 distance: 112 - 113: 45.131 distance: 112 - 118: 21.021 distance: 113 - 114: 14.141 distance: 113 - 116: 30.770 distance: 114 - 115: 20.223 distance: 114 - 119: 45.153 distance: 116 - 117: 31.710 distance: 117 - 118: 34.972 distance: 119 - 120: 44.299 distance: 120 - 121: 50.110 distance: 120 - 123: 32.138 distance: 121 - 122: 29.730 distance: 121 - 130: 40.639 distance: 123 - 124: 19.600 distance: 124 - 125: 15.380 distance: 124 - 126: 18.152 distance: 125 - 127: 23.354 distance: 126 - 128: 9.461 distance: 127 - 129: 7.394 distance: 128 - 129: 16.958 distance: 130 - 131: 11.034 distance: 131 - 132: 6.788 distance: 131 - 134: 20.113 distance: 132 - 133: 8.995 distance: 132 - 138: 12.913 distance: 134 - 135: 7.319 distance: 135 - 136: 9.762 distance: 135 - 137: 16.171