Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 6 20:02:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zes_14692/10_2023/7zes_14692.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zes_14692/10_2023/7zes_14692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zes_14692/10_2023/7zes_14692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zes_14692/10_2023/7zes_14692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zes_14692/10_2023/7zes_14692.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zes_14692/10_2023/7zes_14692.pdb" } resolution = 3.1 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= 0.002 sd= 0.106 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 2 6.06 5 P 10 5.49 5 Mg 2 5.21 5 S 86 5.16 5 C 8604 2.51 5 N 2356 2.21 5 O 2478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 13538 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "B" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "E" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Classifications: {'DNA': 5} Link IDs: {'rna3p': 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: "B" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2033 SG CYS A 287 71.891 74.522 73.975 1.00 67.29 S ATOM 2310 SG CYS A 321 71.507 75.478 77.639 1.00 45.08 S ATOM 2316 SG CYS A 322 71.129 71.926 76.538 1.00 41.17 S ATOM 8698 SG CYS B 287 38.684 34.161 74.110 1.00 65.53 S ATOM 8975 SG CYS B 321 39.255 33.258 77.786 1.00 45.53 S ATOM 8981 SG CYS B 322 39.705 36.860 76.573 1.00 42.58 S Time building chain proxies: 7.09, per 1000 atoms: 0.52 Number of scatterers: 13538 At special positions: 0 Unit cell: (111.922, 109.83, 126.566, 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 2 29.99 S 86 16.00 P 10 15.00 Mg 2 11.99 O 2478 8.00 N 2356 7.00 C 8604 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: 5.14 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 285 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 321 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 287 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 322 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 285 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 287 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 322 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 321 " Number of angles added : 6 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 16 sheets defined 45.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 removed outlier: 3.591A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 55 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 89 through 93 removed outlier: 4.346A pdb=" N PHE A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.558A pdb=" N PHE A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 Proline residue: A 232 - end of helix Proline residue: A 236 - end of helix removed outlier: 3.689A pdb=" N THR A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 280 removed outlier: 3.500A pdb=" N ARG A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 389 through 398 Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 481 through 501 removed outlier: 4.355A pdb=" N ASP A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 removed outlier: 3.573A pdb=" N SER A 540 " --> pdb=" O ALA A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 559 Processing helix chain 'A' and resid 563 through 586 removed outlier: 3.543A pdb=" N GLU A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 590 removed outlier: 3.883A pdb=" N ARG A 590 " --> pdb=" O ARG A 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 587 through 590' Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 633 through 643 removed outlier: 3.612A pdb=" N ARG A 637 " --> pdb=" O ASN A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 657 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 679 through 690 Processing helix chain 'A' and resid 703 through 707 removed outlier: 3.577A pdb=" N THR A 707 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 721 Processing helix chain 'A' and resid 734 through 751 removed outlier: 3.602A pdb=" N VAL A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 761 removed outlier: 4.154A pdb=" N LEU A 761 " --> pdb=" O THR A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 803 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 818 through 831 removed outlier: 3.633A pdb=" N TYR A 824 " --> pdb=" O GLU A 820 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 825 " --> pdb=" O HIS A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 855 through 858 Processing helix chain 'A' and resid 877 through 887 Processing helix chain 'B' and resid 27 through 33 removed outlier: 3.589A pdb=" N LYS B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 55 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 89 through 93 removed outlier: 4.346A pdb=" N PHE B 93 " --> pdb=" O ASP B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 93' Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 190 through 195 removed outlier: 3.557A pdb=" N PHE B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 241 Proline residue: B 232 - end of helix Proline residue: B 236 - end of helix removed outlier: 3.691A pdb=" N THR B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 389 through 398 Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 481 through 501 removed outlier: 4.321A pdb=" N ASP B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 499 " --> pdb=" O LYS B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 540 removed outlier: 3.573A pdb=" N SER B 540 " --> pdb=" O ALA B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 559 Processing helix chain 'B' and resid 563 through 586 removed outlier: 3.542A pdb=" N GLU B 583 " --> pdb=" O ALA B 579 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 590 removed outlier: 3.881A pdb=" N ARG B 590 " --> pdb=" O ARG B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 587 through 590' Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 633 through 643 removed outlier: 3.616A pdb=" N ARG B 637 " --> pdb=" O ASN B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 657 Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 679 through 690 Processing helix chain 'B' and resid 703 through 707 removed outlier: 3.556A pdb=" N THR B 707 " --> pdb=" O TYR B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 721 Processing helix chain 'B' and resid 734 through 751 removed outlier: 3.605A pdb=" N VAL B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 761 removed outlier: 4.155A pdb=" N LEU B 761 " --> pdb=" O THR B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 803 Processing helix chain 'B' and resid 805 through 807 No H-bonds generated for 'chain 'B' and resid 805 through 807' Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 818 through 831 removed outlier: 3.624A pdb=" N TYR B 824 " --> pdb=" O GLU B 820 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 825 " --> pdb=" O HIS B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 834 No H-bonds generated for 'chain 'B' and resid 832 through 834' Processing helix chain 'B' and resid 855 through 858 Processing helix chain 'B' and resid 877 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 23 removed outlier: 6.196A pdb=" N ILE A 19 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ALA A 64 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N VAL A 21 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.567A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 284 Processing sheet with id=AA5, first strand: chain 'A' and resid 332 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 405 through 408 removed outlier: 6.528A pdb=" N ARG A 406 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE A 441 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 408 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS A 459 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU A 472 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU A 515 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR A 474 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.329A pdb=" N ILE A 627 " --> pdb=" O ARG A 647 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLU A 649 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TYR A 629 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU A 628 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 665 " --> pdb=" O TRP A 699 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE A 701 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 667 " --> pdb=" O PHE A 701 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 776 through 779 removed outlier: 7.151A pdb=" N SER A 863 " --> pdb=" O LYS A 890 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N SER A 839 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N SER A 853 " --> pdb=" O SER A 839 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 23 removed outlier: 6.184A pdb=" N ILE B 19 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ALA B 64 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N VAL B 21 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 133 through 136 Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.557A pdb=" N LEU B 199 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LYS B 304 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU B 214 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 283 through 284 Processing sheet with id=AB4, first strand: chain 'B' and resid 332 through 335 Processing sheet with id=AB5, first strand: chain 'B' and resid 405 through 408 removed outlier: 6.543A pdb=" N ARG B 406 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE B 441 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR B 408 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS B 459 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU B 472 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU B 515 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR B 474 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 647 through 650 removed outlier: 6.317A pdb=" N ILE B 627 " --> pdb=" O ARG B 647 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLU B 649 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR B 629 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU B 628 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 665 " --> pdb=" O TRP B 699 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N PHE B 701 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 667 " --> pdb=" O PHE B 701 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 776 through 779 removed outlier: 7.168A pdb=" N SER B 863 " --> pdb=" O LYS B 890 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER B 839 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N SER B 853 " --> pdb=" O SER B 839 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1656 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: 4.75 Time building geometry restraints manager: 5.52 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: 2276 1.32 - 1.44: 3601 1.44 - 1.57: 7827 1.57 - 1.69: 18 1.69 - 1.81: 122 Bond restraints: 13844 Sorted by residual: bond pdb=" C HIS A 598 " pdb=" O HIS A 598 " ideal model delta sigma weight residual 1.232 1.199 0.033 1.20e-02 6.94e+03 7.48e+00 bond pdb=" N ARG B 124 " pdb=" CA ARG B 124 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.33e-02 5.65e+03 6.79e+00 bond pdb=" N ARG A 124 " pdb=" CA ARG A 124 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.33e-02 5.65e+03 6.65e+00 bond pdb=" C VAL A 597 " pdb=" N HIS A 598 " ideal model delta sigma weight residual 1.329 1.305 0.024 1.51e-02 4.39e+03 2.51e+00 bond pdb=" CD2 HIS A 598 " pdb=" NE2 HIS A 598 " ideal model delta sigma weight residual 1.374 1.357 0.017 1.10e-02 8.26e+03 2.31e+00 ... (remaining 13839 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.69: 477 106.69 - 113.54: 7502 113.54 - 120.39: 5214 120.39 - 127.24: 5384 127.24 - 134.09: 151 Bond angle restraints: 18728 Sorted by residual: angle pdb=" C VAL A 731 " pdb=" CA VAL A 731 " pdb=" CB VAL A 731 " ideal model delta sigma weight residual 112.46 108.09 4.37 1.33e+00 5.65e-01 1.08e+01 angle pdb=" C VAL B 731 " pdb=" CA VAL B 731 " pdb=" CB VAL B 731 " ideal model delta sigma weight residual 112.46 108.11 4.35 1.33e+00 5.65e-01 1.07e+01 angle pdb=" N ILE A 193 " pdb=" CA ILE A 193 " pdb=" C ILE A 193 " ideal model delta sigma weight residual 112.35 108.28 4.07 1.41e+00 5.03e-01 8.32e+00 angle pdb=" CA HIS A 598 " pdb=" CB HIS A 598 " pdb=" CG HIS A 598 " ideal model delta sigma weight residual 113.80 116.68 -2.88 1.00e+00 1.00e+00 8.28e+00 angle pdb=" CA MET A 830 " pdb=" CB MET A 830 " pdb=" CG MET A 830 " ideal model delta sigma weight residual 114.10 119.81 -5.71 2.00e+00 2.50e-01 8.14e+00 ... (remaining 18723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 7623 17.48 - 34.95: 606 34.95 - 52.42: 149 52.42 - 69.90: 25 69.90 - 87.37: 13 Dihedral angle restraints: 8416 sinusoidal: 3584 harmonic: 4832 Sorted by residual: dihedral pdb=" CA LEU A 125 " pdb=" C LEU A 125 " pdb=" N CYS A 126 " pdb=" CA CYS A 126 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU B 125 " pdb=" C LEU B 125 " pdb=" N CYS B 126 " pdb=" CA CYS B 126 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLU B 11 " pdb=" C GLU B 11 " pdb=" N PRO B 12 " pdb=" CA PRO B 12 " ideal model delta harmonic sigma weight residual 180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1205 0.031 - 0.062: 570 0.062 - 0.092: 169 0.092 - 0.123: 101 0.123 - 0.154: 13 Chirality restraints: 2058 Sorted by residual: chirality pdb=" CG LEU A 569 " pdb=" CB LEU A 569 " pdb=" CD1 LEU A 569 " pdb=" CD2 LEU A 569 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CG LEU B 569 " pdb=" CB LEU B 569 " pdb=" CD1 LEU B 569 " pdb=" CD2 LEU B 569 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE B 248 " pdb=" N ILE B 248 " pdb=" C ILE B 248 " pdb=" CB ILE B 248 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 2055 not shown) Planarity restraints: 2372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 878 " 0.062 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO A 879 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 879 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 879 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 878 " 0.059 5.00e-02 4.00e+02 8.96e-02 1.29e+01 pdb=" N PRO B 879 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 879 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 879 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 598 " 0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C HIS A 598 " -0.030 2.00e-02 2.50e+03 pdb=" O HIS A 598 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY A 599 " 0.010 2.00e-02 2.50e+03 ... (remaining 2369 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 79 2.55 - 3.14: 10265 3.14 - 3.73: 20108 3.73 - 4.31: 29834 4.31 - 4.90: 50395 Nonbonded interactions: 110681 Sorted by model distance: nonbonded pdb=" OE2 GLU A 214 " pdb="MG MG A1002 " model vdw 1.966 2.170 nonbonded pdb=" OE2 GLU B 214 " pdb="MG MG B1002 " model vdw 1.969 2.170 nonbonded pdb=" OE2 GLU A 209 " pdb="MG MG A1002 " model vdw 2.184 2.170 nonbonded pdb=" NH2 ARG B 797 " pdb=" O LYS B 833 " model vdw 2.231 2.520 nonbonded pdb=" NH2 ARG A 797 " pdb=" O LYS A 833 " model vdw 2.235 2.520 ... (remaining 110676 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' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 1.650 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: 7.650 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 39.170 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 : 0.005 0.052 13844 Z= 0.316 Angle : 0.609 6.626 18728 Z= 0.336 Chirality : 0.043 0.154 2058 Planarity : 0.005 0.093 2372 Dihedral : 13.688 87.374 5292 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1638 helix: 0.35 (0.20), residues: 622 sheet: 1.00 (0.32), residues: 268 loop : -0.01 (0.23), residues: 748 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.443 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2917 time to fit residues: 91.7724 Evaluate side-chains 188 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.507 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 128 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 580 GLN A 618 ASN A 821 HIS B 222 HIS B 580 GLN B 618 ASN B 821 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13844 Z= 0.220 Angle : 0.528 5.898 18728 Z= 0.278 Chirality : 0.042 0.153 2058 Planarity : 0.004 0.060 2372 Dihedral : 7.719 56.714 1918 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.41 % Allowed : 5.82 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1638 helix: 1.38 (0.20), residues: 644 sheet: 0.97 (0.33), residues: 252 loop : 0.08 (0.24), residues: 742 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 213 time to evaluate : 1.505 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 218 average time/residue: 0.3039 time to fit residues: 92.7932 Evaluate side-chains 190 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1206 time to fit residues: 2.6800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 ASN A 821 HIS B 618 ASN B 821 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13844 Z= 0.208 Angle : 0.496 5.652 18728 Z= 0.259 Chirality : 0.041 0.138 2058 Planarity : 0.004 0.043 2372 Dihedral : 7.587 57.415 1918 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.88 % Allowed : 8.19 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.12 (0.21), residues: 1638 helix: 1.60 (0.21), residues: 656 sheet: 0.78 (0.34), residues: 242 loop : 0.03 (0.24), residues: 740 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 196 time to evaluate : 1.626 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 205 average time/residue: 0.3077 time to fit residues: 87.8981 Evaluate side-chains 195 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 189 time to evaluate : 1.518 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1349 time to fit residues: 3.6362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 580 GLN B 618 ASN B 787 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13844 Z= 0.301 Angle : 0.528 5.468 18728 Z= 0.276 Chirality : 0.043 0.147 2058 Planarity : 0.004 0.040 2372 Dihedral : 7.670 59.961 1918 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.29 % Allowed : 9.13 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.21), residues: 1638 helix: 1.47 (0.21), residues: 658 sheet: 0.61 (0.34), residues: 242 loop : -0.09 (0.24), residues: 738 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 189 time to evaluate : 1.436 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 197 average time/residue: 0.3097 time to fit residues: 85.6462 Evaluate side-chains 183 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 175 time to evaluate : 1.626 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1455 time to fit residues: 4.3250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.4025 > 50: distance: 48 - 158: 7.562 distance: 60 - 161: 33.241 distance: 122 - 128: 16.808 distance: 128 - 129: 25.461 distance: 129 - 130: 25.839 distance: 129 - 132: 4.114 distance: 130 - 131: 20.242 distance: 130 - 140: 13.902 distance: 132 - 133: 15.070 distance: 133 - 134: 6.540 distance: 133 - 135: 10.336 distance: 134 - 136: 9.277 distance: 135 - 137: 13.746 distance: 136 - 138: 13.260 distance: 137 - 138: 7.427 distance: 138 - 139: 6.291 distance: 140 - 141: 4.377 distance: 140 - 146: 25.876 distance: 141 - 142: 29.689 distance: 141 - 144: 40.694 distance: 142 - 143: 40.383 distance: 142 - 147: 47.743 distance: 144 - 145: 18.601 distance: 145 - 146: 26.376 distance: 147 - 148: 23.673 distance: 148 - 149: 13.482 distance: 148 - 151: 22.554 distance: 149 - 150: 28.302 distance: 149 - 158: 3.574 distance: 151 - 152: 26.130 distance: 152 - 153: 5.777 distance: 153 - 154: 12.506 distance: 155 - 156: 6.766 distance: 155 - 157: 6.720 distance: 158 - 159: 10.821 distance: 159 - 160: 24.338 distance: 159 - 162: 14.099 distance: 160 - 161: 16.140 distance: 160 - 167: 16.269 distance: 162 - 163: 36.326 distance: 163 - 164: 12.828 distance: 164 - 165: 9.513 distance: 164 - 166: 8.984 distance: 167 - 168: 18.435 distance: 168 - 169: 4.473 distance: 168 - 171: 8.354 distance: 169 - 170: 13.864 distance: 169 - 176: 6.591 distance: 171 - 172: 14.965 distance: 173 - 174: 11.507 distance: 176 - 177: 4.894 distance: 177 - 178: 8.356 distance: 177 - 180: 5.275 distance: 178 - 179: 18.581 distance: 178 - 184: 7.816 distance: 180 - 181: 12.050 distance: 181 - 182: 5.784 distance: 181 - 183: 8.336 distance: 184 - 185: 3.738 distance: 185 - 186: 17.864 distance: 185 - 188: 4.606 distance: 186 - 187: 14.476 distance: 186 - 191: 21.473 distance: 188 - 189: 9.749 distance: 188 - 190: 19.674 distance: 191 - 192: 10.265 distance: 192 - 193: 28.222 distance: 192 - 195: 12.538 distance: 193 - 194: 35.316 distance: 193 - 202: 30.610 distance: 195 - 196: 21.044 distance: 196 - 197: 7.508 distance: 197 - 198: 9.988 distance: 199 - 200: 3.316 distance: 202 - 203: 19.428 distance: 203 - 204: 13.190 distance: 203 - 206: 8.931 distance: 204 - 205: 25.636 distance: 204 - 210: 22.183 distance: 206 - 207: 17.857 distance: 206 - 208: 11.600 distance: 207 - 209: 11.300 distance: 210 - 211: 10.578 distance: 211 - 212: 4.958 distance: 212 - 213: 31.826 distance: 212 - 217: 10.187 distance: 214 - 215: 14.796 distance: 214 - 216: 9.852