Starting phenix.real_space_refine on Thu Sep 26 13:34:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r64_18946/09_2024/8r64_18946.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r64_18946/09_2024/8r64_18946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r64_18946/09_2024/8r64_18946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r64_18946/09_2024/8r64_18946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r64_18946/09_2024/8r64_18946.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r64_18946/09_2024/8r64_18946.cif" } resolution = 3.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 6 5.21 5 S 74 5.16 5 C 8445 2.51 5 N 2353 2.21 5 O 2534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13429 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2300 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 284} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2306 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 284} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2308 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 284} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2314 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 284} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "F" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1971 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 14, 'TRANS': 255} Chain breaks: 3 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 109 Chain: "A" Number of atoms: 1956 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 271, 1951 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 17, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 117 Conformer: "B" Number of residues, atoms: 271, 1951 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 17, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 117 bond proxies already assigned to first conformer: 1979 Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 86 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATHR A 632 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR A 632 " occ=0.50 Time building chain proxies: 9.50, per 1000 atoms: 0.71 Number of scatterers: 13429 At special positions: 0 Unit cell: (135.3, 129.8, 103.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 74 16.00 P 17 15.00 Mg 6 11.99 O 2534 8.00 N 2353 7.00 C 8445 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: 3.61 Conformation dependent library (CDL) restraints added in 2.1 seconds 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 6 sheets defined 63.6% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'B' and resid 380 through 389 Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 406 through 423 removed outlier: 3.868A pdb=" N LYS B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TRP B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Proline residue: B 420 - end of helix Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 446 through 459 removed outlier: 4.227A pdb=" N GLY B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 removed outlier: 3.889A pdb=" N LEU B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 492 Processing helix chain 'B' and resid 514 through 529 removed outlier: 3.613A pdb=" N ARG B 518 " --> pdb=" O HIS B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.768A pdb=" N ARG B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 583 removed outlier: 4.293A pdb=" N LYS B 583 " --> pdb=" O ASN B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 600 Processing helix chain 'B' and resid 604 through 617 removed outlier: 3.511A pdb=" N THR B 609 " --> pdb=" O GLY B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 623 Processing helix chain 'B' and resid 640 through 651 removed outlier: 3.754A pdb=" N PHE B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 650 " --> pdb=" O ASN B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 659 through 671 removed outlier: 4.509A pdb=" N TYR B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 665 " --> pdb=" O GLU B 661 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 669 " --> pdb=" O ASN B 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 removed outlier: 4.068A pdb=" N ARG C 375 " --> pdb=" O VAL C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 389 Processing helix chain 'C' and resid 407 through 423 removed outlier: 4.087A pdb=" N TRP C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 423 through 428 Processing helix chain 'C' and resid 429 through 432 Processing helix chain 'C' and resid 446 through 459 removed outlier: 4.298A pdb=" N GLY C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 471 removed outlier: 3.818A pdb=" N LEU C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 490 removed outlier: 3.583A pdb=" N LYS C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 482 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 514 through 529 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 552 through 559 removed outlier: 3.788A pdb=" N ARG C 558 " --> pdb=" O ALA C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 584 removed outlier: 4.038A pdb=" N LYS C 583 " --> pdb=" O ASN C 579 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU C 584 " --> pdb=" O LEU C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 600 Processing helix chain 'C' and resid 604 through 617 removed outlier: 3.619A pdb=" N LEU C 617 " --> pdb=" O ARG C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 623 Processing helix chain 'C' and resid 626 through 631 removed outlier: 3.736A pdb=" N THR C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 636 removed outlier: 3.613A pdb=" N VAL C 636 " --> pdb=" O PRO C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 651 removed outlier: 3.787A pdb=" N PHE C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG C 649 " --> pdb=" O GLU C 645 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR C 650 " --> pdb=" O ASN C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 658 No H-bonds generated for 'chain 'C' and resid 656 through 658' Processing helix chain 'C' and resid 659 through 671 removed outlier: 4.416A pdb=" N TYR C 663 " --> pdb=" O ASP C 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 377 Processing helix chain 'D' and resid 380 through 390 Processing helix chain 'D' and resid 406 through 423 removed outlier: 4.110A pdb=" N TRP D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) Proline residue: D 420 - end of helix Processing helix chain 'D' and resid 423 through 428 Processing helix chain 'D' and resid 429 through 432 Processing helix chain 'D' and resid 446 through 459 removed outlier: 3.529A pdb=" N ILE D 450 " --> pdb=" O GLY D 446 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 471 removed outlier: 3.624A pdb=" N LEU D 470 " --> pdb=" O SER D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 492 Processing helix chain 'D' and resid 502 through 505 Processing helix chain 'D' and resid 514 through 529 removed outlier: 3.595A pdb=" N ARG D 518 " --> pdb=" O HIS D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 552 through 559 removed outlier: 3.546A pdb=" N ARG D 557 " --> pdb=" O GLU D 553 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG D 558 " --> pdb=" O ALA D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 583 removed outlier: 4.243A pdb=" N LYS D 583 " --> pdb=" O ASN D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 600 Processing helix chain 'D' and resid 604 through 616 removed outlier: 3.579A pdb=" N THR D 609 " --> pdb=" O GLY D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 623 Processing helix chain 'D' and resid 626 through 631 removed outlier: 4.378A pdb=" N THR D 630 " --> pdb=" O ALA D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 649 removed outlier: 3.628A pdb=" N PHE D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 670 removed outlier: 4.262A pdb=" N TYR D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 377 Processing helix chain 'E' and resid 380 through 389 Processing helix chain 'E' and resid 399 through 403 Processing helix chain 'E' and resid 407 through 423 removed outlier: 4.091A pdb=" N TRP E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Proline residue: E 420 - end of helix Processing helix chain 'E' and resid 423 through 428 Processing helix chain 'E' and resid 446 through 458 removed outlier: 3.519A pdb=" N SER E 456 " --> pdb=" O LYS E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 471 removed outlier: 3.947A pdb=" N LEU E 470 " --> pdb=" O SER E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 492 removed outlier: 3.582A pdb=" N LYS E 480 " --> pdb=" O GLY E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 506 removed outlier: 4.325A pdb=" N LEU E 505 " --> pdb=" O GLN E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 530 Processing helix chain 'E' and resid 547 through 551 Processing helix chain 'E' and resid 552 through 559 removed outlier: 3.922A pdb=" N ARG E 558 " --> pdb=" O ALA E 554 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 559 " --> pdb=" O ALA E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 584 removed outlier: 4.188A pdb=" N LYS E 583 " --> pdb=" O ASN E 579 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU E 584 " --> pdb=" O LEU E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 600 Processing helix chain 'E' and resid 604 through 617 removed outlier: 3.518A pdb=" N LEU E 617 " --> pdb=" O ARG E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 623 Processing helix chain 'E' and resid 632 through 636 Processing helix chain 'E' and resid 641 through 650 removed outlier: 3.713A pdb=" N GLU E 645 " --> pdb=" O TYR E 641 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN E 646 " --> pdb=" O ILE E 642 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 670 removed outlier: 4.417A pdb=" N LEU E 660 " --> pdb=" O SER E 656 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU E 661 " --> pdb=" O PRO E 657 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU E 662 " --> pdb=" O LYS E 658 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR E 663 " --> pdb=" O ASP E 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 377 removed outlier: 3.547A pdb=" N ARG F 375 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 391 removed outlier: 3.592A pdb=" N ILE F 391 " --> pdb=" O ILE F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 404 removed outlier: 3.811A pdb=" N ILE F 403 " --> pdb=" O ASN F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.932A pdb=" N TRP F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) Proline residue: F 420 - end of helix Processing helix chain 'F' and resid 423 through 428 removed outlier: 3.700A pdb=" N PHE F 427 " --> pdb=" O ARG F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 459 removed outlier: 3.945A pdb=" N GLY F 459 " --> pdb=" O ALA F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 471 removed outlier: 4.193A pdb=" N LEU F 470 " --> pdb=" O SER F 466 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR F 471 " --> pdb=" O ALA F 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 466 through 471' Processing helix chain 'F' and resid 476 through 492 removed outlier: 3.535A pdb=" N LYS F 480 " --> pdb=" O GLY F 476 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN F 492 " --> pdb=" O VAL F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 506 removed outlier: 4.066A pdb=" N LEU F 505 " --> pdb=" O GLN F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 529 Processing helix chain 'F' and resid 547 through 551 Processing helix chain 'F' and resid 552 through 559 removed outlier: 3.654A pdb=" N ARG F 558 " --> pdb=" O ALA F 554 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 559 " --> pdb=" O ALA F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 582 Processing helix chain 'F' and resid 590 through 600 Processing helix chain 'F' and resid 604 through 617 removed outlier: 3.674A pdb=" N LEU F 617 " --> pdb=" O ARG F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 642 through 650 Processing helix chain 'F' and resid 656 through 670 removed outlier: 4.387A pdb=" N LEU F 660 " --> pdb=" O SER F 656 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU F 661 " --> pdb=" O PRO F 657 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU F 662 " --> pdb=" O LYS F 658 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.739A pdb=" N ILE A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 4.294A pdb=" N ILE A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA A 404 " --> pdb=" O TRP A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 399 through 404' Processing helix chain 'A' and resid 406 through 418 removed outlier: 3.570A pdb=" N LYS A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 459 removed outlier: 4.310A pdb=" N GLY A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 removed outlier: 3.523A pdb=" N LEU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 removed outlier: 3.713A pdb=" N LYS A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 4.012A pdb=" N LEU A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 535 removed outlier: 3.870A pdb=" N SER A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 552 through 559 removed outlier: 4.150A pdb=" N ARG A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 583 removed outlier: 4.116A pdb=" N LYS A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 600 Processing helix chain 'A' and resid 604 through 623 Proline residue: A 619 - end of helix Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 640 through 650 removed outlier: 3.656A pdb=" N PHE A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR A 650 " --> pdb=" O ASN A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 671 Processing sheet with id=AA1, first strand: chain 'B' and resid 461 through 465 removed outlier: 6.211A pdb=" N THR B 461 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE B 498 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE B 463 " --> pdb=" O PHE B 498 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASP B 500 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE B 465 " --> pdb=" O ASP B 500 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 437 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N THR B 545 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU B 439 " --> pdb=" O THR B 545 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 461 through 465 removed outlier: 3.884A pdb=" N ASP C 500 " --> pdb=" O ILE C 465 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C 561 " --> pdb=" O GLY C 436 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 461 through 465 removed outlier: 6.323A pdb=" N THR D 461 " --> pdb=" O VAL D 496 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE D 498 " --> pdb=" O THR D 461 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE D 463 " --> pdb=" O PHE D 498 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP D 500 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE D 465 " --> pdb=" O ASP D 500 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE D 437 " --> pdb=" O GLY D 543 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR D 545 " --> pdb=" O ILE D 437 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU D 439 " --> pdb=" O THR D 545 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU D 438 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 461 through 465 removed outlier: 6.200A pdb=" N THR E 461 " --> pdb=" O VAL E 496 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE E 498 " --> pdb=" O THR E 461 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE E 463 " --> pdb=" O PHE E 498 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA E 495 " --> pdb=" O LEU E 540 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL E 542 " --> pdb=" O ALA E 495 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE E 497 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA E 544 " --> pdb=" O ILE E 497 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE E 499 " --> pdb=" O ALA E 544 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS E 561 " --> pdb=" O GLY E 436 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 461 through 465 removed outlier: 3.639A pdb=" N ALA F 544 " --> pdb=" O ILE F 499 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE F 437 " --> pdb=" O GLY F 543 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THR F 545 " --> pdb=" O ILE F 437 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU F 439 " --> pdb=" O THR F 545 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU F 438 " --> pdb=" O LEU F 563 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 465 removed outlier: 6.262A pdb=" N THR A 461 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE A 498 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE A 463 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP A 500 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE A 465 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA A 495 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL A 542 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE A 497 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ALA A 544 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 499 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY A 436 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU A 563 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 438 " --> pdb=" O LEU A 563 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1836 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: 3.82 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4457 1.34 - 1.46: 2618 1.46 - 1.58: 6446 1.58 - 1.69: 28 1.69 - 1.81: 115 Bond restraints: 13664 Sorted by residual: bond pdb=" C LEU D 528 " pdb=" N ASP D 529 " ideal model delta sigma weight residual 1.328 1.338 -0.010 8.90e-03 1.26e+04 1.37e+00 bond pdb=" CA VAL D 406 " pdb=" CB VAL D 406 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.31e-02 5.83e+03 1.35e+00 bond pdb=" C LEU A 617 " pdb=" N GLY A 618 " ideal model delta sigma weight residual 1.339 1.331 0.008 7.50e-03 1.78e+04 1.24e+00 bond pdb=" CA ASP D 529 " pdb=" CB ASP D 529 " ideal model delta sigma weight residual 1.537 1.521 0.016 1.45e-02 4.76e+03 1.19e+00 bond pdb=" C4 ADP F 702 " pdb=" C5 ADP F 702 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.17e+00 ... (remaining 13659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 18276 1.35 - 2.71: 165 2.71 - 4.06: 101 4.06 - 5.42: 15 5.42 - 6.77: 19 Bond angle restraints: 18576 Sorted by residual: angle pdb=" C3' ATP C 702 " pdb=" C4' ATP C 702 " pdb=" O4' ATP C 702 " ideal model delta sigma weight residual 105.22 101.35 3.87 1.30e+00 5.94e-01 8.89e+00 angle pdb=" C3' ATP E 702 " pdb=" C4' ATP E 702 " pdb=" C5' ATP E 702 " ideal model delta sigma weight residual 115.19 110.36 4.83 1.76e+00 3.23e-01 7.55e+00 angle pdb=" C3' ATP D 702 " pdb=" C4' ATP D 702 " pdb=" O4' ATP D 702 " ideal model delta sigma weight residual 105.22 101.73 3.49 1.30e+00 5.94e-01 7.23e+00 angle pdb=" C3' ATP A 702 " pdb=" C4' ATP A 702 " pdb=" C5' ATP A 702 " ideal model delta sigma weight residual 115.19 110.72 4.47 1.76e+00 3.23e-01 6.45e+00 angle pdb=" C3' ATP D 702 " pdb=" C4' ATP D 702 " pdb=" C5' ATP D 702 " ideal model delta sigma weight residual 115.19 110.76 4.43 1.76e+00 3.23e-01 6.34e+00 ... (remaining 18571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.60: 8284 31.60 - 63.20: 151 63.20 - 94.80: 9 94.80 - 126.39: 1 126.39 - 157.99: 2 Dihedral angle restraints: 8447 sinusoidal: 3375 harmonic: 5072 Sorted by residual: dihedral pdb=" C5' ADP F 702 " pdb=" O5' ADP F 702 " pdb=" PA ADP F 702 " pdb=" O2A ADP F 702 " ideal model delta sinusoidal sigma weight residual -60.00 98.00 -157.99 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O2A ADP F 702 " pdb=" O3A ADP F 702 " pdb=" PA ADP F 702 " pdb=" PB ADP F 702 " ideal model delta sinusoidal sigma weight residual -60.00 81.50 -141.50 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" O1B ADP F 702 " pdb=" O3A ADP F 702 " pdb=" PB ADP F 702 " pdb=" PA ADP F 702 " ideal model delta sinusoidal sigma weight residual -60.00 66.37 -126.37 1 2.00e+01 2.50e-03 3.82e+01 ... (remaining 8444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1874 0.061 - 0.123: 262 0.123 - 0.184: 11 0.184 - 0.245: 2 0.245 - 0.307: 13 Chirality restraints: 2162 Sorted by residual: chirality pdb=" C2' ATP C 702 " pdb=" C1' ATP C 702 " pdb=" C3' ATP C 702 " pdb=" O2' ATP C 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' ATP B 702 " pdb=" C1' ATP B 702 " pdb=" C3' ATP B 702 " pdb=" O2' ATP B 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C2' ATP D 702 " pdb=" C1' ATP D 702 " pdb=" C3' ATP D 702 " pdb=" O2' ATP D 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 2159 not shown) Planarity restraints: 2376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 618 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.53e+00 pdb=" N PRO A 619 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 619 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 619 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP F 419 " 0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO F 420 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO F 420 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 420 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 618 " 0.016 5.00e-02 4.00e+02 2.42e-02 9.39e-01 pdb=" N PRO D 619 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO D 619 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 619 " 0.014 5.00e-02 4.00e+02 ... (remaining 2373 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 99 2.53 - 3.12: 10999 3.12 - 3.72: 20049 3.72 - 4.31: 26854 4.31 - 4.90: 46552 Nonbonded interactions: 104553 Sorted by model distance: nonbonded pdb=" OG1 THR E 448 " pdb="MG MG E 701 " model vdw 1.940 2.170 nonbonded pdb=" OG SER C 516 " pdb=" OE2 GLU G 8 " model vdw 1.953 3.040 nonbonded pdb="MG MG C 701 " pdb=" O2B ATP C 702 " model vdw 1.959 2.170 nonbonded pdb=" OG1 THR A 448 " pdb="MG MG A 701 " model vdw 1.966 2.170 nonbonded pdb="MG MG B 701 " pdb=" O1G ATP B 702 " model vdw 2.037 2.170 ... (remaining 104548 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 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 380 and (name N or name CA or name C or name O or name CB \ )) or resid 381 through 401 or (resid 402 and (name N or name CA or name C or n \ ame O or name CB )) or resid 403 through 406 or (resid 407 and (name N or name C \ A or name C or name O or name CB )) or resid 408 through 448 or (resid 449 and ( \ name N or name CA or name C or name O or name CB )) or resid 450 through 499 or \ (resid 500 and (name N or name CA or name C or name O or name CB )) or resid 501 \ through 528 or (resid 529 and (name N or name CA or name C or name O or name CB \ )) or resid 530 through 568 or (resid 569 through 570 and (name N or name CA or \ name C or name O or name CB )) or resid 571 through 580 or (resid 581 and (name \ N or name CA or name C or name O or name CB )) or resid 582 or (resid 589 throu \ gh 602 and (name N or name CA or name C or name O or name CB )) or resid 603 thr \ ough 612 or (resid 613 through 615 and (name N or name CA or name C or name O or \ name CB )) or resid 616 through 617 or resid 641 or (resid 642 through 650 and \ (name N or name CA or name C or name O or name CB )) or resid 651 or resid 656 t \ hrough 671 or resid 701)) selection = (chain 'B' and ((resid 380 and (name N or name CA or name C or name O or name CB \ )) or resid 381 or (resid 382 and (name N or name CA or name C or name O or nam \ e CB )) or resid 383 through 384 or (resid 385 and (name N or name CA or name C \ or name O or name CB )) or resid 386 through 391 or (resid 392 through 394 and ( \ name N or name CA or name C or name O or name CB )) or resid 395 through 400 or \ (resid 401 through 402 and (name N or name CA or name C or name O or name CB )) \ or resid 403 through 406 or (resid 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 through 414 or (resid 415 and (name N or name CA or \ name C or name O or name CB )) or resid 416 through 418 or resid 434 or (resid \ 435 and (name N or name CA or name C or name O or name CB )) or resid 436 throug \ h 448 or (resid 449 and (name N or name CA or name C or name O or name CB )) or \ resid 450 through 499 or (resid 500 and (name N or name CA or name C or name O o \ r name CB )) or resid 501 through 507 or (resid 508 through 509 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 or (resid 511 and (name N \ or name CA or name C or name O or name CB )) or resid 512 or (resid 513 and (nam \ e N or name CA or name C or name O or name CB )) or resid 514 or (resid 515 and \ (name N or name CA or name C or name O or name CB )) or resid 516 through 517 or \ (resid 518 through 519 and (name N or name CA or name C or name O or name CB )) \ or resid 520 through 522 or (resid 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 528 or (resid 529 and (name N or name CA o \ r name C or name O or name CB )) or resid 530 through 535 or (resid 536 through \ 537 and (name N or name CA or name C or name O or name CB )) or resid 538 throug \ h 552 or (resid 553 through 555 and (name N or name CA or name C or name O or na \ me CB )) or resid 556 through 560 or (resid 561 and (name N or name CA or name C \ or name O or name CB )) or resid 562 through 568 or (resid 569 through 570 and \ (name N or name CA or name C or name O or name CB )) or resid 571 through 573 or \ (resid 574 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 5 through 580 or (resid 581 and (name N or name CA or name C or name O or name C \ B )) or resid 582 or (resid 589 through 602 and (name N or name CA or name C or \ name O or name CB )) or resid 603 through 612 or (resid 613 through 615 and (nam \ e N or name CA or name C or name O or name CB )) or resid 616 through 617 or res \ id 641 or (resid 642 through 650 and (name N or name CA or name C or name O or n \ ame CB )) or resid 651 or resid 656 through 657 or (resid 658 and (name N or nam \ e CA or name C or name O or name CB )) or resid 659 through 663 or (resid 664 an \ d (name N or name CA or name C or name O or name CB )) or resid 665 through 667 \ or (resid 668 and (name N or name CA or name C or name O or name CB )) or resid \ 669 through 671 or resid 701)) selection = (chain 'C' and ((resid 380 and (name N or name CA or name C or name O or name CB \ )) or resid 381 or (resid 382 and (name N or name CA or name C or name O or nam \ e CB )) or resid 383 through 384 or (resid 385 and (name N or name CA or name C \ or name O or name CB )) or resid 386 through 391 or (resid 392 through 394 and ( \ name N or name CA or name C or name O or name CB )) or resid 395 through 401 or \ (resid 402 and (name N or name CA or name C or name O or name CB )) or resid 403 \ through 406 or (resid 407 and (name N or name CA or name C or name O or name CB \ )) or resid 408 through 414 or (resid 415 and (name N or name CA or name C or n \ ame O or name CB )) or resid 416 through 418 or resid 434 or (resid 435 and (nam \ e N or name CA or name C or name O or name CB )) or resid 436 through 448 or (re \ sid 449 and (name N or name CA or name C or name O or name CB )) or resid 450 th \ rough 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) \ or resid 501 through 507 or (resid 508 through 509 and (name N or name CA or na \ me C or name O or name CB )) or (resid 510 through 513 and (name N or name CA or \ name C or name O or name CB )) or resid 514 or (resid 515 and (name N or name C \ A or name C or name O or name CB )) or resid 516 through 517 or (resid 518 throu \ gh 519 and (name N or name CA or name C or name O or name CB )) or resid 520 thr \ ough 522 or (resid 523 and (name N or name CA or name C or name O or name CB )) \ or resid 524 through 528 or (resid 529 and (name N or name CA or name C or name \ O or name CB )) or resid 530 through 535 or (resid 536 through 537 and (name N o \ r name CA or name C or name O or name CB )) or resid 538 through 552 or (resid 5 \ 53 through 555 and (name N or name CA or name C or name O or name CB )) or resid \ 556 through 560 or (resid 561 and (name N or name CA or name C or name O or nam \ e CB )) or resid 562 through 568 or (resid 569 through 570 and (name N or name C \ A or name C or name O or name CB )) or resid 571 through 573 or (resid 574 and ( \ name N or name CA or name C or name O or name CB )) or resid 575 through 580 or \ (resid 581 and (name N or name CA or name C or name O or name CB )) or resid 582 \ or (resid 589 through 602 and (name N or name CA or name C or name O or name CB \ )) or resid 603 through 612 or (resid 613 through 615 and (name N or name CA or \ name C or name O or name CB )) or resid 616 through 617 or resid 641 or (resid \ 642 through 650 and (name N or name CA or name C or name O or name CB )) or resi \ d 651 or resid 656 through 657 or (resid 658 and (name N or name CA or name C or \ name O or name CB )) or resid 659 through 660 or (resid 661 and (name N or name \ CA or name C or name O or name CB )) or resid 662 through 663 or (resid 664 and \ (name N or name CA or name C or name O or name CB )) or resid 665 through 667 o \ r (resid 668 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 69 through 671 or resid 701)) selection = (chain 'D' and (resid 380 through 384 or (resid 385 and (name N or name CA or na \ me C or name O or name CB )) or resid 386 through 391 or (resid 392 through 394 \ and (name N or name CA or name C or name O or name CB )) or resid 395 through 40 \ 0 or (resid 401 through 402 and (name N or name CA or name C or name O or name C \ B )) or resid 403 through 406 or (resid 407 and (name N or name CA or name C or \ name O or name CB )) or resid 408 through 414 or (resid 415 and (name N or name \ CA or name C or name O or name CB )) or resid 416 through 418 or resid 434 or (r \ esid 435 and (name N or name CA or name C or name O or name CB )) or resid 436 t \ hrough 448 or (resid 449 and (name N or name CA or name C or name O or name CB ) \ ) or resid 450 through 499 or (resid 500 and (name N or name CA or name C or nam \ e O or name CB )) or resid 501 through 507 or (resid 508 through 509 and (name N \ or name CA or name C or name O or name CB )) or resid 510 or (resid 511 and (na \ me N or name CA or name C or name O or name CB )) or resid 512 or (resid 513 and \ (name N or name CA or name C or name O or name CB )) or resid 514 or (resid 515 \ and (name N or name CA or name C or name O or name CB )) or resid 516 through 5 \ 17 or (resid 518 through 519 and (name N or name CA or name C or name O or name \ CB )) or resid 520 through 522 or (resid 523 and (name N or name CA or name C or \ name O or name CB )) or resid 524 through 528 or (resid 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 536 or (resid 537 and \ (name N or name CA or name C or name O or name CB )) or resid 538 through 552 o \ r (resid 553 through 555 and (name N or name CA or name C or name O or name CB ) \ ) or resid 556 through 560 or (resid 561 and (name N or name CA or name C or nam \ e O or name CB )) or resid 562 through 568 or (resid 569 through 570 and (name N \ or name CA or name C or name O or name CB )) or resid 571 through 573 or (resid \ 574 and (name N or name CA or name C or name O or name CB )) or resid 575 throu \ gh 580 or (resid 581 and (name N or name CA or name C or name O or name CB )) or \ resid 582 or (resid 589 through 602 and (name N or name CA or name C or name O \ or name CB )) or resid 603 through 612 or (resid 613 through 615 and (name N or \ name CA or name C or name O or name CB )) or resid 616 through 617 or resid 641 \ or (resid 642 through 650 and (name N or name CA or name C or name O or name CB \ )) or resid 651 or resid 656 through 657 or (resid 658 and (name N or name CA or \ name C or name O or name CB )) or resid 659 through 660 or (resid 661 and (name \ N or name CA or name C or name O or name CB )) or resid 662 through 663 or (res \ id 664 and (name N or name CA or name C or name O or name CB )) or resid 665 thr \ ough 667 or (resid 668 and (name N or name CA or name C or name O or name CB )) \ or resid 669 through 671 or resid 701)) selection = (chain 'E' and (resid 380 through 381 or (resid 382 and (name N or name CA or na \ me C or name O or name CB )) or resid 383 through 384 or (resid 385 and (name N \ or name CA or name C or name O or name CB )) or resid 386 through 391 or (resid \ 392 through 394 and (name N or name CA or name C or name O or name CB )) or resi \ d 395 through 400 or (resid 401 through 402 and (name N or name CA or name C or \ name O or name CB )) or resid 403 through 406 or (resid 407 and (name N or name \ CA or name C or name O or name CB )) or resid 408 through 414 or (resid 415 and \ (name N or name CA or name C or name O or name CB )) or resid 416 through 418 or \ resid 434 or (resid 435 and (name N or name CA or name C or name O or name CB ) \ ) or resid 436 through 448 or (resid 449 and (name N or name CA or name C or nam \ e O or name CB )) or resid 450 through 499 or (resid 500 and (name N or name CA \ or name C or name O or name CB )) or resid 501 through 507 or (resid 508 through \ 509 and (name N or name CA or name C or name O or name CB )) or resid 510 or (r \ esid 511 and (name N or name CA or name C or name O or name CB )) or resid 512 o \ r (resid 513 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 14 or (resid 515 and (name N or name CA or name C or name O or name CB )) or res \ id 516 through 517 or (resid 518 through 519 and (name N or name CA or name C or \ name O or name CB )) or resid 520 through 522 or (resid 523 and (name N or name \ CA or name C or name O or name CB )) or resid 524 through 536 or (resid 537 and \ (name N or name CA or name C or name O or name CB )) or resid 538 through 560 o \ r (resid 561 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 62 through 568 or (resid 569 through 570 and (name N or name CA or name C or nam \ e O or name CB )) or resid 571 through 573 or (resid 574 and (name N or name CA \ or name C or name O or name CB )) or resid 575 through 580 or (resid 581 and (na \ me N or name CA or name C or name O or name CB )) or resid 582 or (resid 589 thr \ ough 602 and (name N or name CA or name C or name O or name CB )) or resid 603 t \ hrough 612 or (resid 613 through 615 and (name N or name CA or name C or name O \ or name CB )) or resid 616 through 617 or resid 641 or (resid 642 through 650 an \ d (name N or name CA or name C or name O or name CB )) or resid 651 or resid 656 \ through 657 or (resid 658 and (name N or name CA or name C or name O or name CB \ )) or resid 659 through 660 or (resid 661 and (name N or name CA or name C or n \ ame O or name CB )) or resid 662 through 663 or (resid 664 and (name N or name C \ A or name C or name O or name CB )) or resid 665 through 667 or (resid 668 and ( \ name N or name CA or name C or name O or name CB )) or resid 669 through 671 or \ resid 701)) selection = (chain 'F' and ((resid 380 and (name N or name CA or name C or name O or name CB \ )) or resid 381 or (resid 382 and (name N or name CA or name C or name O or nam \ e CB )) or resid 383 through 391 or (resid 392 through 394 and (name N or name C \ A or name C or name O or name CB )) or resid 395 through 401 or (resid 402 and ( \ name N or name CA or name C or name O or name CB )) or resid 403 through 414 or \ (resid 415 and (name N or name CA or name C or name O or name CB )) or resid 416 \ through 418 or resid 434 or (resid 435 and (name N or name CA or name C or name \ O or name CB )) or resid 436 through 507 or (resid 508 through 509 and (name N \ or name CA or name C or name O or name CB )) or resid 510 or (resid 511 and (nam \ e N or name CA or name C or name O or name CB )) or resid 512 or (resid 513 and \ (name N or name CA or name C or name O or name CB )) or resid 514 or (resid 515 \ and (name N or name CA or name C or name O or name CB )) or resid 516 through 51 \ 7 or (resid 518 through 519 and (name N or name CA or name C or name O or name C \ B )) or resid 520 through 522 or (resid 523 and (name N or name CA or name C or \ name O or name CB )) or resid 524 through 528 or (resid 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 535 or (resid 536 thro \ ugh 537 and (name N or name CA or name C or name O or name CB )) or resid 538 th \ rough 552 or (resid 553 through 555 and (name N or name CA or name C or name O o \ r name CB )) or resid 556 through 560 or (resid 561 and (name N or name CA or na \ me C or name O or name CB )) or resid 562 through 613 or (resid 614 through 615 \ and (name N or name CA or name C or name O or name CB )) or resid 616 through 65 \ 7 or (resid 658 and (name N or name CA or name C or name O or name CB )) or resi \ d 659 through 667 or (resid 668 and (name N or name CA or name C or name O or na \ me CB )) or resid 669 through 671 or resid 701)) } 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=0.50 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: 0.470 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.030 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.060 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 : 0.002 0.031 13664 Z= 0.120 Angle : 0.487 6.771 18576 Z= 0.246 Chirality : 0.046 0.307 2162 Planarity : 0.003 0.031 2376 Dihedral : 11.845 157.994 5147 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.29 % Allowed : 2.61 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.95 % 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: 2.70 (0.21), residues: 1742 helix: 2.55 (0.19), residues: 848 sheet: 1.76 (0.38), residues: 192 loop : 0.98 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 474 HIS 0.001 0.000 HIS A 514 PHE 0.006 0.001 PHE D 440 TYR 0.006 0.001 TYR C 564 ARG 0.002 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 264 time to evaluate : 1.664 Fit side-chains revert: symmetry clash REVERT: C 481 MET cc_start: 0.8964 (mmm) cc_final: 0.8759 (mmm) REVERT: C 524 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8158 (t80) REVERT: D 524 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8383 (t80) REVERT: E 586 CYS cc_start: 0.5232 (p) cc_final: 0.4836 (p) REVERT: F 380 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 390 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8191 (mm-30) REVERT: A 473 LYS cc_start: 0.8233 (pttt) cc_final: 0.7983 (ptmt) REVERT: A 540 LEU cc_start: 0.8798 (tp) cc_final: 0.8591 (tt) outliers start: 4 outliers final: 1 residues processed: 268 average time/residue: 0.2689 time to fit residues: 102.3058 Evaluate side-chains 167 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain D residue 524 PHE Chi-restraints excluded: chain F residue 529 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-dev-5461/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-dev-5461/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: 60.8044 > 50: distance: 35 - 39: 5.537 distance: 39 - 40: 4.080 distance: 40 - 41: 10.895 distance: 40 - 43: 4.117 distance: 41 - 42: 11.408 distance: 41 - 47: 20.113 distance: 43 - 44: 5.236 distance: 44 - 45: 5.754 distance: 44 - 46: 10.283 distance: 48 - 49: 7.419 distance: 48 - 51: 6.809 distance: 49 - 50: 10.849 distance: 49 - 52: 7.988 distance: 52 - 53: 7.954 distance: 53 - 54: 12.058 distance: 53 - 56: 8.729 distance: 54 - 55: 33.190 distance: 54 - 63: 33.007 distance: 56 - 57: 9.167 distance: 57 - 58: 8.781 distance: 57 - 59: 7.614 distance: 58 - 60: 12.790 distance: 59 - 61: 9.247 distance: 60 - 62: 11.257 distance: 61 - 62: 13.333 distance: 63 - 64: 9.327 distance: 64 - 65: 26.613 distance: 64 - 67: 6.129 distance: 65 - 66: 12.160 distance: 65 - 69: 12.036 distance: 66 - 86: 4.149 distance: 67 - 68: 23.243 distance: 69 - 70: 13.746 distance: 70 - 71: 19.847 distance: 71 - 72: 10.178 distance: 71 - 73: 8.510 distance: 73 - 74: 3.244 distance: 74 - 75: 4.503 distance: 74 - 77: 11.429 distance: 75 - 76: 15.879 distance: 75 - 78: 8.713 distance: 76 - 101: 16.847 distance: 78 - 79: 5.149 distance: 79 - 80: 8.365 distance: 79 - 82: 9.960 distance: 80 - 81: 3.083 distance: 80 - 86: 10.828 distance: 81 - 110: 8.578 distance: 82 - 83: 7.329 distance: 83 - 84: 13.693 distance: 83 - 85: 19.261 distance: 86 - 87: 12.322 distance: 87 - 90: 7.306 distance: 88 - 89: 12.572 distance: 88 - 94: 6.918 distance: 89 - 118: 8.041 distance: 90 - 91: 9.383 distance: 91 - 92: 4.492 distance: 92 - 93: 7.333 distance: 94 - 95: 3.507 distance: 95 - 96: 10.019 distance: 95 - 98: 4.737 distance: 96 - 97: 5.655 distance: 96 - 101: 4.500 distance: 97 - 124: 7.628 distance: 98 - 99: 6.858 distance: 101 - 102: 3.774 distance: 102 - 103: 3.509 distance: 102 - 105: 3.048 distance: 103 - 104: 5.539 distance: 103 - 110: 4.797 distance: 105 - 106: 3.560 distance: 106 - 107: 4.004