Starting phenix.real_space_refine on Thu May 22 01:22:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7om0_12982/05_2025/7om0_12982.cif Found real_map, /net/cci-nas-00/data/ceres_data/7om0_12982/05_2025/7om0_12982.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/cci-nas-00/data/ceres_data/7om0_12982/05_2025/7om0_12982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7om0_12982/05_2025/7om0_12982.map" model { file = "/net/cci-nas-00/data/ceres_data/7om0_12982/05_2025/7om0_12982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7om0_12982/05_2025/7om0_12982.cif" } 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 66 5.16 5 C 14072 2.51 5 N 3676 2.21 5 O 4210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22042 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3636 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 426} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.17, per 1000 atoms: 0.60 Number of scatterers: 22042 At special positions: 0 Unit cell: (132.02, 118.9, 130.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 18 15.00 O 4210 8.00 N 3676 7.00 C 14072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.10 Conformation dependent library (CDL) restraints added in 2.6 seconds 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5050 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 36 sheets defined 45.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 316 through 339 Processing helix chain 'A' and resid 349 through 361 Processing helix chain 'A' and resid 387 through 399 removed outlier: 3.607A pdb=" N LEU A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 486 through 502 removed outlier: 3.891A pdb=" N ASN A 502 " --> pdb=" O ASN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 550 through 555 removed outlier: 3.515A pdb=" N VAL A 553 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 555 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.608A pdb=" N LEU A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 624 " --> pdb=" O GLY A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.896A pdb=" N LYS A 644 " --> pdb=" O ASN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 650 through 664 Processing helix chain 'A' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 712 through 719 removed outlier: 3.895A pdb=" N GLU A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'B' and resid 317 through 339 Processing helix chain 'B' and resid 349 through 361 Processing helix chain 'B' and resid 387 through 399 Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 486 through 502 removed outlier: 3.533A pdb=" N ASN B 502 " --> pdb=" O ASN B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 532 Processing helix chain 'B' and resid 550 through 557 removed outlier: 3.837A pdb=" N VAL B 553 " --> pdb=" O LYS B 550 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 556 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 557 " --> pdb=" O LEU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 583 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 640 through 646 removed outlier: 4.004A pdb=" N LYS B 644 " --> pdb=" O ASN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 650 through 664 Processing helix chain 'B' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'B' and resid 687 through 695 Processing helix chain 'B' and resid 706 through 718 removed outlier: 6.261A pdb=" N PHE B 713 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N TYR B 714 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 715 " --> pdb=" O TYR B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 737 Processing helix chain 'F' and resid 317 through 339 Processing helix chain 'F' and resid 349 through 361 Processing helix chain 'F' and resid 387 through 399 Processing helix chain 'F' and resid 403 through 418 Processing helix chain 'F' and resid 475 through 483 Processing helix chain 'F' and resid 486 through 502 Processing helix chain 'F' and resid 520 through 532 Processing helix chain 'F' and resid 550 through 555 removed outlier: 3.588A pdb=" N VAL F 553 " --> pdb=" O LYS F 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU F 555 " --> pdb=" O SER F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 583 Processing helix chain 'F' and resid 618 through 624 removed outlier: 3.530A pdb=" N LEU F 622 " --> pdb=" O THR F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 646 removed outlier: 3.847A pdb=" N LYS F 644 " --> pdb=" O ASN F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 647 through 649 No H-bonds generated for 'chain 'F' and resid 647 through 649' Processing helix chain 'F' and resid 650 through 664 Processing helix chain 'F' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'F' and resid 687 through 696 Processing helix chain 'F' and resid 706 through 719 removed outlier: 6.428A pdb=" N PHE F 713 " --> pdb=" O ILE F 709 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR F 714 " --> pdb=" O VAL F 710 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS F 715 " --> pdb=" O TYR F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 728 through 737 Processing helix chain 'D' and resid 317 through 339 Processing helix chain 'D' and resid 349 through 361 Processing helix chain 'D' and resid 387 through 399 Processing helix chain 'D' and resid 403 through 418 Processing helix chain 'D' and resid 475 through 483 Processing helix chain 'D' and resid 486 through 502 Processing helix chain 'D' and resid 520 through 532 Processing helix chain 'D' and resid 550 through 555 removed outlier: 3.578A pdb=" N VAL D 553 " --> pdb=" O LYS D 550 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 555 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 583 Processing helix chain 'D' and resid 618 through 624 removed outlier: 3.502A pdb=" N LEU D 622 " --> pdb=" O THR D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 646 removed outlier: 3.903A pdb=" N LYS D 644 " --> pdb=" O ASN D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 649 No H-bonds generated for 'chain 'D' and resid 647 through 649' Processing helix chain 'D' and resid 650 through 664 Processing helix chain 'D' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 706 through 719 removed outlier: 7.069A pdb=" N PHE D 713 " --> pdb=" O ILE D 709 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR D 714 " --> pdb=" O VAL D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 737 Processing helix chain 'E' and resid 317 through 339 Processing helix chain 'E' and resid 349 through 361 Processing helix chain 'E' and resid 387 through 399 removed outlier: 3.569A pdb=" N LEU E 398 " --> pdb=" O VAL E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 418 Processing helix chain 'E' and resid 475 through 483 Processing helix chain 'E' and resid 486 through 502 removed outlier: 3.548A pdb=" N MET E 501 " --> pdb=" O ILE E 497 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN E 502 " --> pdb=" O ASN E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 532 Processing helix chain 'E' and resid 552 through 557 removed outlier: 3.833A pdb=" N GLY E 556 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 557 " --> pdb=" O LEU E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 583 Processing helix chain 'E' and resid 618 through 624 removed outlier: 3.565A pdb=" N ARG E 624 " --> pdb=" O GLY E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 646 removed outlier: 4.031A pdb=" N LYS E 644 " --> pdb=" O ASN E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 649 No H-bonds generated for 'chain 'E' and resid 647 through 649' Processing helix chain 'E' and resid 650 through 664 Processing helix chain 'E' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'E' and resid 687 through 695 Processing helix chain 'E' and resid 706 through 712 Processing helix chain 'E' and resid 712 through 719 Processing helix chain 'E' and resid 728 through 737 Processing helix chain 'C' and resid 317 through 339 Processing helix chain 'C' and resid 349 through 361 Processing helix chain 'C' and resid 387 through 399 removed outlier: 3.595A pdb=" N LEU C 398 " --> pdb=" O VAL C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 418 Processing helix chain 'C' and resid 475 through 483 Processing helix chain 'C' and resid 486 through 502 removed outlier: 3.798A pdb=" N ASN C 502 " --> pdb=" O ASN C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 532 Processing helix chain 'C' and resid 550 through 555 removed outlier: 3.603A pdb=" N GLU C 555 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 583 Processing helix chain 'C' and resid 618 through 624 removed outlier: 3.533A pdb=" N LEU C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG C 624 " --> pdb=" O GLY C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 646 removed outlier: 3.893A pdb=" N LYS C 644 " --> pdb=" O ASN C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 650 through 664 Processing helix chain 'C' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'C' and resid 687 through 695 Processing helix chain 'C' and resid 706 through 719 removed outlier: 6.117A pdb=" N PHE C 713 " --> pdb=" O ILE C 709 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N TYR C 714 " --> pdb=" O VAL C 710 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS C 715 " --> pdb=" O TYR C 711 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 716 " --> pdb=" O ALA C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 737 removed outlier: 3.801A pdb=" N PHE C 731 " --> pdb=" O SER C 727 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA4, first strand: chain 'A' and resid 537 through 539 removed outlier: 5.809A pdb=" N ALA A 538 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP A 563 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 560 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N SER A 607 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY A 562 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 514 " --> pdb=" O VAL A 628 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA6, first strand: chain 'A' and resid 586 through 589 removed outlier: 3.582A pdb=" N ALA A 598 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 363 through 365 Processing sheet with id=AA8, first strand: chain 'B' and resid 429 through 431 Processing sheet with id=AA9, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AB1, first strand: chain 'B' and resid 537 through 538 removed outlier: 5.939A pdb=" N ALA B 538 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP B 563 " --> pdb=" O ALA B 538 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP B 564 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ALA B 510 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL B 628 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE B 512 " --> pdb=" O VAL B 628 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 570 through 571 Processing sheet with id=AB3, first strand: chain 'B' and resid 586 through 588 Processing sheet with id=AB4, first strand: chain 'F' and resid 363 through 365 Processing sheet with id=AB5, first strand: chain 'F' and resid 429 through 431 Processing sheet with id=AB6, first strand: chain 'F' and resid 469 through 470 Processing sheet with id=AB7, first strand: chain 'F' and resid 537 through 539 removed outlier: 6.001A pdb=" N ALA F 538 " --> pdb=" O ILE F 561 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASP F 563 " --> pdb=" O ALA F 538 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP F 564 " --> pdb=" O SER F 607 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA F 510 " --> pdb=" O LEU F 626 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL F 628 " --> pdb=" O ALA F 510 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE F 512 " --> pdb=" O VAL F 628 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 570 through 571 Processing sheet with id=AB9, first strand: chain 'F' and resid 586 through 588 Processing sheet with id=AC1, first strand: chain 'D' and resid 363 through 365 Processing sheet with id=AC2, first strand: chain 'D' and resid 429 through 431 Processing sheet with id=AC3, first strand: chain 'D' and resid 469 through 470 Processing sheet with id=AC4, first strand: chain 'D' and resid 537 through 539 removed outlier: 5.956A pdb=" N ALA D 538 " --> pdb=" O ILE D 561 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ALA D 510 " --> pdb=" O LEU D 626 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL D 628 " --> pdb=" O ALA D 510 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE D 512 " --> pdb=" O VAL D 628 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 570 through 571 Processing sheet with id=AC6, first strand: chain 'D' and resid 586 through 589 Processing sheet with id=AC7, first strand: chain 'E' and resid 363 through 364 Processing sheet with id=AC8, first strand: chain 'E' and resid 429 through 431 Processing sheet with id=AC9, first strand: chain 'E' and resid 469 through 470 Processing sheet with id=AD1, first strand: chain 'E' and resid 537 through 539 removed outlier: 5.795A pdb=" N ALA E 538 " --> pdb=" O ILE E 561 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP E 563 " --> pdb=" O ALA E 538 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP E 564 " --> pdb=" O SER E 607 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 514 " --> pdb=" O VAL E 628 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 570 through 571 Processing sheet with id=AD3, first strand: chain 'E' and resid 586 through 588 removed outlier: 3.521A pdb=" N ALA E 598 " --> pdb=" O VAL E 586 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 363 through 364 Processing sheet with id=AD5, first strand: chain 'C' and resid 429 through 431 Processing sheet with id=AD6, first strand: chain 'C' and resid 469 through 470 Processing sheet with id=AD7, first strand: chain 'C' and resid 537 through 539 removed outlier: 5.837A pdb=" N ALA C 538 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP C 563 " --> pdb=" O ALA C 538 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP C 564 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ALA C 510 " --> pdb=" O LEU C 626 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL C 628 " --> pdb=" O ALA C 510 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE C 512 " --> pdb=" O VAL C 628 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 570 through 571 Processing sheet with id=AD9, first strand: chain 'C' and resid 586 through 589 removed outlier: 3.591A pdb=" N ALA C 598 " --> pdb=" O VAL C 586 " (cutoff:3.500A) 900 hydrogen bonds defined for protein. 2586 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: 6.95 Time building geometry restraints manager: 5.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6153 1.33 - 1.45: 3788 1.45 - 1.57: 12425 1.57 - 1.69: 31 1.69 - 1.81: 113 Bond restraints: 22510 Sorted by residual: bond pdb=" O3A ANP C1201 " pdb=" PB ANP C1201 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" O3A ANP B1201 " pdb=" PB ANP B1201 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" O3A ANP F1201 " pdb=" PB ANP F1201 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" O3A ANP A1201 " pdb=" PB ANP A1201 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" O3A ANP D1201 " pdb=" PB ANP D1201 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.18e+01 ... (remaining 22505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 30284 3.56 - 7.13: 107 7.13 - 10.69: 12 10.69 - 14.25: 6 14.25 - 17.82: 6 Bond angle restraints: 30415 Sorted by residual: angle pdb=" PB ANP C1201 " pdb=" N3B ANP C1201 " pdb=" PG ANP C1201 " ideal model delta sigma weight residual 126.95 109.13 17.82 3.00e+00 1.11e-01 3.53e+01 angle pdb=" PB ANP F1201 " pdb=" N3B ANP F1201 " pdb=" PG ANP F1201 " ideal model delta sigma weight residual 126.95 109.26 17.69 3.00e+00 1.11e-01 3.48e+01 angle pdb=" PB ANP A1201 " pdb=" N3B ANP A1201 " pdb=" PG ANP A1201 " ideal model delta sigma weight residual 126.95 109.30 17.65 3.00e+00 1.11e-01 3.46e+01 angle pdb=" PB ANP B1201 " pdb=" N3B ANP B1201 " pdb=" PG ANP B1201 " ideal model delta sigma weight residual 126.95 109.32 17.63 3.00e+00 1.11e-01 3.45e+01 angle pdb=" PB ANP E1201 " pdb=" N3B ANP E1201 " pdb=" PG ANP E1201 " ideal model delta sigma weight residual 126.95 109.33 17.62 3.00e+00 1.11e-01 3.45e+01 ... (remaining 30410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.19: 13279 33.19 - 66.38: 292 66.38 - 99.57: 56 99.57 - 132.75: 0 132.75 - 165.94: 6 Dihedral angle restraints: 13633 sinusoidal: 5812 harmonic: 7821 Sorted by residual: dihedral pdb=" O1B ANP C1201 " pdb=" N3B ANP C1201 " pdb=" PB ANP C1201 " pdb=" PG ANP C1201 " ideal model delta sinusoidal sigma weight residual 35.15 -130.79 165.94 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" O1B ANP B1201 " pdb=" N3B ANP B1201 " pdb=" PB ANP B1201 " pdb=" PG ANP B1201 " ideal model delta sinusoidal sigma weight residual 35.15 -129.46 164.61 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" O1B ANP E1201 " pdb=" N3B ANP E1201 " pdb=" PB ANP E1201 " pdb=" PG ANP E1201 " ideal model delta sinusoidal sigma weight residual 35.15 -129.25 164.40 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 13630 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2727 0.056 - 0.111: 470 0.111 - 0.167: 57 0.167 - 0.222: 2 0.222 - 0.278: 7 Chirality restraints: 3263 Sorted by residual: chirality pdb=" C3' ANP B1201 " pdb=" C2' ANP B1201 " pdb=" C4' ANP B1201 " pdb=" O3' ANP B1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3' ANP C1201 " pdb=" C2' ANP C1201 " pdb=" C4' ANP C1201 " pdb=" O3' ANP C1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' ANP A1201 " pdb=" C2' ANP A1201 " pdb=" C4' ANP A1201 " pdb=" O3' ANP A1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 3260 not shown) Planarity restraints: 3898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 349 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO D 350 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 350 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 350 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 448 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO B 449 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 449 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 449 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 448 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.66e+00 pdb=" N PRO E 449 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 449 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 449 " 0.018 5.00e-02 4.00e+02 ... (remaining 3895 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2104 2.75 - 3.29: 23036 3.29 - 3.82: 36442 3.82 - 4.36: 44988 4.36 - 4.90: 74127 Nonbonded interactions: 180697 Sorted by model distance: nonbonded pdb=" OG SER A 574 " pdb=" OD2 ASP A 616 " model vdw 2.209 3.040 nonbonded pdb=" OE1 GLU E 680 " pdb=" OH TYR E 690 " model vdw 2.210 3.040 nonbonded pdb=" OG SER C 574 " pdb=" OD2 ASP C 616 " model vdw 2.223 3.040 nonbonded pdb=" OG SER F 574 " pdb=" OD2 ASP F 616 " model vdw 2.242 3.040 nonbonded pdb=" OE1 GLU D 547 " pdb=" NZ LYS D 550 " model vdw 2.246 3.120 ... (remaining 180692 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 316 through 750 or resid 754 through 766 or resid 1201)) selection = (chain 'B' and (resid 316 through 750 or resid 754 through 766 or resid 1201)) selection = (chain 'C' and (resid 316 through 750 or resid 754 through 766 or resid 1201)) selection = chain 'D' selection = (chain 'E' and (resid 316 through 750 or resid 754 through 766 or resid 1201)) selection = (chain 'F' and (resid 316 through 750 or resid 754 through 766 or resid 1201)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 47.400 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.004 0.145 22510 Z= 0.242 Angle : 0.633 17.815 30415 Z= 0.324 Chirality : 0.043 0.278 3263 Planarity : 0.003 0.033 3898 Dihedral : 15.336 165.942 8583 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.04 % Allowed : 0.54 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.16), residues: 2597 helix: 2.35 (0.16), residues: 1037 sheet: 0.21 (0.33), residues: 250 loop : -0.28 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 335 HIS 0.006 0.001 HIS B 402 PHE 0.021 0.001 PHE B 713 TYR 0.019 0.001 TYR D 711 ARG 0.002 0.000 ARG C 597 Details of bonding type rmsd hydrogen bonds : bond 0.17284 ( 900) hydrogen bonds : angle 6.13486 ( 2586) covalent geometry : bond 0.00442 (22510) covalent geometry : angle 0.63315 (30415) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 3.813 Fit side-chains REVERT: A 708 TYR cc_start: 0.8627 (p90) cc_final: 0.8240 (p90) REVERT: A 732 TYR cc_start: 0.7985 (t80) cc_final: 0.7683 (t80) REVERT: B 331 MET cc_start: 0.8724 (mtp) cc_final: 0.8450 (mtp) REVERT: B 737 HIS cc_start: 0.8696 (t70) cc_final: 0.8159 (t70) REVERT: F 690 TYR cc_start: 0.9176 (t80) cc_final: 0.8460 (t80) REVERT: F 737 HIS cc_start: 0.8415 (t70) cc_final: 0.7875 (t70) REVERT: D 737 HIS cc_start: 0.8420 (t70) cc_final: 0.7864 (t70) REVERT: C 331 MET cc_start: 0.8938 (mtp) cc_final: 0.8730 (mtp) REVERT: C 690 TYR cc_start: 0.9119 (t80) cc_final: 0.8539 (t80) REVERT: C 737 HIS cc_start: 0.8463 (t70) cc_final: 0.7995 (t70) outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.3195 time to fit residues: 49.8032 Evaluate side-chains 77 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 595 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.0060 chunk 200 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 239 optimal weight: 10.0000 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.082502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.053782 restraints weight = 80911.721| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.49 r_work: 0.2822 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22510 Z= 0.246 Angle : 0.536 5.968 30415 Z= 0.289 Chirality : 0.044 0.190 3263 Planarity : 0.004 0.052 3898 Dihedral : 11.830 159.792 3061 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.45 % Allowed : 3.91 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.16), residues: 2597 helix: 2.21 (0.16), residues: 1094 sheet: 0.30 (0.36), residues: 225 loop : -0.23 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 335 HIS 0.007 0.001 HIS E 402 PHE 0.013 0.001 PHE B 682 TYR 0.013 0.001 TYR F 717 ARG 0.003 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 900) hydrogen bonds : angle 5.12710 ( 2586) covalent geometry : bond 0.00548 (22510) covalent geometry : angle 0.53618 (30415) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 2.627 Fit side-chains REVERT: A 708 TYR cc_start: 0.8531 (p90) cc_final: 0.8301 (p90) REVERT: A 737 HIS cc_start: 0.8393 (t70) cc_final: 0.7969 (m90) REVERT: B 737 HIS cc_start: 0.8555 (t70) cc_final: 0.7762 (t70) REVERT: F 690 TYR cc_start: 0.8925 (t80) cc_final: 0.8171 (t80) REVERT: F 737 HIS cc_start: 0.8404 (t70) cc_final: 0.7740 (t70) REVERT: D 737 HIS cc_start: 0.8519 (t70) cc_final: 0.7876 (t70) REVERT: C 690 TYR cc_start: 0.9056 (t80) cc_final: 0.8327 (t80) REVERT: C 737 HIS cc_start: 0.8596 (t70) cc_final: 0.7964 (t70) outliers start: 11 outliers final: 1 residues processed: 81 average time/residue: 0.2994 time to fit residues: 42.4333 Evaluate side-chains 79 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 595 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 159 optimal weight: 7.9990 chunk 180 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 130 optimal weight: 40.0000 chunk 98 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN E 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.083088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.054300 restraints weight = 79957.802| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.50 r_work: 0.2838 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22510 Z= 0.180 Angle : 0.470 6.405 30415 Z= 0.258 Chirality : 0.042 0.172 3263 Planarity : 0.003 0.050 3898 Dihedral : 10.158 155.929 3061 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.86 % Allowed : 6.18 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.16), residues: 2597 helix: 2.24 (0.16), residues: 1094 sheet: 0.21 (0.36), residues: 220 loop : -0.25 (0.16), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 335 HIS 0.005 0.001 HIS E 402 PHE 0.012 0.001 PHE C 735 TYR 0.024 0.001 TYR D 711 ARG 0.001 0.000 ARG F 703 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 900) hydrogen bonds : angle 4.81305 ( 2586) covalent geometry : bond 0.00401 (22510) covalent geometry : angle 0.47018 (30415) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 2.585 Fit side-chains revert: symmetry clash REVERT: A 708 TYR cc_start: 0.8522 (p90) cc_final: 0.8295 (p90) REVERT: A 737 HIS cc_start: 0.8410 (t70) cc_final: 0.8010 (m90) REVERT: B 737 HIS cc_start: 0.8526 (t70) cc_final: 0.7725 (t70) REVERT: F 690 TYR cc_start: 0.8866 (t80) cc_final: 0.8121 (t80) REVERT: F 737 HIS cc_start: 0.8414 (t70) cc_final: 0.7706 (t70) REVERT: D 737 HIS cc_start: 0.8495 (t70) cc_final: 0.7799 (t70) REVERT: E 737 HIS cc_start: 0.8581 (t70) cc_final: 0.7934 (m90) REVERT: C 690 TYR cc_start: 0.8993 (t80) cc_final: 0.8269 (t80) REVERT: C 737 HIS cc_start: 0.8592 (t70) cc_final: 0.7927 (t70) outliers start: 21 outliers final: 8 residues processed: 87 average time/residue: 0.3035 time to fit residues: 46.4047 Evaluate side-chains 88 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 731 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 241 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.082779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.054561 restraints weight = 83986.625| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.46 r_work: 0.2816 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 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 : 0.006 0.046 22510 Z= 0.247 Angle : 0.522 8.530 30415 Z= 0.284 Chirality : 0.043 0.171 3263 Planarity : 0.003 0.052 3898 Dihedral : 9.885 153.018 3061 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.82 % Allowed : 7.37 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.16), residues: 2597 helix: 1.99 (0.16), residues: 1129 sheet: 0.13 (0.36), residues: 220 loop : -0.36 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 335 HIS 0.004 0.001 HIS E 402 PHE 0.018 0.001 PHE E 713 TYR 0.023 0.001 TYR D 711 ARG 0.002 0.000 ARG F 507 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 900) hydrogen bonds : angle 4.84643 ( 2586) covalent geometry : bond 0.00554 (22510) covalent geometry : angle 0.52168 (30415) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 2.530 Fit side-chains REVERT: A 708 TYR cc_start: 0.8602 (p90) cc_final: 0.8354 (p90) REVERT: B 737 HIS cc_start: 0.8568 (t70) cc_final: 0.7747 (t70) REVERT: F 690 TYR cc_start: 0.8933 (t80) cc_final: 0.8168 (t80) REVERT: F 713 PHE cc_start: 0.9285 (t80) cc_final: 0.9022 (t80) REVERT: F 737 HIS cc_start: 0.8396 (t70) cc_final: 0.7686 (t70) REVERT: D 737 HIS cc_start: 0.8472 (t70) cc_final: 0.7780 (t70) REVERT: E 737 HIS cc_start: 0.8646 (t70) cc_final: 0.7955 (m90) REVERT: C 690 TYR cc_start: 0.9035 (t80) cc_final: 0.8332 (t80) REVERT: C 737 HIS cc_start: 0.8577 (t70) cc_final: 0.7936 (t70) outliers start: 20 outliers final: 8 residues processed: 85 average time/residue: 0.3092 time to fit residues: 45.3123 Evaluate side-chains 86 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 731 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 213 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.084138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.055229 restraints weight = 83749.621| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.61 r_work: 0.2845 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22510 Z= 0.134 Angle : 0.450 7.616 30415 Z= 0.247 Chirality : 0.041 0.163 3263 Planarity : 0.003 0.049 3898 Dihedral : 9.605 150.233 3059 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.62 % Allowed : 8.32 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.16), residues: 2597 helix: 2.27 (0.16), residues: 1099 sheet: 0.04 (0.36), residues: 223 loop : -0.31 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 478 HIS 0.003 0.000 HIS E 402 PHE 0.017 0.001 PHE E 713 TYR 0.023 0.001 TYR D 711 ARG 0.002 0.000 ARG F 703 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 900) hydrogen bonds : angle 4.60589 ( 2586) covalent geometry : bond 0.00296 (22510) covalent geometry : angle 0.44953 (30415) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 2.462 Fit side-chains REVERT: A 708 TYR cc_start: 0.8547 (p90) cc_final: 0.8295 (p90) REVERT: A 737 HIS cc_start: 0.8561 (t70) cc_final: 0.7981 (m90) REVERT: B 737 HIS cc_start: 0.8611 (t70) cc_final: 0.7828 (t70) REVERT: F 690 TYR cc_start: 0.8945 (t80) cc_final: 0.8147 (t80) REVERT: F 737 HIS cc_start: 0.8411 (t70) cc_final: 0.7752 (t70) REVERT: D 737 HIS cc_start: 0.8500 (t70) cc_final: 0.7803 (t70) REVERT: E 737 HIS cc_start: 0.8683 (t70) cc_final: 0.7952 (m90) REVERT: C 690 TYR cc_start: 0.9045 (t80) cc_final: 0.8300 (t80) REVERT: C 737 HIS cc_start: 0.8612 (t70) cc_final: 0.7948 (t70) outliers start: 15 outliers final: 5 residues processed: 79 average time/residue: 0.2887 time to fit residues: 40.4274 Evaluate side-chains 81 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain C residue 731 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 145 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 170 optimal weight: 40.0000 chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 228 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 734 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.083495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.055174 restraints weight = 82523.471| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.48 r_work: 0.2841 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22510 Z= 0.174 Angle : 0.466 8.582 30415 Z= 0.255 Chirality : 0.042 0.159 3263 Planarity : 0.003 0.049 3898 Dihedral : 9.564 150.666 3059 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.95 % Allowed : 8.44 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.16), residues: 2597 helix: 2.33 (0.16), residues: 1092 sheet: 0.02 (0.36), residues: 223 loop : -0.35 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 335 HIS 0.003 0.001 HIS E 402 PHE 0.009 0.001 PHE F 682 TYR 0.020 0.001 TYR F 717 ARG 0.002 0.000 ARG F 703 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 900) hydrogen bonds : angle 4.60779 ( 2586) covalent geometry : bond 0.00389 (22510) covalent geometry : angle 0.46574 (30415) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 2.603 Fit side-chains REVERT: A 708 TYR cc_start: 0.8548 (p90) cc_final: 0.8295 (p90) REVERT: A 737 HIS cc_start: 0.8552 (t70) cc_final: 0.8014 (m90) REVERT: B 737 HIS cc_start: 0.8610 (t70) cc_final: 0.7818 (t70) REVERT: F 690 TYR cc_start: 0.8968 (t80) cc_final: 0.8169 (t80) REVERT: F 737 HIS cc_start: 0.8384 (t70) cc_final: 0.7717 (t70) REVERT: D 737 HIS cc_start: 0.8456 (t70) cc_final: 0.7757 (t70) REVERT: E 737 HIS cc_start: 0.8672 (t70) cc_final: 0.7952 (m90) REVERT: C 690 TYR cc_start: 0.9054 (t80) cc_final: 0.8312 (t80) REVERT: C 737 HIS cc_start: 0.8538 (t70) cc_final: 0.7847 (t70) outliers start: 23 outliers final: 12 residues processed: 88 average time/residue: 0.2842 time to fit residues: 44.4134 Evaluate side-chains 87 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain E residue 689 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 731 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.5406 > 50: distance: 3 - 20: 6.465 distance: 8 - 30: 8.597 distance: 14 - 39: 9.566 distance: 18 - 20: 6.000 distance: 19 - 48: 17.448 distance: 20 - 21: 7.380 distance: 21 - 22: 9.990 distance: 21 - 24: 10.198 distance: 22 - 23: 28.164 distance: 22 - 30: 11.955 distance: 23 - 59: 43.997 distance: 24 - 25: 8.990 distance: 25 - 26: 16.314 distance: 26 - 28: 9.926 distance: 27 - 29: 9.904 distance: 28 - 29: 5.607 distance: 31 - 32: 12.920 distance: 31 - 34: 9.389 distance: 32 - 33: 10.057 distance: 32 - 39: 14.118 distance: 33 - 66: 25.791 distance: 34 - 35: 23.435 distance: 35 - 36: 4.696 distance: 36 - 37: 23.135 distance: 36 - 38: 15.909 distance: 39 - 40: 12.164 distance: 40 - 41: 6.931 distance: 40 - 43: 13.564 distance: 41 - 42: 12.458 distance: 41 - 48: 20.667 distance: 42 - 75: 21.698 distance: 43 - 44: 21.052 distance: 44 - 45: 16.291 distance: 45 - 46: 15.246 distance: 45 - 47: 27.998 distance: 48 - 49: 17.930 distance: 49 - 50: 37.149 distance: 49 - 52: 11.718 distance: 50 - 51: 22.506 distance: 50 - 59: 49.413 distance: 51 - 83: 29.908 distance: 52 - 53: 7.916 distance: 53 - 54: 18.190 distance: 54 - 55: 7.555 distance: 55 - 56: 16.704 distance: 56 - 57: 17.656 distance: 56 - 58: 10.622 distance: 59 - 60: 51.666 distance: 60 - 61: 17.880 distance: 60 - 63: 20.591 distance: 61 - 62: 13.327 distance: 61 - 66: 26.583 distance: 62 - 92: 39.004 distance: 63 - 64: 40.101 distance: 63 - 65: 12.111 distance: 66 - 67: 11.080 distance: 67 - 68: 21.992 distance: 67 - 70: 14.566 distance: 68 - 69: 14.883 distance: 68 - 75: 22.366 distance: 69 - 101: 15.552 distance: 70 - 71: 9.276 distance: 71 - 72: 21.747 distance: 72 - 73: 5.938 distance: 73 - 74: 10.490 distance: 75 - 76: 12.475 distance: 76 - 77: 13.914 distance: 76 - 79: 17.345 distance: 77 - 78: 18.914 distance: 77 - 83: 9.885 distance: 78 - 109: 17.563 distance: 79 - 80: 37.139 distance: 80 - 81: 30.915 distance: 81 - 82: 10.228 distance: 83 - 84: 8.232 distance: 84 - 85: 20.894 distance: 84 - 87: 19.565 distance: 85 - 86: 14.858 distance: 85 - 92: 24.567 distance: 86 - 118: 14.863 distance: 87 - 88: 20.245 distance: 88 - 89: 10.248 distance: 89 - 90: 23.086 distance: 89 - 91: 8.406 distance: 92 - 93: 13.139 distance: 93 - 94: 9.883 distance: 93 - 96: 3.747 distance: 94 - 95: 26.000 distance: 94 - 101: 34.532 distance: 95 - 126: 19.821 distance: 96 - 97: 23.010 distance: 97 - 98: 25.581 distance: 98 - 99: 12.853 distance: 98 - 100: 19.303 distance: 101 - 102: 21.904 distance: 102 - 103: 8.535 distance: 102 - 105: 6.194 distance: 103 - 104: 17.067 distance: 103 - 109: 6.273 distance: 104 - 134: 18.811 distance: 105 - 106: 17.258 distance: 106 - 107: 11.569 distance: 106 - 108: 10.310