Starting phenix.real_space_refine on Sun Nov 17 14:14:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/11_2024/7kej_22839.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/11_2024/7kej_22839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/11_2024/7kej_22839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/11_2024/7kej_22839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/11_2024/7kej_22839.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/11_2024/7kej_22839.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 8718 2.51 5 N 2322 2.21 5 O 2709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13806 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 984 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "K" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "C" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 984 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "A" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "G" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 984 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "J" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.92, per 1000 atoms: 0.43 Number of scatterers: 13806 At special positions: 0 Unit cell: (156.56, 160.68, 124.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2709 8.00 N 2322 7.00 C 8718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.04 Simple disulfide: pdb=" SG CYS E 601 " - pdb=" SG CYS E 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.03 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 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 401 " - " ASN A 257 " " NAG A 402 " - " ASN A 268 " " NAG A 403 " - " ASN A 228 " " NAG B 401 " - " ASN B 257 " " NAG B 402 " - " ASN B 268 " " NAG B 403 " - " ASN B 228 " " NAG C 401 " - " ASN C 257 " " NAG C 402 " - " ASN C 268 " " NAG C 403 " - " ASN C 228 " " NAG M 1 " - " ASN E 563 " " NAG N 1 " - " ASN F 563 " " NAG O 1 " - " ASN D 563 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.2 seconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 30 sheets defined 15.7% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 25 through 28 Processing helix chain 'K' and resid 78 through 82 Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 553 through 575 removed outlier: 4.848A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 598 removed outlier: 3.845A pdb=" N ARG E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'L' and resid 25 through 28 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 553 through 575 removed outlier: 4.847A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.845A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'J' and resid 25 through 28 Processing helix chain 'J' and resid 78 through 82 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 553 through 575 removed outlier: 4.847A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.845A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 36 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 36 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 114 removed outlier: 6.405A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG B 136 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 14.122A pdb=" N THR B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ASP B 237 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 277 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN B 243 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE B 274 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASN H 101 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.070A pdb=" N CYS H 96 " --> pdb=" O TRP H 118 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TRP H 118 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG H 98 " --> pdb=" O ASP H 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU K 108 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL K 12 " --> pdb=" O LEU K 108 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP K 34 " --> pdb=" O VAL K 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU K 108 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL K 12 " --> pdb=" O LEU K 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AB1, first strand: chain 'E' and resid 601 through 602 removed outlier: 6.641A pdb=" N CYS E 601 " --> pdb=" O GLU F 611 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 610 through 611 Processing sheet with id=AB3, first strand: chain 'C' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB6, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.405A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 14.122A pdb=" N THR C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ASP C 237 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL C 277 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN C 243 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE C 274 " --> pdb=" O GLN I 99 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASN I 101 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.070A pdb=" N CYS I 96 " --> pdb=" O TRP I 118 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP I 118 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG I 98 " --> pdb=" O ASP I 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU L 108 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL L 12 " --> pdb=" O LEU L 108 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU L 108 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL L 12 " --> pdb=" O LEU L 108 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AC3, first strand: chain 'F' and resid 601 through 602 removed outlier: 6.641A pdb=" N CYS F 601 " --> pdb=" O GLU D 611 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AC7, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.405A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 14.122A pdb=" N THR A 217 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ASP A 237 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A 277 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN A 243 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE A 274 " --> pdb=" O GLN G 99 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN G 101 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 7.070A pdb=" N CYS G 96 " --> pdb=" O TRP G 118 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP G 118 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG G 98 " --> pdb=" O ASP G 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'J' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU J 108 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL J 12 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP J 34 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU J 108 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL J 12 " --> pdb=" O LEU J 108 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 18 through 23 532 hydrogen bonds defined for protein. 1290 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: 5.94 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2797 1.32 - 1.45: 4352 1.45 - 1.58: 6842 1.58 - 1.72: 55 1.72 - 1.85: 69 Bond restraints: 14115 Sorted by residual: bond pdb=" CB HIS C 154 " pdb=" CG HIS C 154 " ideal model delta sigma weight residual 1.497 1.404 0.093 1.40e-02 5.10e+03 4.41e+01 bond pdb=" CB HIS B 154 " pdb=" CG HIS B 154 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.35e+01 bond pdb=" CB HIS A 154 " pdb=" CG HIS A 154 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.33e+01 bond pdb=" CB TYR B 99 " pdb=" CG TYR B 99 " ideal model delta sigma weight residual 1.512 1.381 0.131 2.20e-02 2.07e+03 3.53e+01 bond pdb=" CB TYR C 99 " pdb=" CG TYR C 99 " ideal model delta sigma weight residual 1.512 1.381 0.131 2.20e-02 2.07e+03 3.52e+01 ... (remaining 14110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 16160 2.24 - 4.48: 2505 4.48 - 6.72: 450 6.72 - 8.97: 55 8.97 - 11.21: 9 Bond angle restraints: 19179 Sorted by residual: angle pdb=" N ARG K 60 " pdb=" CA ARG K 60 " pdb=" C ARG K 60 " ideal model delta sigma weight residual 114.56 103.35 11.21 1.27e+00 6.20e-01 7.79e+01 angle pdb=" N ARG J 60 " pdb=" CA ARG J 60 " pdb=" C ARG J 60 " ideal model delta sigma weight residual 114.56 103.37 11.19 1.27e+00 6.20e-01 7.76e+01 angle pdb=" N ARG L 60 " pdb=" CA ARG L 60 " pdb=" C ARG L 60 " ideal model delta sigma weight residual 114.56 103.37 11.19 1.27e+00 6.20e-01 7.76e+01 angle pdb=" C LEU B 122 " pdb=" N PRO B 123 " pdb=" CA PRO B 123 " ideal model delta sigma weight residual 119.85 127.15 -7.30 1.01e+00 9.80e-01 5.23e+01 angle pdb=" C LEU C 122 " pdb=" N PRO C 123 " pdb=" CA PRO C 123 " ideal model delta sigma weight residual 119.85 127.14 -7.29 1.01e+00 9.80e-01 5.21e+01 ... (remaining 19174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 8340 21.17 - 42.35: 171 42.35 - 63.52: 39 63.52 - 84.70: 30 84.70 - 105.87: 21 Dihedral angle restraints: 8601 sinusoidal: 3645 harmonic: 4956 Sorted by residual: dihedral pdb=" CB CYS B 108 " pdb=" SG CYS B 108 " pdb=" SG CYS B 135 " pdb=" CB CYS B 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.12 -37.12 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS C 108 " pdb=" SG CYS C 108 " pdb=" SG CYS C 135 " pdb=" CB CYS C 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.11 -37.11 1 1.00e+01 1.00e-02 1.94e+01 dihedral pdb=" CB CYS A 108 " pdb=" SG CYS A 108 " pdb=" SG CYS A 135 " pdb=" CB CYS A 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.11 -37.11 1 1.00e+01 1.00e-02 1.94e+01 ... (remaining 8598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1529 0.094 - 0.187: 507 0.187 - 0.281: 92 0.281 - 0.375: 34 0.375 - 0.468: 25 Chirality restraints: 2187 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.02e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 ... (remaining 2184 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 228 " -0.045 2.00e-02 2.50e+03 4.88e-02 2.98e+01 pdb=" CG ASN C 228 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN C 228 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 228 " 0.079 2.00e-02 2.50e+03 pdb=" C1 NAG C 403 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 228 " 0.045 2.00e-02 2.50e+03 4.86e-02 2.96e+01 pdb=" CG ASN B 228 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 228 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 228 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG B 403 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 228 " 0.045 2.00e-02 2.50e+03 4.86e-02 2.95e+01 pdb=" CG ASN A 228 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 228 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 228 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG A 403 " 0.058 2.00e-02 2.50e+03 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 3 1.94 - 2.68: 491 2.68 - 3.42: 17447 3.42 - 4.16: 34283 4.16 - 4.90: 57572 Nonbonded interactions: 109796 Sorted by model distance: nonbonded pdb=" OE1 GLU G 102 " pdb=" OH TYR G 112 " model vdw 1.201 3.040 nonbonded pdb=" OE1 GLU H 102 " pdb=" OH TYR H 112 " model vdw 1.201 3.040 nonbonded pdb=" OE1 GLU I 102 " pdb=" OH TYR I 112 " model vdw 1.202 3.040 nonbonded pdb=" CD GLU G 102 " pdb=" OH TYR G 112 " model vdw 2.293 3.270 nonbonded pdb=" CD GLU I 102 " pdb=" OH TYR I 112 " model vdw 2.293 3.270 ... (remaining 109791 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.240 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.021 0.148 14115 Z= 1.348 Angle : 1.725 11.208 19179 Z= 1.152 Chirality : 0.107 0.468 2187 Planarity : 0.008 0.038 2442 Dihedral : 11.824 105.871 5391 Min Nonbonded Distance : 1.201 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.20 (0.19), residues: 1704 helix: 1.45 (0.35), residues: 156 sheet: 0.90 (0.20), residues: 594 loop : 0.77 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.008 TRP A 86 HIS 0.006 0.002 HIS D 602 PHE 0.020 0.005 PHE C 248 TYR 0.066 0.009 TYR B 99 ARG 0.006 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 ARG cc_start: 0.7902 (tpt90) cc_final: 0.7629 (mpt-90) REVERT: H 13 LYS cc_start: 0.7170 (mttm) cc_final: 0.6827 (mppt) REVERT: H 115 MET cc_start: 0.8962 (mpp) cc_final: 0.8641 (mpp) REVERT: K 16 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6179 (tm-30) REVERT: K 17 THR cc_start: 0.8371 (m) cc_final: 0.7928 (m) REVERT: K 30 TYR cc_start: 0.6837 (m-80) cc_final: 0.6620 (m-80) REVERT: K 74 ILE cc_start: 0.8975 (mt) cc_final: 0.8748 (mt) REVERT: K 91 ASP cc_start: 0.8784 (t0) cc_final: 0.8580 (t0) REVERT: E 527 ILE cc_start: 0.7701 (mm) cc_final: 0.7351 (pt) REVERT: C 278 ASN cc_start: 0.8247 (t0) cc_final: 0.8039 (t0) REVERT: C 281 ILE cc_start: 0.7935 (pt) cc_final: 0.7572 (pt) REVERT: I 13 LYS cc_start: 0.7176 (mttm) cc_final: 0.6767 (mptt) REVERT: I 115 MET cc_start: 0.9000 (mpp) cc_final: 0.8683 (mpp) REVERT: L 16 GLN cc_start: 0.7097 (mm-40) cc_final: 0.6605 (tt0) REVERT: L 28 ARG cc_start: 0.7445 (mtt-85) cc_final: 0.7243 (ttm110) REVERT: L 51 ASN cc_start: 0.8398 (p0) cc_final: 0.8163 (p0) REVERT: L 91 ASP cc_start: 0.8757 (t0) cc_final: 0.8519 (t0) REVERT: F 527 ILE cc_start: 0.7826 (mm) cc_final: 0.7593 (pt) REVERT: F 588 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8900 (mmtp) REVERT: G 13 LYS cc_start: 0.7393 (mttm) cc_final: 0.6930 (mppt) REVERT: G 115 MET cc_start: 0.8951 (mpp) cc_final: 0.8661 (mpp) REVERT: J 16 GLN cc_start: 0.7201 (mm-40) cc_final: 0.6218 (tm-30) REVERT: J 91 ASP cc_start: 0.8823 (t0) cc_final: 0.8595 (t0) REVERT: D 527 ILE cc_start: 0.7508 (mm) cc_final: 0.7250 (pt) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.3124 time to fit residues: 161.9747 Evaluate side-chains 187 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14115 Z= 0.258 Angle : 0.653 10.063 19179 Z= 0.351 Chirality : 0.047 0.237 2187 Planarity : 0.005 0.076 2442 Dihedral : 9.103 80.449 2370 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.79 % Allowed : 7.66 % Favored : 90.55 % 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: 0.93 (0.19), residues: 1704 helix: 2.31 (0.38), residues: 159 sheet: 0.54 (0.19), residues: 645 loop : 0.51 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 86 HIS 0.006 0.001 HIS J 96 PHE 0.019 0.002 PHE F 592 TYR 0.022 0.002 TYR B 261 ARG 0.006 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 ARG cc_start: 0.7942 (tpt90) cc_final: 0.7703 (mpt-90) REVERT: H 13 LYS cc_start: 0.7430 (mttm) cc_final: 0.7003 (mptt) REVERT: H 81 MET cc_start: 0.7607 (tmm) cc_final: 0.6790 (tmm) REVERT: H 82 GLU cc_start: 0.8404 (tp30) cc_final: 0.7879 (tp30) REVERT: K 16 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6282 (tm-30) REVERT: K 57 ILE cc_start: 0.8314 (mm) cc_final: 0.8070 (tp) REVERT: K 97 LEU cc_start: 0.9219 (tp) cc_final: 0.8935 (tp) REVERT: E 527 ILE cc_start: 0.7956 (mm) cc_final: 0.7546 (pt) REVERT: E 611 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6616 (mm-30) REVERT: C 281 ILE cc_start: 0.7889 (pt) cc_final: 0.7663 (pt) REVERT: I 13 LYS cc_start: 0.7327 (mttm) cc_final: 0.6923 (mptt) REVERT: L 16 GLN cc_start: 0.7094 (mm-40) cc_final: 0.6693 (tt0) REVERT: L 51 ASN cc_start: 0.8159 (p0) cc_final: 0.7887 (p0) REVERT: F 527 ILE cc_start: 0.7955 (mm) cc_final: 0.7734 (pt) REVERT: F 577 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8609 (t) REVERT: G 13 LYS cc_start: 0.7283 (mttm) cc_final: 0.6869 (mppt) REVERT: G 46 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7709 (tt0) REVERT: G 81 MET cc_start: 0.8303 (tmm) cc_final: 0.7911 (tmm) REVERT: J 6 GLN cc_start: 0.6629 (mt0) cc_final: 0.6374 (mt0) REVERT: J 16 GLN cc_start: 0.7175 (mm-40) cc_final: 0.6298 (tm-30) REVERT: J 17 THR cc_start: 0.8429 (m) cc_final: 0.7986 (m) REVERT: D 527 ILE cc_start: 0.7796 (mm) cc_final: 0.7547 (pt) REVERT: D 602 HIS cc_start: 0.6018 (OUTLIER) cc_final: 0.4884 (t-90) outliers start: 26 outliers final: 15 residues processed: 242 average time/residue: 0.2516 time to fit residues: 90.1895 Evaluate side-chains 200 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 0.0770 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN H 65 GLN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN E 595 GLN C 44 GLN I 65 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 GLN G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN D 551 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14115 Z= 0.266 Angle : 0.603 8.479 19179 Z= 0.322 Chirality : 0.046 0.204 2187 Planarity : 0.004 0.045 2442 Dihedral : 8.306 72.595 2370 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.14 % Allowed : 9.52 % Favored : 88.34 % 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: 0.56 (0.19), residues: 1704 helix: 1.83 (0.40), residues: 177 sheet: 0.39 (0.20), residues: 615 loop : 0.18 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 86 HIS 0.015 0.002 HIS D 602 PHE 0.016 0.002 PHE B 159 TYR 0.015 0.002 TYR K 30 ARG 0.005 0.001 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: H 13 LYS cc_start: 0.7444 (mttm) cc_final: 0.6923 (mptt) REVERT: H 81 MET cc_start: 0.7677 (tmm) cc_final: 0.6791 (tmm) REVERT: K 16 GLN cc_start: 0.7287 (mm-40) cc_final: 0.6425 (tm-30) REVERT: E 527 ILE cc_start: 0.8226 (mm) cc_final: 0.7896 (pt) REVERT: C 281 ILE cc_start: 0.7929 (pt) cc_final: 0.7712 (pt) REVERT: I 13 LYS cc_start: 0.7500 (mttm) cc_final: 0.6946 (mptt) REVERT: I 48 MET cc_start: 0.7325 (mtm) cc_final: 0.6632 (ttm) REVERT: L 16 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6821 (tt0) REVERT: F 552 ASP cc_start: 0.7840 (t0) cc_final: 0.7497 (t0) REVERT: A 100 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: G 13 LYS cc_start: 0.7554 (mttm) cc_final: 0.6922 (mppt) REVERT: G 46 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7899 (tt0) REVERT: J 16 GLN cc_start: 0.7258 (mm-40) cc_final: 0.6345 (tm-30) REVERT: D 527 ILE cc_start: 0.8027 (mm) cc_final: 0.7816 (pt) outliers start: 31 outliers final: 21 residues processed: 215 average time/residue: 0.2511 time to fit residues: 80.2003 Evaluate side-chains 198 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain I residue 65 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN D 602 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 14115 Z= 0.442 Angle : 0.678 9.049 19179 Z= 0.355 Chirality : 0.049 0.232 2187 Planarity : 0.005 0.051 2442 Dihedral : 7.724 60.617 2370 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.24 % Allowed : 8.83 % Favored : 87.92 % 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: 0.16 (0.19), residues: 1704 helix: 1.61 (0.39), residues: 177 sheet: 0.10 (0.20), residues: 630 loop : -0.10 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.004 0.001 HIS D 602 PHE 0.022 0.003 PHE A 159 TYR 0.014 0.002 TYR A 220 ARG 0.006 0.001 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.8142 (tttt) cc_final: 0.7814 (pttt) REVERT: B 100 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: B 161 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9021 (mt) REVERT: H 13 LYS cc_start: 0.7329 (mttm) cc_final: 0.6770 (mptt) REVERT: H 81 MET cc_start: 0.7824 (tmm) cc_final: 0.6944 (tmm) REVERT: H 82 GLU cc_start: 0.8791 (tp30) cc_final: 0.8361 (mm-30) REVERT: K 16 GLN cc_start: 0.7386 (mm-40) cc_final: 0.6483 (tm-30) REVERT: K 35 TYR cc_start: 0.8978 (m-80) cc_final: 0.8689 (m-10) REVERT: C 100 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: C 161 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9029 (mt) REVERT: C 281 ILE cc_start: 0.8048 (pt) cc_final: 0.7792 (pt) REVERT: I 13 LYS cc_start: 0.7400 (mttm) cc_final: 0.6792 (mptt) REVERT: I 48 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6848 (ttm) REVERT: I 115 MET cc_start: 0.8698 (mpp) cc_final: 0.8171 (mpp) REVERT: L 16 GLN cc_start: 0.7391 (mm-40) cc_final: 0.6952 (tt0) REVERT: L 35 TYR cc_start: 0.8945 (m-80) cc_final: 0.7936 (m-80) REVERT: F 551 GLN cc_start: 0.7994 (mm110) cc_final: 0.7766 (mm-40) REVERT: F 552 ASP cc_start: 0.8060 (t0) cc_final: 0.7741 (t0) REVERT: A 100 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: A 161 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9096 (mt) REVERT: G 13 LYS cc_start: 0.7632 (mttm) cc_final: 0.6931 (mppt) REVERT: G 46 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7924 (tt0) REVERT: J 16 GLN cc_start: 0.7367 (mm-40) cc_final: 0.6982 (tt0) outliers start: 47 outliers final: 30 residues processed: 231 average time/residue: 0.2803 time to fit residues: 97.7276 Evaluate side-chains 214 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-5513/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-5513/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-5513/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-5513/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-5513/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-5513/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-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-5513/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-5513/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-5513/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: 56.3853 > 50: distance: 30 - 89: 5.922 distance: 33 - 103: 6.060 distance: 88 - 94: 3.777 distance: 90 - 91: 3.349 distance: 91 - 92: 3.055 distance: 91 - 93: 4.162 distance: 94 - 95: 3.262 distance: 94 - 180: 4.911 distance: 95 - 98: 8.444 distance: 96 - 103: 6.344 distance: 98 - 99: 5.381 distance: 100 - 101: 5.990 distance: 100 - 102: 3.045 distance: 103 - 104: 9.354 distance: 104 - 105: 9.911 distance: 104 - 107: 7.561 distance: 105 - 111: 3.385 distance: 107 - 108: 9.470 distance: 109 - 110: 8.123 distance: 111 - 112: 9.424 distance: 111 - 158: 11.391 distance: 112 - 113: 7.408 distance: 112 - 115: 8.339 distance: 113 - 114: 15.971 distance: 113 - 116: 8.897 distance: 114 - 155: 15.461 distance: 116 - 117: 24.939 distance: 117 - 118: 21.889 distance: 117 - 120: 17.969 distance: 118 - 119: 10.162 distance: 118 - 123: 23.500 distance: 120 - 121: 14.825 distance: 120 - 122: 20.129 distance: 123 - 124: 16.650 distance: 124 - 125: 21.721 distance: 124 - 127: 12.799 distance: 125 - 126: 5.544 distance: 125 - 134: 14.790 distance: 127 - 128: 13.052 distance: 128 - 129: 5.029 distance: 128 - 130: 13.080 distance: 129 - 131: 11.169 distance: 130 - 132: 7.237 distance: 131 - 133: 8.595 distance: 132 - 133: 4.412 distance: 134 - 135: 13.002 distance: 135 - 136: 7.832 distance: 136 - 137: 26.626 distance: 136 - 138: 18.752 distance: 138 - 139: 9.458 distance: 139 - 140: 15.254 distance: 139 - 142: 20.075 distance: 140 - 141: 6.125 distance: 140 - 147: 13.529 distance: 142 - 143: 7.583 distance: 143 - 144: 13.623 distance: 144 - 145: 23.467 distance: 144 - 146: 3.715 distance: 147 - 148: 13.152 distance: 148 - 149: 20.011 distance: 148 - 151: 11.278 distance: 149 - 150: 9.782 distance: 149 - 155: 7.295 distance: 151 - 152: 16.228 distance: 151 - 153: 12.602 distance: 152 - 154: 19.437 distance: 156 - 157: 3.657 distance: 156 - 159: 8.043 distance: 157 - 158: 10.618 distance: 157 - 165: 8.856 distance: 159 - 160: 17.896 distance: 160 - 161: 15.069 distance: 160 - 162: 13.469 distance: 161 - 163: 9.798 distance: 162 - 164: 7.936 distance: 163 - 164: 12.687