Starting phenix.real_space_refine on Tue Mar 19 17:55:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jym_36726/03_2024/8jym_36726.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jym_36726/03_2024/8jym_36726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jym_36726/03_2024/8jym_36726.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jym_36726/03_2024/8jym_36726.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jym_36726/03_2024/8jym_36726.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jym_36726/03_2024/8jym_36726.pdb" } resolution = 2.79 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= 0.022 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 108 5.16 5 C 15897 2.51 5 N 4092 2.21 5 O 4827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 571": "OD1" <-> "OD2" Residue "D TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 571": "OD1" <-> "OD2" Residue "G TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24924 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8084 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 55, 'TRANS': 977} Chain breaks: 7 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 8084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8084 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 55, 'TRANS': 977} Chain breaks: 7 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "G" Number of atoms: 8084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8084 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 55, 'TRANS': 977} Chain breaks: 7 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 12.59, per 1000 atoms: 0.51 Number of scatterers: 24924 At special positions: 0 Unit cell: (133.665, 140.7, 167.835, 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 108 16.00 O 4827 8.00 N 4092 7.00 C 15897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.04 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.03 Simple disulfide: pdb=" SG CYS G 617 " - pdb=" SG CYS G 649 " distance=2.03 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.03 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 343 " " NAG B 1 " - " ASN A 717 " " NAG C 1 " - " ASN A 801 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 165 " " NAG D1304 " - " ASN D 234 " " NAG D1305 " - " ASN D 282 " " NAG D1306 " - " ASN D 616 " " NAG D1307 " - " ASN D 657 " " NAG D1308 " - " ASN D 709 " " NAG D1309 " - " ASN D1074 " " NAG D1310 " - " ASN D1098 " " NAG D1311 " - " ASN D1134 " " NAG D1312 " - " ASN D 343 " " NAG E 1 " - " ASN D 717 " " NAG F 1 " - " ASN D 801 " " NAG G1301 " - " ASN G 61 " " NAG G1302 " - " ASN G 122 " " NAG G1303 " - " ASN G 165 " " NAG G1304 " - " ASN G 234 " " NAG G1305 " - " ASN G 282 " " NAG G1306 " - " ASN G 616 " " NAG G1307 " - " ASN G 657 " " NAG G1308 " - " ASN G 709 " " NAG G1309 " - " ASN G1074 " " NAG G1310 " - " ASN G1098 " " NAG G1311 " - " ASN G1134 " " NAG G1312 " - " ASN G 343 " " NAG H 1 " - " ASN G 717 " " NAG I 1 " - " ASN G 801 " Time building additional restraints: 8.93 Conformation dependent library (CDL) restraints added in 3.9 seconds 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5820 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 42 sheets defined 23.7% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.567A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.268A pdb=" N ALA A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.657A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.797A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.514A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.157A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.711A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.950A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.508A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.214A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 342 removed outlier: 3.567A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 337 through 342' Processing helix chain 'D' and resid 365 through 372 removed outlier: 4.268A pdb=" N ALA D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.657A pdb=" N SER D 408 " --> pdb=" O ASN D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.797A pdb=" N GLN D 762 " --> pdb=" O SER D 758 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 890 removed outlier: 3.514A pdb=" N GLY D 889 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 912 through 918 removed outlier: 4.158A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.711A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.949A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 removed outlier: 3.508A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.214A pdb=" N GLU D 990 " --> pdb=" O PRO D 986 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU D1017 " --> pdb=" O ILE D1013 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D1033 " --> pdb=" O MET D1029 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 304 Processing helix chain 'G' and resid 337 through 342 removed outlier: 3.566A pdb=" N VAL G 341 " --> pdb=" O PRO G 337 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE G 342 " --> pdb=" O PHE G 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 337 through 342' Processing helix chain 'G' and resid 365 through 372 removed outlier: 4.268A pdb=" N ALA G 372 " --> pdb=" O ILE G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.657A pdb=" N SER G 408 " --> pdb=" O ASN G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 737 through 743 Processing helix chain 'G' and resid 746 through 754 Processing helix chain 'G' and resid 755 through 757 No H-bonds generated for 'chain 'G' and resid 755 through 757' Processing helix chain 'G' and resid 758 through 783 removed outlier: 3.797A pdb=" N GLN G 762 " --> pdb=" O SER G 758 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR G 778 " --> pdb=" O GLN G 774 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 826 Processing helix chain 'G' and resid 866 through 884 Processing helix chain 'G' and resid 886 through 890 removed outlier: 3.514A pdb=" N GLY G 889 " --> pdb=" O TRP G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 908 Processing helix chain 'G' and resid 912 through 918 removed outlier: 4.158A pdb=" N LEU G 916 " --> pdb=" O THR G 912 " (cutoff:3.500A) Processing helix chain 'G' and resid 919 through 941 removed outlier: 3.711A pdb=" N ILE G 934 " --> pdb=" O ALA G 930 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN G 935 " --> pdb=" O ILE G 931 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP G 936 " --> pdb=" O GLY G 932 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR G 941 " --> pdb=" O SER G 937 " (cutoff:3.500A) Processing helix chain 'G' and resid 942 through 944 No H-bonds generated for 'chain 'G' and resid 942 through 944' Processing helix chain 'G' and resid 945 through 965 removed outlier: 3.950A pdb=" N VAL G 951 " --> pdb=" O LYS G 947 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL G 952 " --> pdb=" O LEU G 948 " (cutoff:3.500A) Processing helix chain 'G' and resid 966 through 968 No H-bonds generated for 'chain 'G' and resid 966 through 968' Processing helix chain 'G' and resid 976 through 984 removed outlier: 3.508A pdb=" N ILE G 980 " --> pdb=" O VAL G 976 " (cutoff:3.500A) Processing helix chain 'G' and resid 985 through 1033 removed outlier: 4.214A pdb=" N GLU G 990 " --> pdb=" O PRO G 986 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL G 991 " --> pdb=" O PRO G 987 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN G 992 " --> pdb=" O GLU G 988 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG G 995 " --> pdb=" O VAL G 991 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU G 996 " --> pdb=" O GLN G 992 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU G1017 " --> pdb=" O ILE G1013 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL G1033 " --> pdb=" O MET G1029 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.955A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.930A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.767A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 624 through 626 removed outlier: 4.313A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 325 through 328 Processing sheet with id= 6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.110A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= 8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id= 9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.208A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 711 through 713 Processing sheet with id= 11, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.543A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.652A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id= 14, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id= 15, first strand: chain 'D' and resid 25 through 30 removed outlier: 7.955A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE D 203 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.930A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.767A pdb=" N LEU D 241 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN D 121 " --> pdb=" O ARG D 102 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 624 through 626 removed outlier: 4.313A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'D' and resid 325 through 328 Processing sheet with id= 20, first strand: chain 'D' and resid 354 through 358 removed outlier: 4.110A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'D' and resid 452 through 454 Processing sheet with id= 22, first strand: chain 'D' and resid 473 through 474 Processing sheet with id= 23, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.208A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 711 through 713 Processing sheet with id= 25, first strand: chain 'D' and resid 717 through 728 removed outlier: 3.543A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.652A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D' and resid 1120 through 1121 Processing sheet with id= 28, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id= 29, first strand: chain 'G' and resid 25 through 30 removed outlier: 7.955A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE G 203 " --> pdb=" O VAL G 227 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL G 227 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N SER G 205 " --> pdb=" O PRO G 225 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'G' and resid 48 through 55 removed outlier: 3.930A pdb=" N ASP G 287 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.767A pdb=" N LEU G 241 " --> pdb=" O GLY G 103 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLY G 103 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ARG G 102 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASN G 121 " --> pdb=" O ARG G 102 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'G' and resid 624 through 626 removed outlier: 4.313A pdb=" N VAL G 595 " --> pdb=" O THR G 315 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN G 317 " --> pdb=" O GLY G 593 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY G 593 " --> pdb=" O ASN G 317 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY G 594 " --> pdb=" O GLN G 613 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'G' and resid 325 through 328 Processing sheet with id= 34, first strand: chain 'G' and resid 354 through 358 removed outlier: 4.110A pdb=" N ASN G 354 " --> pdb=" O SER G 399 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER G 399 " --> pdb=" O ASN G 354 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'G' and resid 452 through 454 Processing sheet with id= 36, first strand: chain 'G' and resid 473 through 474 Processing sheet with id= 37, first strand: chain 'G' and resid 654 through 655 removed outlier: 6.208A pdb=" N GLU G 654 " --> pdb=" O ALA G 694 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR G 696 " --> pdb=" O GLU G 654 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'G' and resid 711 through 713 Processing sheet with id= 39, first strand: chain 'G' and resid 717 through 728 removed outlier: 3.542A pdb=" N MET G1050 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR G1067 " --> pdb=" O HIS G1048 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS G1048 " --> pdb=" O TYR G1067 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'G' and resid 733 through 736 removed outlier: 4.652A pdb=" N LYS G 733 " --> pdb=" O LEU G 861 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'G' and resid 1120 through 1121 Processing sheet with id= 42, first strand: chain 'G' and resid 1094 through 1097 939 hydrogen bonds defined for protein. 2574 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: 9.44 Time building geometry restraints manager: 9.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7891 1.34 - 1.46: 6243 1.46 - 1.58: 11225 1.58 - 1.71: 0 1.71 - 1.83: 135 Bond restraints: 25494 Sorted by residual: bond pdb=" C1 NAG D1309 " pdb=" O5 NAG D1309 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C1 NAG G1309 " pdb=" O5 NAG G1309 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" C1 NAG G1301 " pdb=" O5 NAG G1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.29e+00 ... (remaining 25489 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.11: 798 107.11 - 113.83: 14408 113.83 - 120.56: 9461 120.56 - 127.28: 9806 127.28 - 134.00: 222 Bond angle restraints: 34695 Sorted by residual: angle pdb=" N GLN D1002 " pdb=" CA GLN D1002 " pdb=" CB GLN D1002 " ideal model delta sigma weight residual 110.28 115.46 -5.18 1.55e+00 4.16e-01 1.12e+01 angle pdb=" N GLN G1002 " pdb=" CA GLN G1002 " pdb=" CB GLN G1002 " ideal model delta sigma weight residual 110.28 115.46 -5.18 1.55e+00 4.16e-01 1.12e+01 angle pdb=" N GLN A1002 " pdb=" CA GLN A1002 " pdb=" CB GLN A1002 " ideal model delta sigma weight residual 110.28 115.45 -5.17 1.55e+00 4.16e-01 1.11e+01 angle pdb=" N GLY A 526 " pdb=" CA GLY A 526 " pdb=" C GLY A 526 " ideal model delta sigma weight residual 112.34 117.89 -5.55 2.04e+00 2.40e-01 7.39e+00 angle pdb=" N GLY D 526 " pdb=" CA GLY D 526 " pdb=" C GLY D 526 " ideal model delta sigma weight residual 112.34 117.88 -5.54 2.04e+00 2.40e-01 7.37e+00 ... (remaining 34690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 14441 17.70 - 35.40: 1159 35.40 - 53.09: 171 53.09 - 70.79: 36 70.79 - 88.49: 24 Dihedral angle restraints: 15831 sinusoidal: 6795 harmonic: 9036 Sorted by residual: dihedral pdb=" CB CYS D 480 " pdb=" SG CYS D 480 " pdb=" SG CYS D 488 " pdb=" CB CYS D 488 " ideal model delta sinusoidal sigma weight residual 93.00 37.75 55.25 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 37.76 55.24 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS G 480 " pdb=" SG CYS G 480 " pdb=" SG CYS G 488 " pdb=" CB CYS G 488 " ideal model delta sinusoidal sigma weight residual 93.00 37.76 55.24 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 15828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2831 0.040 - 0.079: 809 0.079 - 0.119: 388 0.119 - 0.158: 49 0.158 - 0.198: 3 Chirality restraints: 4080 Sorted by residual: chirality pdb=" C1 NAG D1308 " pdb=" ND2 ASN D 709 " pdb=" C2 NAG D1308 " pdb=" O5 NAG D1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" C1 NAG G1308 " pdb=" ND2 ASN G 709 " pdb=" C2 NAG G1308 " pdb=" O5 NAG G1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.69e-01 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.58e-01 ... (remaining 4077 not shown) Planarity restraints: 4458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 906 " -0.013 2.00e-02 2.50e+03 1.35e-02 3.19e+00 pdb=" CG PHE D 906 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE D 906 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE D 906 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE D 906 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 906 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 906 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.013 2.00e-02 2.50e+03 1.34e-02 3.13e+00 pdb=" CG PHE A 906 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 906 " 0.013 2.00e-02 2.50e+03 1.34e-02 3.13e+00 pdb=" CG PHE G 906 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE G 906 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE G 906 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE G 906 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 906 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 906 " 0.000 2.00e-02 2.50e+03 ... (remaining 4455 not shown) Histogram of nonbonded interaction distances: 0.55 - 1.42: 36 1.42 - 2.29: 87 2.29 - 3.16: 19884 3.16 - 4.03: 58106 4.03 - 4.90: 110435 Warning: very small nonbonded interaction distances. Nonbonded interactions: 188548 Sorted by model distance: nonbonded pdb=" N VAL A 382 " pdb=" NH2 ARG G 983 " model vdw 0.546 3.200 nonbonded pdb=" NH2 ARG A 983 " pdb=" N VAL D 382 " model vdw 0.546 3.200 nonbonded pdb=" NH2 ARG D 983 " pdb=" N VAL G 382 " model vdw 0.546 3.200 nonbonded pdb=" NH1 ARG A 983 " pdb=" CA VAL D 382 " model vdw 0.706 3.550 nonbonded pdb=" CA VAL A 382 " pdb=" NH1 ARG G 983 " model vdw 0.706 3.550 ... (remaining 188543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 12.970 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 62.160 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.140 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 0.041 25494 Z= 0.254 Angle : 0.551 5.547 34695 Z= 0.287 Chirality : 0.045 0.198 4080 Planarity : 0.004 0.037 4416 Dihedral : 12.783 88.491 9894 Min Nonbonded Distance : 0.546 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.19 (0.15), residues: 3051 helix: 2.27 (0.22), residues: 612 sheet: 0.97 (0.20), residues: 666 loop : -1.05 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 886 HIS 0.002 0.001 HIS G1064 PHE 0.031 0.001 PHE D 906 TYR 0.015 0.001 TYR D1067 ARG 0.001 0.000 ARG G1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8151 (p90) cc_final: 0.7420 (p90) REVERT: A 586 ASP cc_start: 0.7772 (m-30) cc_final: 0.7553 (m-30) REVERT: A 979 ASP cc_start: 0.8141 (t70) cc_final: 0.7889 (t0) REVERT: A 985 ASP cc_start: 0.8106 (p0) cc_final: 0.7839 (p0) REVERT: D 351 TYR cc_start: 0.8277 (p90) cc_final: 0.7526 (p90) REVERT: D 586 ASP cc_start: 0.7663 (m-30) cc_final: 0.7339 (m-30) REVERT: D 755 GLN cc_start: 0.9178 (mt0) cc_final: 0.8956 (mt0) REVERT: D 979 ASP cc_start: 0.7981 (t70) cc_final: 0.7733 (t0) REVERT: D 985 ASP cc_start: 0.8128 (p0) cc_final: 0.7848 (p0) REVERT: G 351 TYR cc_start: 0.8255 (p90) cc_final: 0.7564 (p90) REVERT: G 979 ASP cc_start: 0.8192 (t70) cc_final: 0.7970 (t0) REVERT: G 985 ASP cc_start: 0.8102 (p0) cc_final: 0.7886 (p0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 1.2402 time to fit residues: 275.2117 Evaluate side-chains 120 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.0570 chunk 234 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 242 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 180 optimal weight: 0.5980 chunk 280 optimal weight: 2.9990 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 856 ASN A1010 GLN D 339 HIS ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 856 ASN D1010 GLN G 339 HIS G 613 GLN G 856 ASN G1010 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25494 Z= 0.197 Angle : 0.520 6.811 34695 Z= 0.278 Chirality : 0.044 0.214 4080 Planarity : 0.004 0.050 4416 Dihedral : 7.100 55.957 4329 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.44 % Allowed : 6.97 % Favored : 92.59 % 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: 0.24 (0.15), residues: 3051 helix: 2.45 (0.22), residues: 612 sheet: 1.02 (0.20), residues: 684 loop : -1.10 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 436 HIS 0.003 0.001 HIS G1064 PHE 0.019 0.001 PHE A 906 TYR 0.018 0.001 TYR A 160 ARG 0.008 0.000 ARG D 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7917 (p90) cc_final: 0.7514 (p90) REVERT: A 586 ASP cc_start: 0.7743 (m-30) cc_final: 0.7521 (m-30) REVERT: A 624 ILE cc_start: 0.8311 (pt) cc_final: 0.7912 (pp) REVERT: A 979 ASP cc_start: 0.7760 (t70) cc_final: 0.7455 (t0) REVERT: D 53 ASP cc_start: 0.8121 (t70) cc_final: 0.7792 (t0) REVERT: D 351 TYR cc_start: 0.8032 (p90) cc_final: 0.7601 (p90) REVERT: D 755 GLN cc_start: 0.9144 (mt0) cc_final: 0.8926 (mt0) REVERT: D 979 ASP cc_start: 0.7780 (t70) cc_final: 0.7524 (t0) REVERT: G 351 TYR cc_start: 0.8065 (p90) cc_final: 0.7665 (p90) REVERT: G 624 ILE cc_start: 0.8352 (pt) cc_final: 0.8058 (pp) REVERT: G 979 ASP cc_start: 0.7874 (t70) cc_final: 0.7642 (t0) REVERT: G 1017 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8325 (tt0) outliers start: 12 outliers final: 2 residues processed: 138 average time/residue: 1.1290 time to fit residues: 187.1765 Evaluate side-chains 124 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain G residue 1002 GLN Chi-restraints excluded: chain G residue 1017 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 281 optimal weight: 4.9990 chunk 303 optimal weight: 0.8980 chunk 250 optimal weight: 9.9990 chunk 278 optimal weight: 0.0050 chunk 95 optimal weight: 3.9990 chunk 225 optimal weight: 30.0000 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 613 GLN G 613 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25494 Z= 0.149 Angle : 0.480 6.148 34695 Z= 0.254 Chirality : 0.044 0.221 4080 Planarity : 0.004 0.038 4416 Dihedral : 6.591 55.581 4329 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.70 % Allowed : 8.41 % Favored : 90.89 % 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: 0.34 (0.15), residues: 3051 helix: 2.61 (0.22), residues: 612 sheet: 1.03 (0.20), residues: 687 loop : -1.05 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 436 HIS 0.003 0.000 HIS A 207 PHE 0.017 0.001 PHE A 133 TYR 0.016 0.001 TYR D1067 ARG 0.004 0.000 ARG D 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7712 (m-30) cc_final: 0.7510 (m-30) REVERT: A 624 ILE cc_start: 0.8266 (pt) cc_final: 0.7874 (pp) REVERT: A 979 ASP cc_start: 0.7980 (t70) cc_final: 0.7652 (t0) REVERT: A 988 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8425 (tm-30) REVERT: D 53 ASP cc_start: 0.8153 (t70) cc_final: 0.7805 (t0) REVERT: D 335 LEU cc_start: 0.8365 (mm) cc_final: 0.7982 (tm) REVERT: D 755 GLN cc_start: 0.9156 (mt0) cc_final: 0.8950 (mt0) REVERT: D 855 PHE cc_start: 0.7563 (m-80) cc_final: 0.7090 (m-80) REVERT: D 979 ASP cc_start: 0.7925 (t70) cc_final: 0.7655 (t0) REVERT: G 351 TYR cc_start: 0.8056 (p90) cc_final: 0.7634 (p90) REVERT: G 624 ILE cc_start: 0.8376 (pt) cc_final: 0.8077 (pp) REVERT: G 979 ASP cc_start: 0.8093 (t70) cc_final: 0.7868 (t0) REVERT: G 1017 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8348 (pt0) outliers start: 19 outliers final: 10 residues processed: 137 average time/residue: 1.1535 time to fit residues: 188.0540 Evaluate side-chains 129 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 1002 GLN Chi-restraints excluded: chain G residue 1017 GLU Chi-restraints excluded: chain G residue 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.4980 chunk 211 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 267 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25494 Z= 0.206 Angle : 0.494 7.238 34695 Z= 0.262 Chirality : 0.044 0.204 4080 Planarity : 0.004 0.036 4416 Dihedral : 6.316 56.277 4329 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.81 % Allowed : 10.25 % Favored : 88.94 % 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: 0.33 (0.15), residues: 3051 helix: 2.55 (0.22), residues: 618 sheet: 1.01 (0.20), residues: 684 loop : -1.05 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 436 HIS 0.003 0.001 HIS G1064 PHE 0.020 0.001 PHE G 429 TYR 0.017 0.001 TYR D1067 ARG 0.002 0.000 ARG D 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7731 (m-30) cc_final: 0.7509 (m-30) REVERT: A 624 ILE cc_start: 0.8221 (pt) cc_final: 0.7843 (pp) REVERT: A 979 ASP cc_start: 0.8137 (t70) cc_final: 0.7836 (t0) REVERT: A 988 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8452 (tm-30) REVERT: D 53 ASP cc_start: 0.8133 (t70) cc_final: 0.7796 (t0) REVERT: D 335 LEU cc_start: 0.8356 (mm) cc_final: 0.7999 (tm) REVERT: D 755 GLN cc_start: 0.9160 (mt0) cc_final: 0.8953 (mt0) REVERT: D 979 ASP cc_start: 0.7960 (t70) cc_final: 0.7716 (t0) REVERT: G 342 PHE cc_start: 0.8499 (m-80) cc_final: 0.8222 (m-80) REVERT: G 351 TYR cc_start: 0.8067 (p90) cc_final: 0.7646 (p90) REVERT: G 624 ILE cc_start: 0.8341 (pt) cc_final: 0.8026 (pp) REVERT: G 1017 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8428 (pt0) outliers start: 22 outliers final: 6 residues processed: 137 average time/residue: 1.1508 time to fit residues: 188.1720 Evaluate side-chains 120 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain G residue 1002 GLN Chi-restraints excluded: chain G residue 1017 GLU Chi-restraints excluded: chain G residue 1092 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.757 > 50: distance: 4 - 100: 20.857 distance: 16 - 89: 23.201 distance: 19 - 86: 26.412 distance: 62 - 66: 29.362 distance: 66 - 67: 15.224 distance: 67 - 68: 6.379 distance: 68 - 69: 41.423 distance: 68 - 74: 33.820 distance: 70 - 71: 16.696 distance: 71 - 72: 13.204 distance: 71 - 73: 48.207 distance: 74 - 75: 15.774 distance: 75 - 76: 40.603 distance: 76 - 77: 47.298 distance: 76 - 78: 14.423 distance: 78 - 79: 30.641 distance: 79 - 80: 13.913 distance: 79 - 82: 8.494 distance: 80 - 81: 41.588 distance: 80 - 86: 24.899 distance: 82 - 83: 36.926 distance: 83 - 84: 40.801 distance: 83 - 85: 11.119 distance: 86 - 87: 15.782 distance: 87 - 88: 35.978 distance: 87 - 90: 30.791 distance: 88 - 89: 22.251 distance: 88 - 93: 12.103 distance: 90 - 91: 7.855 distance: 90 - 92: 15.949 distance: 93 - 94: 35.064 distance: 94 - 95: 41.266 distance: 94 - 97: 5.708 distance: 95 - 96: 21.857 distance: 95 - 100: 26.240 distance: 97 - 98: 28.450 distance: 100 - 101: 35.582 distance: 101 - 102: 29.146 distance: 101 - 104: 56.358 distance: 102 - 103: 49.710 distance: 102 - 108: 31.045 distance: 104 - 105: 32.142 distance: 105 - 106: 9.214 distance: 105 - 107: 50.687 distance: 108 - 109: 33.792 distance: 108 - 114: 16.104 distance: 109 - 110: 53.656 distance: 109 - 112: 19.351 distance: 110 - 111: 47.841 distance: 110 - 115: 47.675 distance: 112 - 113: 27.461 distance: 113 - 114: 25.240 distance: 115 - 116: 41.469 distance: 115 - 121: 10.602 distance: 116 - 117: 36.766 distance: 116 - 119: 16.162 distance: 117 - 118: 9.474 distance: 117 - 122: 44.881 distance: 119 - 120: 12.518 distance: 120 - 121: 26.698 distance: 122 - 123: 17.431 distance: 123 - 124: 14.460 distance: 123 - 126: 9.219 distance: 124 - 130: 12.781 distance: 126 - 127: 9.531 distance: 127 - 128: 24.401 distance: 127 - 129: 21.918 distance: 130 - 131: 13.696 distance: 131 - 132: 17.271 distance: 131 - 134: 17.338 distance: 132 - 133: 13.911 distance: 132 - 138: 22.385 distance: 134 - 135: 41.451 distance: 135 - 136: 7.608 distance: 135 - 137: 29.477