Starting phenix.real_space_refine on Fri Jun 20 08:12:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m15_30037/06_2025/6m15_30037_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m15_30037/06_2025/6m15_30037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m15_30037/06_2025/6m15_30037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m15_30037/06_2025/6m15_30037.map" model { file = "/net/cci-nas-00/data/ceres_data/6m15_30037/06_2025/6m15_30037_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m15_30037/06_2025/6m15_30037_neut.cif" } resolution = 2.38 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= 0.008 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 129 5.16 5 C 14889 2.51 5 N 3840 2.21 5 O 4613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23471 Number of models: 1 Model: "" Number of chains: 30 Chain: "B" Number of atoms: 7467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7467 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 925} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 7467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7467 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 925} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 7467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7467 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 925} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "D" 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: "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: "G" 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: "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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 14.71, per 1000 atoms: 0.63 Number of scatterers: 23471 At special positions: 0 Unit cell: (132.625, 126.259, 162.333, 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 129 16.00 O 4613 8.00 N 3840 7.00 C 14889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 17 " - pdb=" SG CYS B 56 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 244 " distance=2.02 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 397 " distance=2.04 Simple disulfide: pdb=" SG CYS B 409 " - pdb=" SG CYS B 458 " distance=2.05 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 509 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 590 " - pdb=" SG CYS B 612 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 696 " - pdb=" SG CYS B 706 " distance=2.04 Simple disulfide: pdb=" SG CYS B 884 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 934 " - pdb=" SG CYS B 943 " distance=2.03 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 244 " distance=2.02 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 341 " - pdb=" SG CYS A 397 " distance=2.04 Simple disulfide: pdb=" SG CYS A 409 " - pdb=" SG CYS A 458 " distance=2.05 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 509 " distance=2.02 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 590 " - pdb=" SG CYS A 612 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 696 " - pdb=" SG CYS A 706 " distance=2.04 Simple disulfide: pdb=" SG CYS A 884 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 934 " - pdb=" SG CYS A 943 " distance=2.03 Simple disulfide: pdb=" SG CYS C 17 " - pdb=" SG CYS C 56 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 234 " - pdb=" SG CYS C 244 " distance=2.02 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 285 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 369 " distance=2.03 Simple disulfide: pdb=" SG CYS C 341 " - pdb=" SG CYS C 397 " distance=2.04 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 458 " distance=2.05 Simple disulfide: pdb=" SG CYS C 482 " - pdb=" SG CYS C 509 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 590 " - pdb=" SG CYS C 612 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 601 " distance=2.03 Simple disulfide: pdb=" SG CYS C 696 " - pdb=" SG CYS C 706 " distance=2.04 Simple disulfide: pdb=" SG CYS C 884 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 934 " - pdb=" SG CYS C 943 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A1203 " - " ASN A 985 " " NAG A1204 " - " ASN A 37 " " NAG A1207 " - " ASN A 118 " " NAG A1210 " - " ASN A 273 " " NAG A1213 " - " ASN A 356 " " NAG A1214 " - " ASN A 427 " " NAG A1218 " - " ASN A 523 " " NAG A1221 " - " ASN A 922 " " NAG B1203 " - " ASN B 985 " " NAG B1204 " - " ASN B 37 " " NAG B1207 " - " ASN B 118 " " NAG B1210 " - " ASN B 273 " " NAG B1213 " - " ASN B 356 " " NAG B1214 " - " ASN B 427 " " NAG B1218 " - " ASN B 523 " " NAG B1221 " - " ASN B 922 " " NAG C1203 " - " ASN C 985 " " NAG C1204 " - " ASN C 37 " " NAG C1207 " - " ASN C 118 " " NAG C1210 " - " ASN C 273 " " NAG C1213 " - " ASN C 356 " " NAG C1214 " - " ASN C 427 " " NAG C1218 " - " ASN C 523 " " NAG C1221 " - " ASN C 922 " " NAG D 1 " - " ASN B 955 " " NAG E 1 " - " ASN B 102 " " NAG F 1 " - " ASN B 152 " " NAG G 1 " - " ASN B 303 " " NAG H 1 " - " ASN B 501 " " NAG I 1 " - " ASN B 652 " " NAG J 1 " - " ASN B 971 " " NAG K 1 " - " ASN A 955 " " NAG L 1 " - " ASN A 102 " " NAG M 1 " - " ASN A 152 " " NAG N 1 " - " ASN A 303 " " NAG O 1 " - " ASN A 501 " " NAG P 1 " - " ASN A 652 " " NAG Q 1 " - " ASN A 971 " " NAG R 1 " - " ASN C 955 " " NAG S 1 " - " ASN C 102 " " NAG T 1 " - " ASN C 152 " " NAG U 1 " - " ASN C 303 " " NAG V 1 " - " ASN C 501 " " NAG W 1 " - " ASN C 652 " " NAG X 1 " - " ASN C 971 " Time building additional restraints: 6.64 Conformation dependent library (CDL) restraints added in 2.9 seconds 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5352 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 36 sheets defined 25.0% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'B' and resid 21 through 29 removed outlier: 3.776A pdb=" N ASN B 26 " --> pdb=" O ARG B 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 27 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 237 through 247 removed outlier: 3.542A pdb=" N LEU B 242 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.550A pdb=" N THR B 308 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 316 removed outlier: 3.955A pdb=" N TYR B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 497 through 501 removed outlier: 3.580A pdb=" N ASN B 501 " --> pdb=" O PRO B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 595 Processing helix chain 'B' and resid 598 through 603 Processing helix chain 'B' and resid 604 through 608 removed outlier: 3.502A pdb=" N ARG B 607 " --> pdb=" O LEU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 638 removed outlier: 3.583A pdb=" N ARG B 620 " --> pdb=" O GLU B 616 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 681 Processing helix chain 'B' and resid 688 through 700 Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'B' and resid 768 through 785 Processing helix chain 'B' and resid 786 through 789 Processing helix chain 'B' and resid 794 through 817 removed outlier: 3.623A pdb=" N VAL B 803 " --> pdb=" O ALA B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 836 Processing helix chain 'B' and resid 837 through 885 removed outlier: 4.364A pdb=" N ASN B 872 " --> pdb=" O ALA B 868 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 875 " --> pdb=" O ARG B 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.776A pdb=" N ASN A 26 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 27 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 237 through 247 removed outlier: 3.543A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.550A pdb=" N THR A 308 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.955A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 497 through 501 removed outlier: 3.581A pdb=" N ASN A 501 " --> pdb=" O PRO A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 595 Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 604 through 608 removed outlier: 3.501A pdb=" N ARG A 607 " --> pdb=" O LEU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 638 removed outlier: 3.583A pdb=" N ARG A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 688 through 700 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 749 through 761 Processing helix chain 'A' and resid 768 through 785 Processing helix chain 'A' and resid 786 through 789 Processing helix chain 'A' and resid 794 through 817 removed outlier: 3.623A pdb=" N VAL A 803 " --> pdb=" O ALA A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 836 Processing helix chain 'A' and resid 837 through 885 removed outlier: 4.364A pdb=" N ASN A 872 " --> pdb=" O ALA A 868 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 875 " --> pdb=" O ARG A 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 removed outlier: 3.776A pdb=" N ASN C 26 " --> pdb=" O ARG C 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 237 through 247 removed outlier: 3.543A pdb=" N LEU C 242 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.550A pdb=" N THR C 308 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 316 removed outlier: 3.955A pdb=" N TYR C 315 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 497 through 501 removed outlier: 3.580A pdb=" N ASN C 501 " --> pdb=" O PRO C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 595 Processing helix chain 'C' and resid 598 through 603 Processing helix chain 'C' and resid 604 through 608 removed outlier: 3.501A pdb=" N ARG C 607 " --> pdb=" O LEU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 638 removed outlier: 3.583A pdb=" N ARG C 620 " --> pdb=" O GLU C 616 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 681 Processing helix chain 'C' and resid 688 through 700 Processing helix chain 'C' and resid 721 through 725 Processing helix chain 'C' and resid 749 through 761 Processing helix chain 'C' and resid 768 through 785 Processing helix chain 'C' and resid 786 through 789 Processing helix chain 'C' and resid 794 through 817 removed outlier: 3.623A pdb=" N VAL C 803 " --> pdb=" O ALA C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 836 Processing helix chain 'C' and resid 837 through 885 removed outlier: 4.364A pdb=" N ASN C 872 " --> pdb=" O ALA C 868 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 875 " --> pdb=" O ARG C 871 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 35 removed outlier: 6.829A pdb=" N GLY B 34 " --> pdb=" O TYR C 438 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 437 " --> pdb=" O LYS C 444 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LYS C 444 " --> pdb=" O VAL C 455 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 44 removed outlier: 7.437A pdb=" N SER B 217 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR B 233 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 219 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR B 231 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 221 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 removed outlier: 4.022A pdb=" N TYR B 163 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.497A pdb=" N VAL B 119 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER B 154 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 121 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN B 152 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 123 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU B 148 " --> pdb=" O ARG B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 254 through 260 removed outlier: 5.612A pdb=" N VAL B 255 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE B 467 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER B 257 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 465 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 265 through 268 removed outlier: 5.738A pdb=" N LYS B 444 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 437 " --> pdb=" O LYS B 444 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 275 through 276 removed outlier: 6.823A pdb=" N SER B 275 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS B 300 " --> pdb=" O CYS B 397 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 297 removed outlier: 6.688A pdb=" N ILE B 381 " --> pdb=" O ASN B 375 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 368 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 514 through 521 removed outlier: 4.479A pdb=" N ARG B 544 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASN B 518 " --> pdb=" O ARG B 544 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN B 923 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HIS B 570 " --> pdb=" O PRO B 921 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 572 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 919 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 574 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR B 917 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU B 576 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE B 915 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE B 578 " --> pdb=" O MET B 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET B 913 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN B 580 " --> pdb=" O GLY B 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY B 911 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 919 " --> pdb=" O HIS B 900 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N HIS B 900 " --> pdb=" O LEU B 919 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN B 923 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HIS B 570 " --> pdb=" O PRO B 921 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 572 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 919 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 574 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR B 917 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU B 576 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE B 915 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE B 578 " --> pdb=" O MET B 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET B 913 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN B 580 " --> pdb=" O GLY B 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY B 911 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 930 " --> pdb=" O LEU B 951 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 951 " --> pdb=" O THR B 930 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 585 through 588 Processing sheet with id=AB4, first strand: chain 'B' and resid 977 through 980 removed outlier: 3.725A pdb=" N CYS B 943 " --> pdb=" O VAL B 980 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 39 through 44 removed outlier: 7.437A pdb=" N SER A 217 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR A 233 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 219 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR A 231 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 221 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 54 through 55 removed outlier: 4.023A pdb=" N TYR A 163 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 64 through 68 removed outlier: 6.498A pdb=" N VAL A 119 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 154 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 121 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN A 152 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 123 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 148 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 254 through 260 removed outlier: 5.612A pdb=" N VAL A 255 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE A 467 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER A 257 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 465 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 265 through 268 removed outlier: 5.738A pdb=" N LYS A 444 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 437 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 275 through 276 removed outlier: 6.823A pdb=" N SER A 275 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS A 300 " --> pdb=" O CYS A 397 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 294 through 297 removed outlier: 6.688A pdb=" N ILE A 381 " --> pdb=" O ASN A 375 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 368 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 514 through 521 removed outlier: 4.480A pdb=" N ARG A 544 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN A 518 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN A 923 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS A 570 " --> pdb=" O PRO A 921 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU A 572 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 919 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU A 574 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR A 917 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU A 576 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 915 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE A 578 " --> pdb=" O MET A 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET A 913 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN A 580 " --> pdb=" O GLY A 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A 911 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 919 " --> pdb=" O HIS A 900 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS A 900 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN A 923 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS A 570 " --> pdb=" O PRO A 921 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU A 572 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 919 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU A 574 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR A 917 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU A 576 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 915 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE A 578 " --> pdb=" O MET A 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET A 913 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN A 580 " --> pdb=" O GLY A 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A 911 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 930 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU A 951 " --> pdb=" O THR A 930 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 585 through 588 Processing sheet with id=AC7, first strand: chain 'A' and resid 977 through 980 removed outlier: 3.726A pdb=" N CYS A 943 " --> pdb=" O VAL A 980 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 39 through 44 removed outlier: 7.437A pdb=" N SER C 217 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR C 233 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU C 219 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR C 231 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 221 " --> pdb=" O THR C 229 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 54 through 55 removed outlier: 4.022A pdb=" N TYR C 163 " --> pdb=" O THR C 76 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.498A pdb=" N VAL C 119 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER C 154 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 121 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN C 152 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 123 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU C 148 " --> pdb=" O ARG C 125 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 254 through 260 removed outlier: 5.612A pdb=" N VAL C 255 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE C 467 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER C 257 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 465 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 275 through 276 removed outlier: 6.822A pdb=" N SER C 275 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS C 300 " --> pdb=" O CYS C 397 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 294 through 297 removed outlier: 6.688A pdb=" N ILE C 381 " --> pdb=" O ASN C 375 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 368 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 514 through 521 removed outlier: 4.480A pdb=" N ARG C 544 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASN C 518 " --> pdb=" O ARG C 544 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE C 532 " --> pdb=" O LEU C 528 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN C 923 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS C 570 " --> pdb=" O PRO C 921 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C 572 " --> pdb=" O LEU C 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 919 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 574 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C 917 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU C 576 " --> pdb=" O PHE C 915 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE C 915 " --> pdb=" O GLU C 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 578 " --> pdb=" O MET C 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET C 913 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLN C 580 " --> pdb=" O GLY C 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY C 911 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU C 919 " --> pdb=" O HIS C 900 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N HIS C 900 " --> pdb=" O LEU C 919 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN C 923 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS C 570 " --> pdb=" O PRO C 921 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C 572 " --> pdb=" O LEU C 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 919 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 574 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C 917 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU C 576 " --> pdb=" O PHE C 915 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE C 915 " --> pdb=" O GLU C 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 578 " --> pdb=" O MET C 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET C 913 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLN C 580 " --> pdb=" O GLY C 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY C 911 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C 930 " --> pdb=" O LEU C 951 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU C 951 " --> pdb=" O THR C 930 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 585 through 588 Processing sheet with id=AD9, first strand: chain 'C' and resid 977 through 980 removed outlier: 3.725A pdb=" N CYS C 943 " --> pdb=" O VAL C 980 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2499 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: 10.64 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6974 1.34 - 1.47: 6652 1.47 - 1.59: 10143 1.59 - 1.72: 0 1.72 - 1.85: 168 Bond restraints: 23937 Sorted by residual: bond pdb=" C1 NAG A1217 " pdb=" O5 NAG A1217 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 NAG B1217 " pdb=" O5 NAG B1217 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 NAG C1217 " pdb=" O5 NAG C1217 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 BMA Q 3 " pdb=" C2 BMA Q 3 " ideal model delta sigma weight residual 1.519 1.587 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1 BMA X 3 " pdb=" C2 BMA X 3 " ideal model delta sigma weight residual 1.519 1.587 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 23932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 30797 2.11 - 4.22: 1603 4.22 - 6.33: 171 6.33 - 8.44: 15 8.44 - 10.55: 24 Bond angle restraints: 32610 Sorted by residual: angle pdb=" CA TYR B 91 " pdb=" CB TYR B 91 " pdb=" CG TYR B 91 " ideal model delta sigma weight residual 113.90 124.10 -10.20 1.80e+00 3.09e-01 3.21e+01 angle pdb=" CA TYR C 91 " pdb=" CB TYR C 91 " pdb=" CG TYR C 91 " ideal model delta sigma weight residual 113.90 124.10 -10.20 1.80e+00 3.09e-01 3.21e+01 angle pdb=" CA TYR A 91 " pdb=" CB TYR A 91 " pdb=" CG TYR A 91 " ideal model delta sigma weight residual 113.90 124.09 -10.19 1.80e+00 3.09e-01 3.21e+01 angle pdb=" C ASP C 339 " pdb=" N ASP C 340 " pdb=" CA ASP C 340 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C ASP B 339 " pdb=" N ASP B 340 " pdb=" CA ASP B 340 " ideal model delta sigma weight residual 121.54 130.49 -8.95 1.91e+00 2.74e-01 2.20e+01 ... (remaining 32605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.14: 14454 22.14 - 44.29: 330 44.29 - 66.43: 129 66.43 - 88.57: 42 88.57 - 110.72: 48 Dihedral angle restraints: 15003 sinusoidal: 6633 harmonic: 8370 Sorted by residual: dihedral pdb=" CB CYS C 409 " pdb=" SG CYS C 409 " pdb=" SG CYS C 458 " pdb=" CB CYS C 458 " ideal model delta sinusoidal sigma weight residual 93.00 4.26 88.74 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B 409 " pdb=" SG CYS B 409 " pdb=" SG CYS B 458 " pdb=" CB CYS B 458 " ideal model delta sinusoidal sigma weight residual 93.00 4.28 88.72 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS A 409 " pdb=" SG CYS A 409 " pdb=" SG CYS A 458 " pdb=" CB CYS A 458 " ideal model delta sinusoidal sigma weight residual 93.00 4.29 88.71 1 1.00e+01 1.00e-02 9.38e+01 ... (remaining 15000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 3699 0.129 - 0.258: 177 0.258 - 0.388: 12 0.388 - 0.517: 0 0.517 - 0.646: 6 Chirality restraints: 3894 Sorted by residual: chirality pdb=" C1 NAG A1204 " pdb=" ND2 ASN A 37 " pdb=" C2 NAG A1204 " pdb=" O5 NAG A1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C1 NAG B1204 " pdb=" ND2 ASN B 37 " pdb=" C2 NAG B1204 " pdb=" O5 NAG B1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C1 NAG C1204 " pdb=" ND2 ASN C 37 " pdb=" C2 NAG C1204 " pdb=" O5 NAG C1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.04e+01 ... (remaining 3891 not shown) Planarity restraints: 4128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 389 " -0.025 2.00e-02 2.50e+03 2.74e-02 1.31e+01 pdb=" CG PHE A 389 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 389 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 389 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 389 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 389 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 389 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 389 " 0.024 2.00e-02 2.50e+03 2.73e-02 1.31e+01 pdb=" CG PHE B 389 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE B 389 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE B 389 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 389 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 389 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 389 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 389 " -0.024 2.00e-02 2.50e+03 2.72e-02 1.30e+01 pdb=" CG PHE C 389 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE C 389 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE C 389 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 389 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE C 389 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 389 " -0.008 2.00e-02 2.50e+03 ... (remaining 4125 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 619 2.69 - 3.24: 20897 3.24 - 3.80: 36560 3.80 - 4.35: 49327 4.35 - 4.90: 80692 Nonbonded interactions: 188095 Sorted by model distance: nonbonded pdb=" O ARG B 607 " pdb=" CG GLU C 820 " model vdw 2.141 3.440 nonbonded pdb=" CG GLU A 820 " pdb=" O ARG C 607 " model vdw 2.142 3.440 nonbonded pdb=" CG GLU B 820 " pdb=" O ARG A 607 " model vdw 2.148 3.440 nonbonded pdb=" OG1 THR B 31 " pdb=" O ARG B 33 " model vdw 2.335 3.040 nonbonded pdb=" OG1 THR C 31 " pdb=" O ARG C 33 " model vdw 2.336 3.040 ... (remaining 188090 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: 0.15 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 1.020 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 57.250 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.170 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:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.009 0.134 24051 Z= 0.399 Angle : 1.094 13.530 32907 Z= 0.587 Chirality : 0.070 0.646 3894 Planarity : 0.007 0.066 4083 Dihedral : 13.409 110.717 9516 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.12 % Allowed : 1.24 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.14), residues: 2877 helix: -2.92 (0.13), residues: 645 sheet: -1.04 (0.18), residues: 747 loop : -1.19 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A 127 HIS 0.021 0.004 HIS C 500 PHE 0.060 0.006 PHE B 389 TYR 0.060 0.005 TYR B 233 ARG 0.025 0.002 ARG C 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 45) link_NAG-ASN : angle 3.82370 ( 135) link_BETA1-4 : bond 0.01782 ( 24) link_BETA1-4 : angle 3.35912 ( 72) hydrogen bonds : bond 0.24943 ( 919) hydrogen bonds : angle 8.53657 ( 2499) SS BOND : bond 0.00709 ( 45) SS BOND : angle 2.68855 ( 90) covalent geometry : bond 0.00904 (23937) covalent geometry : angle 1.04981 (32610) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 357 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7913 (mtm-85) REVERT: B 545 MET cc_start: 0.8491 (mtp) cc_final: 0.8246 (mtp) REVERT: A 853 MET cc_start: 0.8993 (mtp) cc_final: 0.8760 (mtm) REVERT: C 122 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7827 (mtt-85) REVERT: C 754 MET cc_start: 0.8929 (mmt) cc_final: 0.8728 (mmt) outliers start: 3 outliers final: 0 residues processed: 360 average time/residue: 1.4679 time to fit residues: 598.6916 Evaluate side-chains 242 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 GLN B 210 ASN ** B 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 ASN B 655 GLN B 710 HIS B 810 GLN B 878 GLN B 907 ASN B 976 ASN A 99 HIS A 159 GLN A 210 ASN ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 HIS A 526 ASN A 710 HIS A 765 GLN A 810 GLN A 907 ASN C 99 HIS C 159 GLN C 210 ASN ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 GLN C 500 HIS C 526 ASN C 710 HIS C 766 ASN C 810 GLN C 897 GLN C 907 ASN C 976 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.101042 restraints weight = 23311.734| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.73 r_work: 0.2936 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24051 Z= 0.146 Angle : 0.710 12.051 32907 Z= 0.351 Chirality : 0.050 0.426 3894 Planarity : 0.005 0.050 4083 Dihedral : 11.820 68.962 4644 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.40 % Allowed : 5.32 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.64 (0.15), residues: 2877 helix: 0.25 (0.19), residues: 654 sheet: -0.28 (0.19), residues: 729 loop : -0.73 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 127 HIS 0.009 0.002 HIS C 500 PHE 0.023 0.002 PHE C 430 TYR 0.025 0.002 TYR A 91 ARG 0.003 0.000 ARG A 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 45) link_NAG-ASN : angle 2.44755 ( 135) link_BETA1-4 : bond 0.01116 ( 24) link_BETA1-4 : angle 2.40613 ( 72) hydrogen bonds : bond 0.06245 ( 919) hydrogen bonds : angle 5.70206 ( 2499) SS BOND : bond 0.00402 ( 45) SS BOND : angle 2.18839 ( 90) covalent geometry : bond 0.00316 (23937) covalent geometry : angle 0.67664 (32610) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 MET cc_start: 0.6814 (ttt) cc_final: 0.6452 (ttt) REVERT: B 282 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: B 405 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8046 (ttm170) REVERT: B 459 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7031 (m-80) REVERT: B 520 THR cc_start: 0.8607 (p) cc_final: 0.8399 (p) REVERT: B 620 ARG cc_start: 0.8726 (ttm110) cc_final: 0.8498 (ttm110) REVERT: A 405 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7961 (ttm170) REVERT: A 459 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.6839 (m-80) REVERT: A 485 LEU cc_start: 0.8398 (mm) cc_final: 0.8079 (mt) REVERT: C 206 MET cc_start: 0.6690 (ttt) cc_final: 0.6461 (ttt) REVERT: C 214 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: C 330 GLU cc_start: 0.8420 (tp30) cc_final: 0.8090 (mm-30) REVERT: C 340 ASP cc_start: 0.7719 (t0) cc_final: 0.7450 (t0) REVERT: C 454 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8663 (tt0) REVERT: C 459 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: C 545 MET cc_start: 0.9026 (mtp) cc_final: 0.8785 (mtp) REVERT: C 754 MET cc_start: 0.9376 (mmt) cc_final: 0.9129 (mmt) outliers start: 34 outliers final: 9 residues processed: 273 average time/residue: 1.4026 time to fit residues: 436.9575 Evaluate side-chains 250 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 838 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 18 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 265 optimal weight: 0.0040 chunk 73 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 HIS B 326 ASN ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 GLN B 766 ASN B 805 ASN A 326 ASN A 483 ASN A 765 GLN A 805 ASN A 892 ASN C 99 HIS C 326 ASN C 766 ASN C 805 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.098206 restraints weight = 23150.282| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.72 r_work: 0.2886 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24051 Z= 0.206 Angle : 0.773 13.252 32907 Z= 0.383 Chirality : 0.055 0.736 3894 Planarity : 0.005 0.048 4083 Dihedral : 10.828 65.062 4644 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.85 % Allowed : 5.97 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.15), residues: 2877 helix: 1.28 (0.20), residues: 636 sheet: -0.24 (0.19), residues: 720 loop : -0.59 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 127 HIS 0.008 0.002 HIS B 500 PHE 0.025 0.002 PHE C 430 TYR 0.035 0.002 TYR B 91 ARG 0.006 0.001 ARG C 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 45) link_NAG-ASN : angle 2.70841 ( 135) link_BETA1-4 : bond 0.01116 ( 24) link_BETA1-4 : angle 2.40446 ( 72) hydrogen bonds : bond 0.06605 ( 919) hydrogen bonds : angle 5.70791 ( 2499) SS BOND : bond 0.00585 ( 45) SS BOND : angle 2.55429 ( 90) covalent geometry : bond 0.00480 (23937) covalent geometry : angle 0.73660 (32610) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8426 (mtm180) REVERT: B 206 MET cc_start: 0.7015 (ttt) cc_final: 0.6672 (ttt) REVERT: B 340 ASP cc_start: 0.7989 (t0) cc_final: 0.7778 (t0) REVERT: B 405 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8081 (ttm170) REVERT: B 459 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: B 583 MET cc_start: 0.8805 (mtm) cc_final: 0.8540 (ttp) REVERT: B 818 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8999 (pp) REVERT: A 279 GLN cc_start: 0.8874 (mm110) cc_final: 0.8607 (mm-40) REVERT: A 405 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8010 (ttm170) REVERT: A 459 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7483 (m-80) REVERT: A 485 LEU cc_start: 0.8554 (mm) cc_final: 0.8219 (mm) REVERT: C 99 HIS cc_start: 0.8418 (m-70) cc_final: 0.8101 (m90) REVERT: C 206 MET cc_start: 0.6783 (ttt) cc_final: 0.6541 (ttt) REVERT: C 459 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: C 545 MET cc_start: 0.9019 (mtp) cc_final: 0.8734 (mtp) REVERT: C 754 MET cc_start: 0.9397 (mmt) cc_final: 0.9155 (mmt) outliers start: 45 outliers final: 15 residues processed: 277 average time/residue: 1.4759 time to fit residues: 468.3489 Evaluate side-chains 261 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 838 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 120 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 68 optimal weight: 0.0370 chunk 257 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 overall best weight: 4.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 GLN B 892 ASN A 765 GLN C 766 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.096658 restraints weight = 23420.374| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.74 r_work: 0.2864 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 24051 Z= 0.265 Angle : 0.839 14.507 32907 Z= 0.418 Chirality : 0.058 0.731 3894 Planarity : 0.005 0.049 4083 Dihedral : 10.275 66.607 4644 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.85 % Allowed : 6.59 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.11 (0.15), residues: 2877 helix: 1.35 (0.20), residues: 633 sheet: -0.22 (0.19), residues: 720 loop : -0.55 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 169 HIS 0.009 0.002 HIS B 500 PHE 0.027 0.003 PHE C 430 TYR 0.038 0.003 TYR A 91 ARG 0.007 0.001 ARG A 671 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 45) link_NAG-ASN : angle 2.97735 ( 135) link_BETA1-4 : bond 0.01174 ( 24) link_BETA1-4 : angle 2.53555 ( 72) hydrogen bonds : bond 0.07020 ( 919) hydrogen bonds : angle 5.86666 ( 2499) SS BOND : bond 0.00820 ( 45) SS BOND : angle 2.94704 ( 90) covalent geometry : bond 0.00625 (23937) covalent geometry : angle 0.79742 (32610) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8454 (mtm180) REVERT: B 206 MET cc_start: 0.7177 (ttt) cc_final: 0.6853 (ttt) REVERT: B 214 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8058 (pp20) REVERT: B 340 ASP cc_start: 0.8076 (t70) cc_final: 0.7851 (t0) REVERT: B 405 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8098 (ttm170) REVERT: B 459 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: B 596 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7365 (p0) REVERT: A 214 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8105 (pp20) REVERT: A 279 GLN cc_start: 0.8903 (mm110) cc_final: 0.8644 (mm-40) REVERT: A 405 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8148 (ttm170) REVERT: A 459 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: C 122 ARG cc_start: 0.8970 (mtt180) cc_final: 0.8737 (mtt-85) REVERT: C 161 LYS cc_start: 0.7503 (mtmt) cc_final: 0.7208 (mttm) REVERT: C 206 MET cc_start: 0.6963 (ttt) cc_final: 0.6723 (ttt) REVERT: C 459 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: C 545 MET cc_start: 0.8938 (mtp) cc_final: 0.8675 (mtp) REVERT: C 754 MET cc_start: 0.9404 (mmt) cc_final: 0.9166 (mmt) REVERT: C 837 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8149 (p0) outliers start: 45 outliers final: 16 residues processed: 272 average time/residue: 1.5127 time to fit residues: 468.3790 Evaluate side-chains 263 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 837 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 57.9451 > 50: distance: 13 - 185: 33.573 distance: 27 - 171: 19.548 distance: 30 - 168: 4.034 distance: 41 - 155: 20.926 distance: 44 - 152: 22.511 distance: 79 - 161: 13.252 distance: 89 - 143: 21.030 distance: 92 - 140: 15.437 distance: 106 - 127: 22.145 distance: 109 - 124: 19.244 distance: 116 - 120: 6.313 distance: 120 - 121: 11.917 distance: 121 - 122: 18.451 distance: 122 - 123: 16.096 distance: 122 - 124: 5.088 distance: 124 - 125: 8.197 distance: 125 - 126: 15.867 distance: 125 - 128: 8.194 distance: 126 - 127: 11.186 distance: 126 - 133: 14.761 distance: 128 - 129: 5.468 distance: 129 - 130: 6.576 distance: 131 - 132: 17.092 distance: 133 - 134: 33.236 distance: 134 - 135: 38.542 distance: 134 - 137: 12.501 distance: 135 - 136: 12.753 distance: 135 - 140: 23.418 distance: 137 - 139: 12.993 distance: 141 - 142: 14.022 distance: 141 - 144: 6.094 distance: 142 - 143: 8.022 distance: 142 - 152: 3.076 distance: 144 - 145: 4.920 distance: 145 - 146: 3.488 distance: 145 - 147: 8.473 distance: 146 - 148: 12.152 distance: 147 - 149: 8.165 distance: 148 - 150: 6.857 distance: 149 - 150: 3.661 distance: 150 - 151: 7.890 distance: 152 - 153: 9.992 distance: 153 - 154: 4.453 distance: 153 - 156: 7.933 distance: 154 - 155: 4.939 distance: 154 - 161: 13.482 distance: 156 - 157: 14.275 distance: 157 - 158: 8.711 distance: 158 - 159: 6.734 distance: 158 - 160: 12.921 distance: 161 - 162: 9.628 distance: 162 - 163: 15.625 distance: 162 - 165: 18.896 distance: 163 - 164: 7.988 distance: 163 - 168: 19.724 distance: 165 - 166: 26.612 distance: 165 - 167: 17.282 distance: 168 - 169: 6.695 distance: 169 - 170: 11.186 distance: 169 - 172: 28.359 distance: 170 - 171: 12.618 distance: 170 - 173: 17.205 distance: 173 - 174: 12.043 distance: 173 - 179: 21.106 distance: 174 - 175: 6.162 distance: 174 - 177: 20.229 distance: 175 - 176: 22.560 distance: 175 - 180: 5.970 distance: 177 - 178: 16.171 distance: 178 - 179: 15.078 distance: 180 - 181: 9.858 distance: 181 - 182: 14.774 distance: 181 - 184: 11.129 distance: 182 - 183: 22.598 distance: 182 - 186: 10.797 distance: 184 - 185: 13.022 distance: 186 - 187: 12.272 distance: 187 - 188: 5.614 distance: 187 - 190: 18.893 distance: 188 - 189: 4.853 distance: 188 - 197: 5.955 distance: 190 - 191: 7.880 distance: 191 - 192: 8.546 distance: 191 - 193: 9.719 distance: 192 - 194: 10.183 distance: 193 - 195: 8.860 distance: 194 - 196: 10.333 distance: 195 - 196: 8.551