Starting phenix.real_space_refine on Thu Jan 23 01:45:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u0n_20608/01_2025/6u0n_20608_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u0n_20608/01_2025/6u0n_20608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u0n_20608/01_2025/6u0n_20608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u0n_20608/01_2025/6u0n_20608.map" model { file = "/net/cci-nas-00/data/ceres_data/6u0n_20608/01_2025/6u0n_20608_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u0n_20608/01_2025/6u0n_20608_neut.cif" } resolution = 3.5 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= 0.003 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 118 5.16 5 C 12153 2.51 5 N 3304 2.21 5 O 3747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 19322 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2781 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 10, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2774 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 4 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2724 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 21, 'TRANS': 341} Chain breaks: 4 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 763 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 967 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYS:plan-2': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 28 Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 985 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYS:plan-2': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 780 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 786 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 780 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 110, 780 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 790 Chain: "P" Number of atoms: 987 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 981 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'TYS:plan-2': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 132, 981 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'TYS:plan-2': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 997 Chain: "Q" Number of atoms: 792 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 786 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 110, 786 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 796 Chain: "X" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 991 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "Y" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 940 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "Z" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 927 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 55 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: "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: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: "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 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASER L 70 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER L 70 " occ=0.50 residue: pdb=" N ACYS P 92 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS P 92 " occ=0.50 residue: pdb=" N ASER Q 70 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER Q 70 " occ=0.50 Time building chain proxies: 13.73, per 1000 atoms: 0.71 Number of scatterers: 19322 At special positions: 0 Unit cell: (146.923, 149.037, 167.006, 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 118 16.00 O 3747 8.00 N 3304 7.00 C 12153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS X 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.04 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS Y 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS Z 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 84 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 84 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG ACYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG BCYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS X 598 " - pdb=" SG CYS X 604 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN N 4 " - " MAN N 5 " " MAN O 4 " - " MAN O 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 603 " - " ASN A 355 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 363 " " NAG A 608 " - " ASN A 448 " " NAG A 609 " - " ASN A 88 " " NAG A 610 " - " ASN A 234 " " NAG B 601 " - " ASN B 448 " " NAG B 602 " - " ASN B 386 " " NAG B 603 " - " ASN B 88 " " NAG B 604 " - " ASN B 392 " " NAG B 610 " - " ASN B 276 " " NAG B 611 " - " ASN B 295 " " NAG B 612 " - " ASN B 332 " " NAG B 613 " - " ASN B 363 " " NAG B 614 " - " ASN B 339 " " NAG C 606 " - " ASN C 276 " " NAG C 607 " - " ASN C 295 " " NAG C 608 " - " ASN C 332 " " NAG C 609 " - " ASN C 363 " " NAG C 610 " - " ASN C 339 " " NAG C 611 " - " ASN C 448 " " NAG C 612 " - " ASN C 386 " " NAG C 613 " - " ASN C 88 " " NAG C 614 " - " ASN C 392 " " NAG G 1 " - " ASN A 276 " " NAG K 1 " - " ASN A 386 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN B 262 " " NAG O 1 " - " ASN C 262 " Time building additional restraints: 4.97 Conformation dependent library (CDL) restraints added in 2.6 seconds 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4586 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 51 sheets defined 15.5% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.596A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.720A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.586A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.688A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.812A pdb=" N TRP B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 110 removed outlier: 3.929A pdb=" N ASP B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 350 removed outlier: 3.503A pdb=" N ASN B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 350 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'C' and resid 101 through 109 removed outlier: 4.272A pdb=" N ASP C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 353 removed outlier: 4.031A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.502A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.738A pdb=" N TRP D 62 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 63 " --> pdb=" O SER D 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 removed outlier: 3.613A pdb=" N LEU E 61 " --> pdb=" O ARG E 58 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP E 62 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP E 63 " --> pdb=" O SER E 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 64 removed outlier: 3.573A pdb=" N TRP F 62 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.204A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 96 through 100A removed outlier: 4.257A pdb=" N GLY H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA H 100A" --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 98 through 100A Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.528A pdb=" N THR P 87 " --> pdb=" O SER P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 100 removed outlier: 4.305A pdb=" N GLY P 99 " --> pdb=" O SER P 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.884A pdb=" N ASP Q 82 " --> pdb=" O GLN Q 79 " (cutoff:3.500A) Processing helix chain 'X' and resid 516 through 523 removed outlier: 3.640A pdb=" N LEU X 520 " --> pdb=" O GLY X 516 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU X 523 " --> pdb=" O PHE X 519 " (cutoff:3.500A) Processing helix chain 'X' and resid 529 through 535 Processing helix chain 'X' and resid 536 through 545 removed outlier: 3.843A pdb=" N ARG X 542 " --> pdb=" O THR X 538 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN X 543 " --> pdb=" O VAL X 539 " (cutoff:3.500A) Processing helix chain 'X' and resid 569 through 574 Processing helix chain 'X' and resid 578 through 594 removed outlier: 3.564A pdb=" N TYR X 586 " --> pdb=" O ALA X 582 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG X 588 " --> pdb=" O GLU X 584 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP X 589 " --> pdb=" O ARG X 585 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN X 590 " --> pdb=" O TYR X 586 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU X 592 " --> pdb=" O ARG X 588 " (cutoff:3.500A) Processing helix chain 'X' and resid 618 through 622 Processing helix chain 'X' and resid 628 through 633 removed outlier: 4.005A pdb=" N ASP X 632 " --> pdb=" O TRP X 628 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS X 633 " --> pdb=" O LEU X 629 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 628 through 633' Processing helix chain 'X' and resid 641 through 649 removed outlier: 3.595A pdb=" N GLU X 647 " --> pdb=" O TYR X 643 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU X 648 " --> pdb=" O GLY X 644 " (cutoff:3.500A) Processing helix chain 'Y' and resid 529 through 537 removed outlier: 3.706A pdb=" N SER Y 534 " --> pdb=" O MET Y 530 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET Y 535 " --> pdb=" O GLY Y 531 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR Y 536 " --> pdb=" O ALA Y 532 " (cutoff:3.500A) Processing helix chain 'Y' and resid 538 through 543 removed outlier: 4.368A pdb=" N ASN Y 543 " --> pdb=" O VAL Y 539 " (cutoff:3.500A) Processing helix chain 'Y' and resid 569 through 574 Processing helix chain 'Y' and resid 576 through 588 removed outlier: 3.504A pdb=" N LEU Y 581 " --> pdb=" O GLN Y 577 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA Y 582 " --> pdb=" O ALA Y 578 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL Y 583 " --> pdb=" O ARG Y 579 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR Y 586 " --> pdb=" O ALA Y 582 " (cutoff:3.500A) Processing helix chain 'Y' and resid 589 through 596 removed outlier: 3.532A pdb=" N LEU Y 593 " --> pdb=" O ASP Y 589 " (cutoff:3.500A) Processing helix chain 'Y' and resid 620 through 625 removed outlier: 3.651A pdb=" N ASP Y 624 " --> pdb=" O SER Y 620 " (cutoff:3.500A) Processing helix chain 'Y' and resid 627 through 635 removed outlier: 3.549A pdb=" N GLU Y 634 " --> pdb=" O GLN Y 630 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE Y 635 " --> pdb=" O TRP Y 631 " (cutoff:3.500A) Processing helix chain 'Y' and resid 638 through 658 removed outlier: 3.638A pdb=" N GLY Y 644 " --> pdb=" O GLN Y 640 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU Y 645 " --> pdb=" O ILE Y 641 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU Y 646 " --> pdb=" O ILE Y 642 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU Y 648 " --> pdb=" O GLY Y 644 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN Y 650 " --> pdb=" O LEU Y 646 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN Y 658 " --> pdb=" O GLU Y 654 " (cutoff:3.500A) Processing helix chain 'Z' and resid 529 through 534 Processing helix chain 'Z' and resid 563 through 575 removed outlier: 3.746A pdb=" N LEU Z 568 " --> pdb=" O HIS Z 564 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR Z 569 " --> pdb=" O LEU Z 565 " (cutoff:3.500A) Processing helix chain 'Z' and resid 576 through 596 removed outlier: 3.809A pdb=" N LEU Z 581 " --> pdb=" O GLN Z 577 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR Z 586 " --> pdb=" O ALA Z 582 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN Z 591 " --> pdb=" O LEU Z 587 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU Z 592 " --> pdb=" O ARG Z 588 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP Z 596 " --> pdb=" O LEU Z 592 " (cutoff:3.500A) Processing helix chain 'Z' and resid 627 through 635 Processing helix chain 'Z' and resid 638 through 654 removed outlier: 4.023A pdb=" N GLY Z 644 " --> pdb=" O GLN Z 640 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU Z 645 " --> pdb=" O ILE Z 641 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN Z 650 " --> pdb=" O LEU Z 646 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN Z 653 " --> pdb=" O SER Z 649 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 498 through 499 removed outlier: 4.330A pdb=" N VAL A 36 " --> pdb=" O THR X 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.760A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.663A pdb=" N GLN A 432 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.125A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.036A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.238A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 359 through 360 Processing sheet with id=AA6, first strand: chain 'A' and resid 272 through 273 removed outlier: 11.257A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.238A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.036A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 414 Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 375 Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.860A pdb=" N PHE B 53 " --> pdb=" O CYS B 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 91 through 93 removed outlier: 3.591A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 196 through 202 removed outlier: 3.571A pdb=" N THR B 123 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 121 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 120 " --> pdb=" O MET B 434 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 432 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 242 through 245 Processing sheet with id=AB4, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.713A pdb=" N ARG B 273 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR B 467 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 466 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 413 through 418 removed outlier: 3.500A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 413 through 418 removed outlier: 3.500A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 375 through 377 Processing sheet with id=AB8, first strand: chain 'C' and resid 494 through 497 removed outlier: 5.733A pdb=" N VAL C 36 " --> pdb=" O THR Z 606 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR Z 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.508A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 83 through 86 removed outlier: 4.874A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.679A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.777A pdb=" N GLN C 432 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AC5, first strand: chain 'C' and resid 414 through 417 removed outlier: 3.844A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG C 298 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 393 through 395 removed outlier: 3.601A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.801A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 2 through 5 removed outlier: 4.230A pdb=" N LYS D 2 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN D 94 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP D 28 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN D 40 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 14 through 15 Processing sheet with id=AD1, first strand: chain 'E' and resid 2 through 5 removed outlier: 6.497A pdb=" N LYS E 2 " --> pdb=" O GLN E 94 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU E 96 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL E 4 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS E 84 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU E 85 " --> pdb=" O HIS E 27 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS E 27 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP E 28 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 37 " --> pdb=" O TRP E 28 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN E 40 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AD3, first strand: chain 'F' and resid 2 through 5 removed outlier: 6.634A pdb=" N LYS F 2 " --> pdb=" O GLN F 94 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LEU F 96 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL F 4 " --> pdb=" O LEU F 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 12 through 13 Processing sheet with id=AD5, first strand: chain 'F' and resid 16 through 17 removed outlier: 3.858A pdb=" N CYS F 16 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.766A pdb=" N GLU H 10 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.515A pdb=" N VAL H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.572A pdb=" N LEU I 82 " --> pdb=" O VAL I 18 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.512A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY I 50 " --> pdb=" O HIS I 58 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.745A pdb=" N VAL I 102 " --> pdb=" O SER I 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.250A pdb=" N VAL J 11 " --> pdb=" O THR J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'J' and resid 19 through 23 removed outlier: 3.580A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE J 75 " --> pdb=" O VAL J 19 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.705A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR J 90 " --> pdb=" O VAL J 97 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 12 through 13 removed outlier: 3.971A pdb=" N ALA L 13 " --> pdb=" O THR L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AE8, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.752A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 95B" --> pdb=" O ASP L 92 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.752A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR L 86 " --> pdb=" O SER L 102 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 5 through 6 removed outlier: 3.631A pdb=" N VAL P 20 " --> pdb=" O LEU P 80 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 5 through 6 removed outlier: 3.631A pdb=" N VAL P 20 " --> pdb=" O LEU P 80 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR P 77 " --> pdb=" O ASP P 72 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.925A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU P 46 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 23 through 24 Processing sheet with id=AF5, first strand: chain 'Q' and resid 45 through 48 removed outlier: 7.267A pdb=" N TRP Q 35 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR Q 36 " --> pdb=" O TYR Q 87 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 45 through 48 removed outlier: 7.267A pdb=" N TRP Q 35 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR Q 36 " --> pdb=" O TYR Q 87 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1259 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.62 Time building geometry restraints manager: 5.66 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: 6124 1.34 - 1.46: 4779 1.46 - 1.58: 8670 1.58 - 1.70: 6 1.70 - 1.82: 145 Bond restraints: 19724 Sorted by residual: bond pdb=" O3 TYS P 100F" pdb=" S TYS P 100F" ideal model delta sigma weight residual 1.458 1.633 -0.175 2.00e-02 2.50e+03 7.65e+01 bond pdb=" O1 TYS I 100F" pdb=" S TYS I 100F" ideal model delta sigma weight residual 1.462 1.634 -0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" O2 TYS I 100I" pdb=" S TYS I 100I" ideal model delta sigma weight residual 1.461 1.632 -0.171 2.00e-02 2.50e+03 7.31e+01 bond pdb=" O1 TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.462 1.632 -0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" O3 TYS P 100I" pdb=" S TYS P 100I" ideal model delta sigma weight residual 1.458 1.627 -0.169 2.00e-02 2.50e+03 7.16e+01 ... (remaining 19719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 25831 2.10 - 4.20: 866 4.20 - 6.30: 117 6.30 - 8.39: 31 8.39 - 10.49: 13 Bond angle restraints: 26858 Sorted by residual: angle pdb=" C GLU J 50 " pdb=" N ASN J 51 " pdb=" CA ASN J 51 " ideal model delta sigma weight residual 121.54 131.04 -9.50 1.91e+00 2.74e-01 2.48e+01 angle pdb=" C GLU Q 50 " pdb=" N ASN Q 51 " pdb=" CA ASN Q 51 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C GLU L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 angle pdb=" N SER C 56 " pdb=" CA SER C 56 " pdb=" C SER C 56 " ideal model delta sigma weight residual 111.02 116.22 -5.20 1.25e+00 6.40e-01 1.73e+01 angle pdb=" C LYS C 335 " pdb=" N ALA C 336 " pdb=" CA ALA C 336 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 ... (remaining 26853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 11314 21.85 - 43.70: 786 43.70 - 65.54: 87 65.54 - 87.39: 38 87.39 - 109.24: 14 Dihedral angle restraints: 12239 sinusoidal: 5119 harmonic: 7120 Sorted by residual: dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS X 605 " pdb=" CB CYS X 605 " ideal model delta sinusoidal sigma weight residual -86.00 -12.87 -73.13 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS Z 605 " pdb=" CB CYS Z 605 " ideal model delta sinusoidal sigma weight residual -86.00 -18.96 -67.04 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS B 378 " pdb=" SG CYS B 378 " pdb=" SG CYS B 445 " pdb=" CB CYS B 445 " ideal model delta sinusoidal sigma weight residual -86.00 -139.10 53.10 1 1.00e+01 1.00e-02 3.84e+01 ... (remaining 12236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 3142 0.141 - 0.282: 48 0.282 - 0.423: 5 0.423 - 0.564: 1 0.564 - 0.705: 2 Chirality restraints: 3198 Sorted by residual: chirality pdb=" C1 NAG B 613 " pdb=" ND2 ASN B 363 " pdb=" C2 NAG B 613 " pdb=" O5 NAG B 613 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" C1 NAG C 609 " pdb=" ND2 ASN C 363 " pdb=" C2 NAG C 609 " pdb=" O5 NAG C 609 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG B 603 " pdb=" ND2 ASN B 88 " pdb=" C2 NAG B 603 " pdb=" O5 NAG B 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.96e+00 ... (remaining 3195 not shown) Planarity restraints: 3375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 448 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" C ASN B 448 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN B 448 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE B 449 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 75 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO C 76 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 243 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C SER A 243 " 0.045 2.00e-02 2.50e+03 pdb=" O SER A 243 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 244 " -0.015 2.00e-02 2.50e+03 ... (remaining 3372 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4080 2.77 - 3.31: 16535 3.31 - 3.84: 31150 3.84 - 4.37: 35387 4.37 - 4.90: 62412 Nonbonded interactions: 149564 Sorted by model distance: nonbonded pdb=" O LYS B 229 " pdb=" OG SER B 241 " model vdw 2.242 3.040 nonbonded pdb=" O SER C 56 " pdb=" OG SER C 56 " model vdw 2.283 3.040 nonbonded pdb=" O LEU B 369 " pdb=" OG1 THR B 373 " model vdw 2.306 3.040 nonbonded pdb=" O SER E 23 " pdb=" OG SER E 23 " model vdw 2.326 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" O ALA A 497 " model vdw 2.328 3.040 ... (remaining 149559 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 46 or (resid 47 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 61 or (resid 62 and (na \ me N or name CA or name C or name O or name CB )) or resid 63 or (resid 64 and ( \ name N or name CA or name C or name O or name CB )) or resid 65 through 77 or (r \ esid 78 and (name N or name CA or name C or name O or name CB )) or resid 79 or \ (resid 80 and (name N or name CA or name C or name O or name CB )) or resid 81 t \ hrough 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) \ or resid 93 through 124 or (resid 125 and (name N or name CA or name C or name O \ or name CB )) or resid 126 or (resid 127 and (name N or name CA or name C or na \ me O or name CB )) or (resid 194 through 195 and (name N or name CA or name C or \ name O or name CB )) or resid 196 through 206 or (resid 207 through 208 and (na \ me N or name CA or name C or name O or name CB )) or resid 209 through 229 or (r \ esid 230 through 232 and (name N or name CA or name C or name O or name CB )) or \ resid 233 through 349 or (resid 350 and (name N or name CA or name C or name O \ or name CB )) or resid 351 through 397 or (resid 412 and (name N or name CA or n \ ame C or name O or name CB )) or resid 413 through 458 or resid 460 through 465 \ or (resid 466 through 467 and (name N or name CA or name C or name O or name CB \ )) or resid 468 through 491 or (resid 492 and (name N or name CA or name C or na \ me O or name CB )) or resid 493 through 499 or (resid 500 and (name N or name CA \ or name C or name O or name CB )) or resid 501 through 502 or resid 603 through \ 610)) selection = (chain 'B' and (resid 35 through 56 or (resid 57 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 61 or (resid 62 and (na \ me N or name CA or name C or name O or name CB )) or resid 63 or (resid 64 and ( \ name N or name CA or name C or name O or name CB )) or resid 65 through 96 or (r \ esid 97 and (name N or name CA or name C or name O or name CB )) or resid 98 thr \ ough 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) \ or resid 118 through 124 or (resid 125 and (name N or name CA or name C or name \ O or name CB )) or resid 126 through 127 or (resid 194 through 195 and (name N o \ r name CA or name C or name O or name CB )) or resid 196 through 202 or (resid 2 \ 03 through 204 and (name N or name CA or name C or name O or name CB )) or resid \ 205 through 206 or (resid 207 through 208 and (name N or name CA or name C or n \ ame O or name CB )) or resid 209 through 231 or (resid 232 and (name N or name C \ A or name C or name O or name CB )) or resid 233 through 300 or resid 325 throug \ h 357 or (resid 358 and (name N or name CA or name C or name O or name CB )) or \ resid 359 through 369 or (resid 370 and (name N or name CA or name C or name O o \ r name CB )) or resid 371 through 395 or (resid 396 and (name N or name CA or na \ me C or name O or name CB )) or resid 397 through 439 or (resid 440 and (name N \ or name CA or name C or name O or name CB )) or resid 441 through 456 or (resid \ 457 and (name N or name CA or name C or name O or name CB )) or resid 458 or res \ id 463 through 464 or (resid 465 and (name N or name CA or name C or name O or n \ ame CB or name OG1)) or (resid 466 through 467 and (name N or name CA or name C \ or name O or name CB )) or resid 468 through 491 or (resid 492 and (name N or na \ me CA or name C or name O or name CB )) or resid 493 through 499 or (resid 500 a \ nd (name N or name CA or name C or name O or name CB )) or resid 501 through 502 \ or resid 602 through 612)) selection = (chain 'C' and (resid 35 through 56 or (resid 57 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 91 or (resid 92 and (na \ me N or name CA or name C or name O or name CB )) or resid 93 through 116 or (re \ sid 117 and (name N or name CA or name C or name O or name CB )) or resid 118 th \ rough 229 or (resid 230 through 232 and (name N or name CA or name C or name O o \ r name CB )) or resid 233 through 300 or resid 325 through 349 or (resid 350 and \ (name N or name CA or name C or name O or name CB )) or resid 351 through 357 o \ r (resid 358 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 59 through 397 or (resid 412 and (name N or name CA or name C or name O or name \ CB )) or resid 413 through 439 or (resid 440 and (name N or name CA or name C or \ name O or name CB )) or resid 441 through 458 or resid 460 through 465 or (resi \ d 466 through 467 and (name N or name CA or name C or name O or name CB )) or re \ sid 468 through 502 or resid 607 through 612)) } ncs_group { reference = (chain 'D' and (resid 1 through 20 or (resid 21 through 22 and (name N or name C \ A or name C or name O or name CB or name CG or name CD )) or resid 23 through 86 \ or (resid 87 and (name N or name CA or name C or name O or name CB )) or resid \ 88 through 90 or (resid 91 and (name N or name CA or name C or name O or name CB \ )) or resid 92 through 97)) selection = chain 'E' selection = (chain 'F' and (resid 1 through 20 or (resid 21 through 22 and (name N or name C \ A or name C or name O or name CB or name CG or name CD )) or resid 23 through 86 \ or (resid 87 and (name N or name CA or name C or name O or name CB )) or resid \ 88 through 90 or (resid 91 and (name N or name CA or name C or name O or name CB \ )) or resid 92 through 97)) } ncs_group { reference = chain 'G' selection = chain 'K' } ncs_group { reference = (chain 'H' and (resid 2 through 91 or resid 93 through 104 or (resid 105 and (na \ me N or name CA or name C or name O or name CB )) or resid 106 through 112)) selection = (chain 'I' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 or (resid 12 through 13 and (name N or name \ CA or name C or name O or name CB )) or resid 14 through 18 or (resid 19 and (na \ me N or name CA or name C or name O or name CB )) or resid 20 through 91 or resi \ d 93 through 100Q or (resid 101 and (name N or name CA or name C or name O or na \ me CB )) or resid 102 through 112)) selection = (chain 'P' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 91 or resid 93 through 100O or (res \ id 100P and (name N or name CA or name C or name O or name CB )) or resid 100Q o \ r (resid 101 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 02 through 104 or (resid 105 and (name N or name CA or name C or name O or name \ CB )) or resid 106 through 112)) } ncs_group { reference = (chain 'J' and (resid 2 through 51 or (resid 52 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 59 or (resid 60 through \ 61 and (name N or name CA or name C or name O or name CB )) or resid 62 through \ 69 or resid 71 through 107)) selection = (chain 'L' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 69 or resid 71 through 107)) selection = (chain 'Q' and (resid 2 through 51 or (resid 52 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 59 or (resid 60 through \ 61 and (name N or name CA or name C or name O or name CB )) or resid 62 through \ 69 or resid 71 through 107)) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'X' and (resid 521 through 528 or (resid 529 and (name N or name CA or na \ me C or name O or name CB )) or resid 530 through 539 or (resid 540 and (name N \ or name CA or name C or name O or name CB )) or (resid 542 and (name N or name C \ A or name C or name O or name CB )) or (resid 560 through 563 and (name N or nam \ e CA or name C or name O or name CB )) or resid 564 through 600 or (resid 601 an \ d (name N or name CA or name C or name O or name CB )) or resid 602 through 606 \ or (resid 607 and (name N or name CA or name C or name O or name CB )) or resid \ 608 through 616 or (resid 617 and (name N or name CA or name C or name O or name \ CB )) or resid 618 through 629 or (resid 630 and (name N or name CA or name C o \ r name O or name CB )) or resid 631 through 632 or (resid 633 and (name N or nam \ e CA or name C or name O or name CB )) or resid 634 through 636 or (resid 637 an \ d (name N or name CA or name C or name O or name CB )) or resid 638 through 639 \ or (resid 640 through 641 and (name N or name CA or name C or name O or name CB \ )) or resid 642 through 647 or (resid 648 and (name N or name CA or name C or na \ me O or name CB )) or resid 649 through 650 or (resid 651 and (name N or name CA \ or name C or name O or name CB )) or resid 652 through 653)) selection = (chain 'Y' and (resid 521 through 528 or (resid 529 and (name N or name CA or na \ me C or name O or name CB )) or resid 530 through 540 or resid 542 or (resid 560 \ through 563 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 64 through 606 or (resid 607 and (name N or name CA or name C or name O or name \ CB )) or resid 608 through 629 or (resid 630 and (name N or name CA or name C or \ name O or name CB )) or resid 631 through 632 or (resid 633 and (name N or name \ CA or name C or name O or name CB )) or resid 634 through 639 or (resid 640 thr \ ough 641 and (name N or name CA or name C or name O or name CB )) or resid 642 t \ hrough 649 or (resid 650 through 651 and (name N or name CA or name C or name O \ or name CB )) or resid 652 or (resid 653 and (name N or name CA or name C or nam \ e O or name CB )))) selection = (chain 'Z' and (resid 521 through 557 or resid 560 through 600 or (resid 601 and \ (name N or name CA or name C or name O or name CB )) or resid 602 through 616 o \ r (resid 617 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 18 through 636 or (resid 637 and (name N or name CA or name C or name O or name \ CB )) or resid 638 through 649 or (resid 650 through 651 and (name N or name CA \ or name C or name O or name CB )) or resid 652 through 653)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 46.580 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.008 0.175 19724 Z= 0.517 Angle : 0.908 10.493 26858 Z= 0.471 Chirality : 0.059 0.705 3198 Planarity : 0.006 0.066 3346 Dihedral : 15.218 109.240 7539 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.58 % Favored : 90.34 % Rotamer: Outliers : 0.56 % Allowed : 6.51 % Favored : 92.93 % 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: -5.29 (0.13), residues: 2420 helix: -4.82 (0.08), residues: 401 sheet: -2.85 (0.17), residues: 736 loop : -3.51 (0.13), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP X 614 HIS 0.007 0.001 HIS A 352 PHE 0.021 0.002 PHE A 376 TYR 0.019 0.002 TYR B 484 ARG 0.005 0.000 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 444 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8648 (mttt) cc_final: 0.8250 (mttp) REVERT: A 62 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7964 (mm-30) REVERT: A 479 TRP cc_start: 0.7378 (m-10) cc_final: 0.7023 (m-10) REVERT: B 340 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7841 (tp30) REVERT: B 377 ASN cc_start: 0.7613 (t0) cc_final: 0.7323 (t0) REVERT: D 89 GLN cc_start: 0.9021 (mt0) cc_final: 0.8364 (mp10) REVERT: F 70 ILE cc_start: 0.8945 (mm) cc_final: 0.8739 (mm) REVERT: F 94 GLN cc_start: 0.8795 (pt0) cc_final: 0.8563 (pm20) REVERT: H 79 TYR cc_start: 0.7890 (m-80) cc_final: 0.7624 (m-10) REVERT: I 10 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8070 (mm-30) REVERT: J 21 ILE cc_start: 0.9191 (mm) cc_final: 0.8973 (mp) REVERT: J 92 ASP cc_start: 0.8236 (t0) cc_final: 0.7605 (p0) REVERT: L 45 LYS cc_start: 0.9028 (ttpt) cc_final: 0.8802 (tttt) REVERT: L 90 THR cc_start: 0.8044 (t) cc_final: 0.7576 (m) REVERT: L 95 LEU cc_start: 0.9257 (mp) cc_final: 0.8841 (tp) REVERT: P 38 ARG cc_start: 0.6821 (ptt180) cc_final: 0.6398 (ptm-80) REVERT: P 61 GLN cc_start: 0.8644 (tp40) cc_final: 0.8303 (tp-100) REVERT: P 66 ARG cc_start: 0.8428 (mtp180) cc_final: 0.8170 (ptm160) REVERT: P 82 ARG cc_start: 0.7052 (ptt-90) cc_final: 0.6771 (mpt180) REVERT: P 82 LEU cc_start: 0.8655 (mt) cc_final: 0.7086 (mp) REVERT: P 101 ASP cc_start: 0.8675 (t70) cc_final: 0.8367 (t0) outliers start: 11 outliers final: 6 residues processed: 452 average time/residue: 0.3510 time to fit residues: 240.7716 Evaluate side-chains 359 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 353 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 102 optimal weight: 0.0170 chunk 62 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 overall best weight: 1.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 66 HIS A 67 ASN A 279 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 478 ASN B 279 ASN C 72 HIS C 258 GLN C 280 ASN C 422 GLN E 27 HIS ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN F 32 ASN I 6 GLN I 58 HIS I 95 ASN J 37 GLN L 31 ASN L 37 GLN P 81 HIS Q 31 ASN Q 37 GLN X 590 GLN X 625 ASN Y 562 GLN Y 564 HIS Y 590 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.111488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.079093 restraints weight = 113430.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.081493 restraints weight = 38649.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.082426 restraints weight = 24400.156| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19724 Z= 0.331 Angle : 0.677 8.256 26858 Z= 0.352 Chirality : 0.050 0.601 3198 Planarity : 0.005 0.062 3346 Dihedral : 9.825 80.924 3517 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.22 % Allowed : 15.24 % Favored : 82.53 % 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: -4.47 (0.14), residues: 2420 helix: -3.86 (0.15), residues: 380 sheet: -2.42 (0.18), residues: 774 loop : -3.05 (0.15), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 479 HIS 0.010 0.001 HIS E 27 PHE 0.021 0.002 PHE Q 62 TYR 0.022 0.002 TYR J 87 ARG 0.015 0.001 ARG Q 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 376 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8289 (mttt) cc_final: 0.7939 (mttp) REVERT: A 62 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8097 (mm-30) REVERT: A 479 TRP cc_start: 0.7530 (m-10) cc_final: 0.7297 (m-90) REVERT: A 492 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7794 (mt-10) REVERT: B 377 ASN cc_start: 0.7768 (t0) cc_final: 0.7525 (t0) REVERT: C 92 GLU cc_start: 0.7650 (tp30) cc_final: 0.7422 (tp30) REVERT: D 89 GLN cc_start: 0.8839 (mt0) cc_final: 0.8164 (mp10) REVERT: E 23 SER cc_start: 0.8987 (t) cc_final: 0.8761 (p) REVERT: F 70 ILE cc_start: 0.9036 (mm) cc_final: 0.8724 (mt) REVERT: F 94 GLN cc_start: 0.8936 (pt0) cc_final: 0.8560 (pm20) REVERT: I 10 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8047 (mm-30) REVERT: I 23 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7883 (tm-30) REVERT: I 46 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7662 (tm-30) REVERT: I 62 LYS cc_start: 0.8900 (ttpp) cc_final: 0.8565 (ttpp) REVERT: J 87 TYR cc_start: 0.7483 (m-80) cc_final: 0.7221 (m-10) REVERT: J 92 ASP cc_start: 0.8394 (t0) cc_final: 0.7431 (p0) REVERT: L 32 ASP cc_start: 0.7836 (p0) cc_final: 0.7572 (p0) REVERT: L 45 LYS cc_start: 0.9058 (ttpt) cc_final: 0.8656 (tttt) REVERT: L 90 THR cc_start: 0.8427 (t) cc_final: 0.8019 (m) REVERT: L 95 LEU cc_start: 0.9271 (mp) cc_final: 0.8821 (tp) REVERT: L 103 LYS cc_start: 0.8719 (mppt) cc_final: 0.8196 (mppt) REVERT: P 62 LYS cc_start: 0.8969 (pttm) cc_final: 0.8753 (pttm) REVERT: P 64 ARG cc_start: 0.7774 (mtt-85) cc_final: 0.7406 (mtt-85) REVERT: P 66 ARG cc_start: 0.8817 (mtp180) cc_final: 0.8531 (ptm160) REVERT: P 76 ARG cc_start: 0.8337 (mtm110) cc_final: 0.8133 (ptp-110) REVERT: P 82 ARG cc_start: 0.7413 (ptt-90) cc_final: 0.6875 (mpt180) REVERT: P 100 MET cc_start: 0.8488 (mtm) cc_final: 0.8069 (mtt) REVERT: P 101 ASP cc_start: 0.8696 (t70) cc_final: 0.8458 (t0) REVERT: Q 66 LYS cc_start: 0.9223 (ttpp) cc_final: 0.8861 (ttmm) REVERT: Q 72 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7656 (p) outliers start: 44 outliers final: 27 residues processed: 403 average time/residue: 0.3013 time to fit residues: 186.4263 Evaluate side-chains 373 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 345 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 595 ILE Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Z residue 606 THR Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 10 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 178 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 235 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 283 ASN C 258 GLN C 425 ASN E 40 GLN F 32 ASN H 39 GLN I 6 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN L 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.116887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.084540 restraints weight = 74217.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.087234 restraints weight = 33514.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.089116 restraints weight = 20604.350| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19724 Z= 0.216 Angle : 0.608 9.011 26858 Z= 0.313 Chirality : 0.048 0.564 3198 Planarity : 0.004 0.063 3346 Dihedral : 8.596 76.058 3514 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.88 % Allowed : 17.47 % Favored : 79.66 % 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: -3.97 (0.15), residues: 2420 helix: -3.08 (0.19), residues: 391 sheet: -2.02 (0.19), residues: 754 loop : -2.91 (0.15), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Z 571 HIS 0.009 0.001 HIS P 81 PHE 0.014 0.001 PHE P 63 TYR 0.014 0.001 TYR B 484 ARG 0.004 0.000 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 376 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8211 (mttt) cc_final: 0.7911 (mttp) REVERT: A 62 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7855 (mm-30) REVERT: B 377 ASN cc_start: 0.7667 (t0) cc_final: 0.7412 (t0) REVERT: D 89 GLN cc_start: 0.8865 (mt0) cc_final: 0.7861 (mp10) REVERT: E 23 SER cc_start: 0.8876 (t) cc_final: 0.8614 (p) REVERT: F 32 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7693 (t0) REVERT: F 70 ILE cc_start: 0.9083 (mm) cc_final: 0.8737 (mt) REVERT: F 94 GLN cc_start: 0.8929 (pt0) cc_final: 0.8599 (pm20) REVERT: H 100 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7901 (pmm) REVERT: I 10 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8046 (mm-30) REVERT: I 23 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7825 (tm-30) REVERT: I 46 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7581 (tm-30) REVERT: I 62 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8533 (ttpp) REVERT: J 49 TYR cc_start: 0.7613 (p90) cc_final: 0.7408 (p90) REVERT: J 92 ASP cc_start: 0.8290 (t0) cc_final: 0.7403 (p0) REVERT: L 45 LYS cc_start: 0.9151 (ttpt) cc_final: 0.8824 (tttt) REVERT: L 90 THR cc_start: 0.8407 (t) cc_final: 0.7972 (m) REVERT: L 95 LEU cc_start: 0.9196 (mp) cc_final: 0.8693 (tp) REVERT: P 46 GLU cc_start: 0.7532 (mp0) cc_final: 0.7230 (mp0) REVERT: P 66 ARG cc_start: 0.8688 (mtp180) cc_final: 0.8323 (ptm160) REVERT: P 82 ARG cc_start: 0.7277 (ptt-90) cc_final: 0.6824 (mpt180) REVERT: P 100 MET cc_start: 0.8445 (mtm) cc_final: 0.8060 (mtt) REVERT: P 101 ASP cc_start: 0.8614 (t70) cc_final: 0.8366 (t0) REVERT: Q 72 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7641 (p) REVERT: Z 626 MET cc_start: 0.7507 (ttt) cc_final: 0.6649 (ttt) outliers start: 57 outliers final: 31 residues processed: 415 average time/residue: 0.2844 time to fit residues: 183.5291 Evaluate side-chains 376 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 342 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Z residue 608 VAL Chi-restraints excluded: chain Z residue 652 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 219 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN F 32 ASN L 17 GLN L 31 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 652 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.115069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.081241 restraints weight = 96137.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085322 restraints weight = 39289.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086488 restraints weight = 20631.692| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19724 Z= 0.337 Angle : 0.643 7.957 26858 Z= 0.329 Chirality : 0.049 0.553 3198 Planarity : 0.004 0.059 3346 Dihedral : 7.968 78.831 3514 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 3.13 % Allowed : 19.18 % Favored : 77.69 % 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: -3.70 (0.16), residues: 2420 helix: -2.60 (0.22), residues: 387 sheet: -1.99 (0.19), residues: 764 loop : -2.71 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 96 HIS 0.005 0.001 HIS I 81 PHE 0.012 0.001 PHE A 53 TYR 0.023 0.002 TYR L 49 ARG 0.004 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 359 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 91 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7246 (mm-30) REVERT: B 377 ASN cc_start: 0.7686 (t0) cc_final: 0.7447 (t0) REVERT: D 89 GLN cc_start: 0.8633 (mt0) cc_final: 0.8116 (mp10) REVERT: E 23 SER cc_start: 0.8881 (t) cc_final: 0.8632 (p) REVERT: F 32 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7696 (t0) REVERT: F 70 ILE cc_start: 0.9156 (mm) cc_final: 0.8826 (mt) REVERT: F 94 GLN cc_start: 0.8969 (pt0) cc_final: 0.8566 (pm20) REVERT: I 10 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8101 (mm-30) REVERT: I 23 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7724 (tm-30) REVERT: I 38 ARG cc_start: 0.8043 (ptt180) cc_final: 0.7840 (ptt180) REVERT: I 46 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7837 (tm-30) REVERT: I 62 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8484 (ttpp) REVERT: J 92 ASP cc_start: 0.8363 (t0) cc_final: 0.7440 (p0) REVERT: L 32 ASP cc_start: 0.7785 (p0) cc_final: 0.7540 (p0) REVERT: L 36 TYR cc_start: 0.8239 (m-80) cc_final: 0.7663 (m-80) REVERT: L 45 LYS cc_start: 0.9169 (ttpt) cc_final: 0.8840 (ttpp) REVERT: L 90 THR cc_start: 0.8424 (t) cc_final: 0.7962 (m) REVERT: P 66 ARG cc_start: 0.8797 (mtp180) cc_final: 0.8426 (ptm160) REVERT: P 100 MET cc_start: 0.8432 (mtm) cc_final: 0.8164 (mtt) REVERT: P 101 ASP cc_start: 0.8708 (t70) cc_final: 0.8445 (t0) REVERT: Q 72 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7491 (p) outliers start: 62 outliers final: 41 residues processed: 396 average time/residue: 0.2959 time to fit residues: 184.4025 Evaluate side-chains 384 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 341 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 595 ILE Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Y residue 646 LEU Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN F 32 ASN J 30 ASN L 31 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.113694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.078949 restraints weight = 101112.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.082994 restraints weight = 38353.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085624 restraints weight = 19253.065| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19724 Z= 0.232 Angle : 0.601 9.316 26858 Z= 0.307 Chirality : 0.047 0.542 3198 Planarity : 0.004 0.062 3346 Dihedral : 7.199 78.541 3514 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.23 % Allowed : 20.55 % Favored : 76.22 % 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: -3.34 (0.16), residues: 2420 helix: -2.19 (0.24), residues: 381 sheet: -1.69 (0.19), residues: 739 loop : -2.57 (0.15), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Z 571 HIS 0.005 0.001 HIS I 81 PHE 0.011 0.001 PHE A 53 TYR 0.015 0.001 TYR B 484 ARG 0.007 0.000 ARG P 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 364 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8228 (mttt) cc_final: 0.7887 (mttp) REVERT: A 91 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7263 (mm-30) REVERT: B 377 ASN cc_start: 0.7857 (t0) cc_final: 0.7589 (t0) REVERT: D 89 GLN cc_start: 0.8874 (mt0) cc_final: 0.8183 (mp10) REVERT: E 23 SER cc_start: 0.8894 (t) cc_final: 0.8651 (p) REVERT: F 32 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7562 (t0) REVERT: F 70 ILE cc_start: 0.9157 (mm) cc_final: 0.8831 (mt) REVERT: F 94 GLN cc_start: 0.8965 (pt0) cc_final: 0.8531 (pm20) REVERT: I 10 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8114 (mm-30) REVERT: I 23 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7701 (tm-30) REVERT: I 46 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7886 (tm-30) REVERT: I 62 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8527 (ttpp) REVERT: J 92 ASP cc_start: 0.8356 (t0) cc_final: 0.7404 (p0) REVERT: L 32 ASP cc_start: 0.7825 (p0) cc_final: 0.7578 (p0) REVERT: L 36 TYR cc_start: 0.8422 (m-80) cc_final: 0.7661 (m-80) REVERT: L 45 LYS cc_start: 0.9172 (ttpt) cc_final: 0.8862 (tttt) REVERT: L 90 THR cc_start: 0.8408 (t) cc_final: 0.7926 (m) REVERT: L 95 LEU cc_start: 0.9205 (mp) cc_final: 0.8633 (tp) REVERT: P 46 GLU cc_start: 0.7493 (mp0) cc_final: 0.7222 (mp0) REVERT: P 64 ARG cc_start: 0.8061 (ptp90) cc_final: 0.7837 (ptp90) REVERT: P 100 MET cc_start: 0.8450 (mtm) cc_final: 0.8144 (mtt) REVERT: P 101 ASP cc_start: 0.8714 (t70) cc_final: 0.8481 (t0) REVERT: Q 72 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7526 (p) outliers start: 64 outliers final: 47 residues processed: 405 average time/residue: 0.2816 time to fit residues: 181.1838 Evaluate side-chains 398 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 349 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Y residue 646 LEU Chi-restraints excluded: chain Z residue 573 ILE Chi-restraints excluded: chain Z residue 608 VAL Chi-restraints excluded: chain Z residue 652 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 69.2785 > 50: distance: 52 - 57: 34.138 distance: 57 - 58: 29.281 distance: 58 - 59: 45.226 distance: 58 - 61: 8.372 distance: 59 - 60: 50.084 distance: 59 - 67: 50.845 distance: 61 - 62: 11.123 distance: 62 - 63: 53.031 distance: 62 - 64: 51.797 distance: 63 - 65: 49.748 distance: 64 - 66: 13.173 distance: 65 - 66: 58.772 distance: 67 - 68: 38.636 distance: 68 - 69: 16.992 distance: 69 - 70: 51.645 distance: 69 - 71: 36.998 distance: 71 - 72: 24.400 distance: 72 - 73: 55.349 distance: 72 - 75: 21.927 distance: 73 - 74: 69.202 distance: 75 - 76: 25.919 distance: 75 - 77: 41.251 distance: 76 - 78: 24.298 distance: 80 - 81: 47.209 distance: 80 - 83: 56.348 distance: 81 - 82: 10.296 distance: 81 - 88: 28.364 distance: 83 - 84: 42.156 distance: 84 - 85: 23.510 distance: 85 - 86: 16.012 distance: 86 - 87: 19.889 distance: 88 - 89: 52.468 distance: 88 - 94: 41.410 distance: 89 - 90: 68.094 distance: 89 - 92: 42.749 distance: 90 - 91: 54.372 distance: 90 - 95: 53.150 distance: 92 - 93: 44.071 distance: 93 - 94: 30.024 distance: 95 - 96: 13.885 distance: 96 - 97: 24.253 distance: 96 - 99: 4.869 distance: 97 - 98: 32.211 distance: 97 - 102: 20.158 distance: 99 - 100: 34.696 distance: 99 - 101: 36.939 distance: 102 - 103: 22.802 distance: 103 - 104: 15.175 distance: 103 - 106: 39.080 distance: 104 - 105: 36.960 distance: 104 - 109: 30.682 distance: 106 - 107: 45.834 distance: 106 - 108: 50.615 distance: 109 - 110: 42.999 distance: 110 - 111: 15.443 distance: 110 - 113: 28.770 distance: 111 - 112: 25.409 distance: 111 - 115: 29.726 distance: 113 - 114: 51.040 distance: 115 - 116: 38.113 distance: 116 - 117: 54.711 distance: 116 - 119: 13.172 distance: 117 - 118: 20.491 distance: 117 - 122: 33.145 distance: 119 - 120: 11.791 distance: 119 - 121: 20.808 distance: 122 - 123: 39.376 distance: 123 - 124: 41.680 distance: 123 - 126: 16.017 distance: 124 - 125: 38.871 distance: 124 - 131: 26.010 distance: 126 - 127: 30.930 distance: 127 - 128: 39.749 distance: 128 - 129: 26.490 distance: 128 - 130: 13.264