Starting phenix.real_space_refine on Fri Apr 5 21:11:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/04_2024/7m18_23615_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/04_2024/7m18_23615.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/04_2024/7m18_23615_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/04_2024/7m18_23615_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/04_2024/7m18_23615_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/04_2024/7m18_23615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/04_2024/7m18_23615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/04_2024/7m18_23615_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/04_2024/7m18_23615_updated.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.484 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: 6 Type Number sf(0) Gaussians P 40 5.49 5 S 360 5.16 5 Cl 8 4.86 5 C 34048 2.51 5 N 9200 2.21 5 O 10408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 123": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D GLU 421": "OE1" <-> "OE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 376": "OE1" <-> "OE2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F GLU 421": "OE1" <-> "OE2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "H GLU 376": "OE1" <-> "OE2" Residue "H GLU 383": "OE1" <-> "OE2" Residue "H GLU 421": "OE1" <-> "OE2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G GLU 429": "OE1" <-> "OE2" Residue "J GLU 123": "OE1" <-> "OE2" Residue "J GLU 205": "OE1" <-> "OE2" Residue "J GLU 376": "OE1" <-> "OE2" Residue "J GLU 383": "OE1" <-> "OE2" Residue "J GLU 421": "OE1" <-> "OE2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "I GLU 429": "OE1" <-> "OE2" Residue "L GLU 123": "OE1" <-> "OE2" Residue "L GLU 205": "OE1" <-> "OE2" Residue "L GLU 376": "OE1" <-> "OE2" Residue "L GLU 383": "OE1" <-> "OE2" Residue "L GLU 421": "OE1" <-> "OE2" Residue "K GLU 183": "OE1" <-> "OE2" Residue "K GLU 429": "OE1" <-> "OE2" Residue "N GLU 123": "OE1" <-> "OE2" Residue "N GLU 205": "OE1" <-> "OE2" Residue "N GLU 376": "OE1" <-> "OE2" Residue "N GLU 383": "OE1" <-> "OE2" Residue "N GLU 421": "OE1" <-> "OE2" Residue "M GLU 183": "OE1" <-> "OE2" Residue "M GLU 429": "OE1" <-> "OE2" Residue "P GLU 123": "OE1" <-> "OE2" Residue "P GLU 205": "OE1" <-> "OE2" Residue "P GLU 376": "OE1" <-> "OE2" Residue "P GLU 383": "OE1" <-> "OE2" Residue "P GLU 421": "OE1" <-> "OE2" Residue "O GLU 183": "OE1" <-> "OE2" Residue "O GLU 429": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 54064 Number of models: 1 Model: "" Number of chains: 32 Chain: "B" Number of atoms: 3312 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 3379 Chain: "A" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3340 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 3312 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 3379 Chain: "C" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3340 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "F" Number of atoms: 3312 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 3379 Chain: "E" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3340 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "H" Number of atoms: 3312 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 3379 Chain: "G" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3340 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "J" Number of atoms: 3312 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 3379 Chain: "I" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3340 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 3312 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 3379 Chain: "K" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3340 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "N" Number of atoms: 3312 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 3379 Chain: "M" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3340 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "P" Number of atoms: 3312 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 427, 3310 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 3379 Chain: "O" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3340 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'GDP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'GDP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'GDP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'GDP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'GDP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'GDP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'GDP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'GDP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 31.68, per 1000 atoms: 0.59 Number of scatterers: 54064 At special positions: 0 Unit cell: (302.1, 302.1, 69.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 8 17.00 S 360 16.00 P 40 15.00 O 10408 8.00 N 9200 7.00 C 34048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.76 Conformation dependent library (CDL) restraints added in 11.2 seconds 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 264 helices and 32 sheets defined 42.2% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.56 Creating SS restraints... Processing helix chain 'B' and resid 11 through 28 removed outlier: 3.756A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 73 through 78 removed outlier: 4.793A pdb=" N SER B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 126 removed outlier: 3.740A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASN B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 181 through 195 removed outlier: 4.058A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 211 Processing helix chain 'B' and resid 222 through 241 removed outlier: 3.683A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 326 through 336 Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.961A pdb=" N GLN B 384 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ALA B 387 " --> pdb=" O GLN B 384 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG B 390 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 405 through 426 Processing helix chain 'A' and resid 11 through 27 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.662A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 183 through 193 removed outlier: 4.261A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 244 removed outlier: 5.560A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.233A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 382 through 399 removed outlier: 3.563A pdb=" N GLU A 386 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 397 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.803A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 434 Processing helix chain 'D' and resid 11 through 28 removed outlier: 3.756A pdb=" N LYS D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 73 through 78 removed outlier: 4.793A pdb=" N SER D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 126 removed outlier: 3.740A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASN D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 Processing helix chain 'D' and resid 181 through 195 removed outlier: 4.057A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 211 Processing helix chain 'D' and resid 222 through 241 removed outlier: 3.683A pdb=" N LEU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 286 through 293 Processing helix chain 'D' and resid 305 through 307 No H-bonds generated for 'chain 'D' and resid 305 through 307' Processing helix chain 'D' and resid 326 through 336 Processing helix chain 'D' and resid 372 through 391 removed outlier: 3.961A pdb=" N GLN D 384 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ALA D 387 " --> pdb=" O GLN D 384 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG D 390 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 401 Processing helix chain 'D' and resid 405 through 426 Processing helix chain 'C' and resid 11 through 27 Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 145 through 160 removed outlier: 4.662A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 183 through 193 removed outlier: 4.262A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 224 through 244 removed outlier: 5.561A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 288 through 296 removed outlier: 4.233A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 382 through 399 removed outlier: 3.564A pdb=" N GLU C 386 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C 397 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR C 399 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.803A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 434 Processing helix chain 'F' and resid 11 through 28 removed outlier: 3.756A pdb=" N LYS F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 73 through 78 removed outlier: 4.793A pdb=" N SER F 78 " --> pdb=" O ASP F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 126 removed outlier: 3.740A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU F 125 " --> pdb=" O ARG F 121 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASN F 126 " --> pdb=" O LYS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 158 Processing helix chain 'F' and resid 181 through 195 removed outlier: 4.058A pdb=" N HIS F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 211 Processing helix chain 'F' and resid 222 through 241 removed outlier: 3.683A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR F 238 " --> pdb=" O SER F 234 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU F 240 " --> pdb=" O VAL F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 257 Processing helix chain 'F' and resid 286 through 293 Processing helix chain 'F' and resid 305 through 307 No H-bonds generated for 'chain 'F' and resid 305 through 307' Processing helix chain 'F' and resid 326 through 336 Processing helix chain 'F' and resid 372 through 391 removed outlier: 3.961A pdb=" N GLN F 384 " --> pdb=" O ILE F 381 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ALA F 387 " --> pdb=" O GLN F 384 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 401 Processing helix chain 'F' and resid 405 through 426 Processing helix chain 'E' and resid 11 through 27 Processing helix chain 'E' and resid 48 through 51 Processing helix chain 'E' and resid 75 through 79 Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 115 through 128 Processing helix chain 'E' and resid 145 through 160 removed outlier: 4.662A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 183 through 193 removed outlier: 4.261A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 224 through 244 removed outlier: 5.560A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 288 through 296 removed outlier: 4.233A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 335 Processing helix chain 'E' and resid 382 through 399 removed outlier: 3.563A pdb=" N GLU E 386 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU E 397 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR E 399 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 removed outlier: 4.803A pdb=" N GLU E 411 " --> pdb=" O TRP E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 434 Processing helix chain 'H' and resid 11 through 28 removed outlier: 3.756A pdb=" N LYS H 19 " --> pdb=" O GLN H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 73 through 78 removed outlier: 4.793A pdb=" N SER H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 126 removed outlier: 3.740A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU H 125 " --> pdb=" O ARG H 121 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASN H 126 " --> pdb=" O LYS H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 158 Processing helix chain 'H' and resid 181 through 195 removed outlier: 4.057A pdb=" N HIS H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU H 194 " --> pdb=" O HIS H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 211 Processing helix chain 'H' and resid 222 through 241 removed outlier: 3.683A pdb=" N LEU H 228 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR H 238 " --> pdb=" O SER H 234 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU H 240 " --> pdb=" O VAL H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 257 Processing helix chain 'H' and resid 286 through 293 Processing helix chain 'H' and resid 305 through 307 No H-bonds generated for 'chain 'H' and resid 305 through 307' Processing helix chain 'H' and resid 326 through 336 Processing helix chain 'H' and resid 372 through 391 removed outlier: 3.961A pdb=" N GLN H 384 " --> pdb=" O ILE H 381 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ALA H 387 " --> pdb=" O GLN H 384 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG H 390 " --> pdb=" O ALA H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 401 Processing helix chain 'H' and resid 405 through 426 Processing helix chain 'G' and resid 11 through 27 Processing helix chain 'G' and resid 48 through 51 Processing helix chain 'G' and resid 75 through 79 Processing helix chain 'G' and resid 103 through 108 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 115 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 4.662A pdb=" N THR G 150 " --> pdb=" O GLY G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 183 through 193 removed outlier: 4.262A pdb=" N THR G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 215 Processing helix chain 'G' and resid 224 through 244 removed outlier: 5.561A pdb=" N SER G 241 " --> pdb=" O SER G 237 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU G 242 " --> pdb=" O ILE G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 288 through 296 removed outlier: 4.233A pdb=" N PHE G 296 " --> pdb=" O THR G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 309 No H-bonds generated for 'chain 'G' and resid 307 through 309' Processing helix chain 'G' and resid 325 through 335 Processing helix chain 'G' and resid 382 through 399 removed outlier: 3.564A pdb=" N GLU G 386 " --> pdb=" O ALA G 383 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU G 397 " --> pdb=" O LYS G 394 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR G 399 " --> pdb=" O ASP G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 411 removed outlier: 4.803A pdb=" N GLU G 411 " --> pdb=" O TRP G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 434 Processing helix chain 'J' and resid 11 through 28 removed outlier: 3.756A pdb=" N LYS J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 49 No H-bonds generated for 'chain 'J' and resid 47 through 49' Processing helix chain 'J' and resid 73 through 78 removed outlier: 4.793A pdb=" N SER J 78 " --> pdb=" O ASP J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 126 removed outlier: 3.740A pdb=" N ASP J 114 " --> pdb=" O ALA J 110 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU J 125 " --> pdb=" O ARG J 121 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASN J 126 " --> pdb=" O LYS J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 158 Processing helix chain 'J' and resid 181 through 195 removed outlier: 4.058A pdb=" N HIS J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN J 191 " --> pdb=" O LEU J 187 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU J 194 " --> pdb=" O HIS J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 211 Processing helix chain 'J' and resid 222 through 241 removed outlier: 3.683A pdb=" N LEU J 228 " --> pdb=" O ASP J 224 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER J 234 " --> pdb=" O SER J 230 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR J 237 " --> pdb=" O MET J 233 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR J 238 " --> pdb=" O SER J 234 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER J 239 " --> pdb=" O GLY J 235 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU J 240 " --> pdb=" O VAL J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 257 Processing helix chain 'J' and resid 286 through 293 Processing helix chain 'J' and resid 305 through 307 No H-bonds generated for 'chain 'J' and resid 305 through 307' Processing helix chain 'J' and resid 326 through 336 Processing helix chain 'J' and resid 372 through 391 removed outlier: 3.961A pdb=" N GLN J 384 " --> pdb=" O ILE J 381 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ALA J 387 " --> pdb=" O GLN J 384 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG J 390 " --> pdb=" O ALA J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 401 Processing helix chain 'J' and resid 405 through 426 Processing helix chain 'I' and resid 11 through 27 Processing helix chain 'I' and resid 48 through 51 Processing helix chain 'I' and resid 75 through 79 Processing helix chain 'I' and resid 103 through 108 Processing helix chain 'I' and resid 111 through 113 No H-bonds generated for 'chain 'I' and resid 111 through 113' Processing helix chain 'I' and resid 115 through 128 Processing helix chain 'I' and resid 145 through 160 removed outlier: 4.662A pdb=" N THR I 150 " --> pdb=" O GLY I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 177 No H-bonds generated for 'chain 'I' and resid 175 through 177' Processing helix chain 'I' and resid 183 through 193 removed outlier: 4.261A pdb=" N THR I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 215 Processing helix chain 'I' and resid 224 through 244 removed outlier: 5.560A pdb=" N SER I 241 " --> pdb=" O SER I 237 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU I 242 " --> pdb=" O ILE I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 288 through 296 removed outlier: 4.233A pdb=" N PHE I 296 " --> pdb=" O THR I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 309 No H-bonds generated for 'chain 'I' and resid 307 through 309' Processing helix chain 'I' and resid 325 through 335 Processing helix chain 'I' and resid 382 through 399 removed outlier: 3.563A pdb=" N GLU I 386 " --> pdb=" O ALA I 383 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU I 397 " --> pdb=" O LYS I 394 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR I 399 " --> pdb=" O ASP I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 411 removed outlier: 4.803A pdb=" N GLU I 411 " --> pdb=" O TRP I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 434 Processing helix chain 'L' and resid 11 through 28 removed outlier: 3.756A pdb=" N LYS L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 49 No H-bonds generated for 'chain 'L' and resid 47 through 49' Processing helix chain 'L' and resid 73 through 78 removed outlier: 4.793A pdb=" N SER L 78 " --> pdb=" O ASP L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 126 removed outlier: 3.740A pdb=" N ASP L 114 " --> pdb=" O ALA L 110 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER L 115 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU L 125 " --> pdb=" O ARG L 121 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASN L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 158 Processing helix chain 'L' and resid 181 through 195 removed outlier: 4.057A pdb=" N HIS L 190 " --> pdb=" O THR L 186 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN L 191 " --> pdb=" O LEU L 187 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU L 194 " --> pdb=" O HIS L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 211 Processing helix chain 'L' and resid 222 through 241 removed outlier: 3.683A pdb=" N LEU L 228 " --> pdb=" O ASP L 224 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER L 234 " --> pdb=" O SER L 230 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR L 237 " --> pdb=" O MET L 233 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR L 238 " --> pdb=" O SER L 234 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER L 239 " --> pdb=" O GLY L 235 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU L 240 " --> pdb=" O VAL L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 257 Processing helix chain 'L' and resid 286 through 293 Processing helix chain 'L' and resid 305 through 307 No H-bonds generated for 'chain 'L' and resid 305 through 307' Processing helix chain 'L' and resid 326 through 336 Processing helix chain 'L' and resid 372 through 391 removed outlier: 3.961A pdb=" N GLN L 384 " --> pdb=" O ILE L 381 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ALA L 387 " --> pdb=" O GLN L 384 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG L 390 " --> pdb=" O ALA L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 401 Processing helix chain 'L' and resid 405 through 426 Processing helix chain 'K' and resid 11 through 27 Processing helix chain 'K' and resid 48 through 51 Processing helix chain 'K' and resid 75 through 79 Processing helix chain 'K' and resid 103 through 108 Processing helix chain 'K' and resid 111 through 113 No H-bonds generated for 'chain 'K' and resid 111 through 113' Processing helix chain 'K' and resid 115 through 128 Processing helix chain 'K' and resid 145 through 160 removed outlier: 4.662A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 177 No H-bonds generated for 'chain 'K' and resid 175 through 177' Processing helix chain 'K' and resid 183 through 193 removed outlier: 4.262A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 215 Processing helix chain 'K' and resid 224 through 244 removed outlier: 5.561A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 259 Processing helix chain 'K' and resid 288 through 296 removed outlier: 4.233A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 309 No H-bonds generated for 'chain 'K' and resid 307 through 309' Processing helix chain 'K' and resid 325 through 335 Processing helix chain 'K' and resid 382 through 399 removed outlier: 3.564A pdb=" N GLU K 386 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU K 397 " --> pdb=" O LYS K 394 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR K 399 " --> pdb=" O ASP K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 411 removed outlier: 4.803A pdb=" N GLU K 411 " --> pdb=" O TRP K 407 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 434 Processing helix chain 'N' and resid 11 through 28 removed outlier: 3.756A pdb=" N LYS N 19 " --> pdb=" O GLN N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 49 No H-bonds generated for 'chain 'N' and resid 47 through 49' Processing helix chain 'N' and resid 73 through 78 removed outlier: 4.793A pdb=" N SER N 78 " --> pdb=" O ASP N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 126 removed outlier: 3.740A pdb=" N ASP N 114 " --> pdb=" O ALA N 110 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER N 115 " --> pdb=" O GLU N 111 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU N 125 " --> pdb=" O ARG N 121 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASN N 126 " --> pdb=" O LYS N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 158 Processing helix chain 'N' and resid 181 through 195 removed outlier: 4.058A pdb=" N HIS N 190 " --> pdb=" O THR N 186 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN N 191 " --> pdb=" O LEU N 187 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU N 194 " --> pdb=" O HIS N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 211 Processing helix chain 'N' and resid 222 through 241 removed outlier: 3.683A pdb=" N LEU N 228 " --> pdb=" O ASP N 224 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER N 234 " --> pdb=" O SER N 230 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR N 237 " --> pdb=" O MET N 233 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR N 238 " --> pdb=" O SER N 234 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER N 239 " --> pdb=" O GLY N 235 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU N 240 " --> pdb=" O VAL N 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 257 Processing helix chain 'N' and resid 286 through 293 Processing helix chain 'N' and resid 305 through 307 No H-bonds generated for 'chain 'N' and resid 305 through 307' Processing helix chain 'N' and resid 326 through 336 Processing helix chain 'N' and resid 372 through 391 removed outlier: 3.961A pdb=" N GLN N 384 " --> pdb=" O ILE N 381 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ALA N 387 " --> pdb=" O GLN N 384 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG N 390 " --> pdb=" O ALA N 387 " (cutoff:3.500A) Processing helix chain 'N' and resid 395 through 401 Processing helix chain 'N' and resid 405 through 426 Processing helix chain 'M' and resid 11 through 27 Processing helix chain 'M' and resid 48 through 51 Processing helix chain 'M' and resid 75 through 79 Processing helix chain 'M' and resid 103 through 108 Processing helix chain 'M' and resid 111 through 113 No H-bonds generated for 'chain 'M' and resid 111 through 113' Processing helix chain 'M' and resid 115 through 128 Processing helix chain 'M' and resid 145 through 160 removed outlier: 4.662A pdb=" N THR M 150 " --> pdb=" O GLY M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 177 No H-bonds generated for 'chain 'M' and resid 175 through 177' Processing helix chain 'M' and resid 183 through 193 removed outlier: 4.261A pdb=" N THR M 193 " --> pdb=" O LEU M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 215 Processing helix chain 'M' and resid 224 through 244 removed outlier: 5.560A pdb=" N SER M 241 " --> pdb=" O SER M 237 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU M 242 " --> pdb=" O ILE M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 259 Processing helix chain 'M' and resid 288 through 296 removed outlier: 4.233A pdb=" N PHE M 296 " --> pdb=" O THR M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 309 No H-bonds generated for 'chain 'M' and resid 307 through 309' Processing helix chain 'M' and resid 325 through 335 Processing helix chain 'M' and resid 382 through 399 removed outlier: 3.563A pdb=" N GLU M 386 " --> pdb=" O ALA M 383 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU M 397 " --> pdb=" O LYS M 394 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR M 399 " --> pdb=" O ASP M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 411 removed outlier: 4.803A pdb=" N GLU M 411 " --> pdb=" O TRP M 407 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 434 Processing helix chain 'P' and resid 11 through 28 removed outlier: 3.756A pdb=" N LYS P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 49 No H-bonds generated for 'chain 'P' and resid 47 through 49' Processing helix chain 'P' and resid 73 through 78 removed outlier: 4.793A pdb=" N SER P 78 " --> pdb=" O ASP P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 126 removed outlier: 3.740A pdb=" N ASP P 114 " --> pdb=" O ALA P 110 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER P 115 " --> pdb=" O GLU P 111 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU P 125 " --> pdb=" O ARG P 121 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASN P 126 " --> pdb=" O LYS P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 158 Processing helix chain 'P' and resid 181 through 195 removed outlier: 4.057A pdb=" N HIS P 190 " --> pdb=" O THR P 186 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN P 191 " --> pdb=" O LEU P 187 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU P 194 " --> pdb=" O HIS P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 204 through 211 Processing helix chain 'P' and resid 222 through 241 removed outlier: 3.683A pdb=" N LEU P 228 " --> pdb=" O ASP P 224 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER P 234 " --> pdb=" O SER P 230 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR P 237 " --> pdb=" O MET P 233 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR P 238 " --> pdb=" O SER P 234 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER P 239 " --> pdb=" O GLY P 235 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU P 240 " --> pdb=" O VAL P 236 " (cutoff:3.500A) Processing helix chain 'P' and resid 250 through 257 Processing helix chain 'P' and resid 286 through 293 Processing helix chain 'P' and resid 305 through 307 No H-bonds generated for 'chain 'P' and resid 305 through 307' Processing helix chain 'P' and resid 326 through 336 Processing helix chain 'P' and resid 372 through 391 removed outlier: 3.961A pdb=" N GLN P 384 " --> pdb=" O ILE P 381 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ALA P 387 " --> pdb=" O GLN P 384 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG P 390 " --> pdb=" O ALA P 387 " (cutoff:3.500A) Processing helix chain 'P' and resid 395 through 401 Processing helix chain 'P' and resid 405 through 426 Processing helix chain 'O' and resid 11 through 27 Processing helix chain 'O' and resid 48 through 51 Processing helix chain 'O' and resid 75 through 79 Processing helix chain 'O' and resid 103 through 108 Processing helix chain 'O' and resid 111 through 113 No H-bonds generated for 'chain 'O' and resid 111 through 113' Processing helix chain 'O' and resid 115 through 128 Processing helix chain 'O' and resid 145 through 160 removed outlier: 4.662A pdb=" N THR O 150 " --> pdb=" O GLY O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 175 through 177 No H-bonds generated for 'chain 'O' and resid 175 through 177' Processing helix chain 'O' and resid 183 through 193 removed outlier: 4.262A pdb=" N THR O 193 " --> pdb=" O LEU O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 215 Processing helix chain 'O' and resid 224 through 244 removed outlier: 5.561A pdb=" N SER O 241 " --> pdb=" O SER O 237 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU O 242 " --> pdb=" O ILE O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 252 through 259 Processing helix chain 'O' and resid 288 through 296 removed outlier: 4.233A pdb=" N PHE O 296 " --> pdb=" O THR O 292 " (cutoff:3.500A) Processing helix chain 'O' and resid 307 through 309 No H-bonds generated for 'chain 'O' and resid 307 through 309' Processing helix chain 'O' and resid 325 through 335 Processing helix chain 'O' and resid 382 through 399 removed outlier: 3.564A pdb=" N GLU O 386 " --> pdb=" O ALA O 383 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU O 397 " --> pdb=" O LYS O 394 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR O 399 " --> pdb=" O ASP O 396 " (cutoff:3.500A) Processing helix chain 'O' and resid 405 through 411 removed outlier: 4.803A pdb=" N GLU O 411 " --> pdb=" O TRP O 407 " (cutoff:3.500A) Processing helix chain 'O' and resid 416 through 434 Processing sheet with id= A, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= B, first strand: chain 'B' and resid 364 through 368 removed outlier: 3.920A pdb=" N ILE B 368 " --> pdb=" O ALA B 314 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA B 352 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 2 through 8 removed outlier: 6.486A pdb=" N CYS B 129 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL B 5 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLN B 131 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 12.125A pdb=" N ILE B 7 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N PHE B 133 " --> pdb=" O ILE B 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 5 through 8 removed outlier: 6.809A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 51 through 53 Processing sheet with id= F, first strand: chain 'D' and resid 364 through 368 removed outlier: 3.920A pdb=" N ILE D 368 " --> pdb=" O ALA D 314 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA D 352 " --> pdb=" O PHE D 317 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 2 through 8 removed outlier: 6.485A pdb=" N CYS D 129 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL D 5 " --> pdb=" O CYS D 129 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLN D 131 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 12.125A pdb=" N ILE D 7 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N PHE D 133 " --> pdb=" O ILE D 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 5 through 8 removed outlier: 6.809A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 51 through 53 Processing sheet with id= J, first strand: chain 'F' and resid 364 through 368 removed outlier: 3.920A pdb=" N ILE F 368 " --> pdb=" O ALA F 314 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA F 352 " --> pdb=" O PHE F 317 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 2 through 8 removed outlier: 6.486A pdb=" N CYS F 129 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL F 5 " --> pdb=" O CYS F 129 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLN F 131 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 12.125A pdb=" N ILE F 7 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N PHE F 133 " --> pdb=" O ILE F 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 5 through 8 removed outlier: 6.809A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 51 through 53 Processing sheet with id= N, first strand: chain 'H' and resid 364 through 368 removed outlier: 3.920A pdb=" N ILE H 368 " --> pdb=" O ALA H 314 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA H 352 " --> pdb=" O PHE H 317 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 2 through 8 removed outlier: 6.485A pdb=" N CYS H 129 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL H 5 " --> pdb=" O CYS H 129 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLN H 131 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 12.125A pdb=" N ILE H 7 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N PHE H 133 " --> pdb=" O ILE H 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 5 through 8 removed outlier: 6.809A pdb=" N LEU G 167 " --> pdb=" O VAL G 137 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 51 through 53 Processing sheet with id= R, first strand: chain 'J' and resid 364 through 368 removed outlier: 3.920A pdb=" N ILE J 368 " --> pdb=" O ALA J 314 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA J 352 " --> pdb=" O PHE J 317 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 2 through 8 removed outlier: 6.486A pdb=" N CYS J 129 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL J 5 " --> pdb=" O CYS J 129 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLN J 131 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 12.125A pdb=" N ILE J 7 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N PHE J 133 " --> pdb=" O ILE J 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'I' and resid 5 through 8 removed outlier: 6.809A pdb=" N LEU I 167 " --> pdb=" O VAL I 137 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 51 through 53 Processing sheet with id= V, first strand: chain 'L' and resid 364 through 368 removed outlier: 3.920A pdb=" N ILE L 368 " --> pdb=" O ALA L 314 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA L 352 " --> pdb=" O PHE L 317 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 2 through 8 removed outlier: 6.485A pdb=" N CYS L 129 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL L 5 " --> pdb=" O CYS L 129 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLN L 131 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 12.125A pdb=" N ILE L 7 " --> pdb=" O GLN L 131 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N PHE L 133 " --> pdb=" O ILE L 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'K' and resid 5 through 8 removed outlier: 6.809A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'N' and resid 51 through 53 Processing sheet with id= Z, first strand: chain 'N' and resid 364 through 368 removed outlier: 3.920A pdb=" N ILE N 368 " --> pdb=" O ALA N 314 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA N 352 " --> pdb=" O PHE N 317 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'N' and resid 2 through 8 removed outlier: 6.486A pdb=" N CYS N 129 " --> pdb=" O GLU N 3 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL N 5 " --> pdb=" O CYS N 129 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLN N 131 " --> pdb=" O VAL N 5 " (cutoff:3.500A) removed outlier: 12.125A pdb=" N ILE N 7 " --> pdb=" O GLN N 131 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N PHE N 133 " --> pdb=" O ILE N 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'M' and resid 5 through 8 removed outlier: 6.809A pdb=" N LEU M 167 " --> pdb=" O VAL M 137 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'P' and resid 51 through 53 Processing sheet with id= AD, first strand: chain 'P' and resid 364 through 368 removed outlier: 3.920A pdb=" N ILE P 368 " --> pdb=" O ALA P 314 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA P 352 " --> pdb=" O PHE P 317 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'P' and resid 2 through 8 removed outlier: 6.485A pdb=" N CYS P 129 " --> pdb=" O GLU P 3 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL P 5 " --> pdb=" O CYS P 129 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLN P 131 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 12.125A pdb=" N ILE P 7 " --> pdb=" O GLN P 131 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N PHE P 133 " --> pdb=" O ILE P 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'O' and resid 5 through 8 removed outlier: 6.809A pdb=" N LEU O 167 " --> pdb=" O VAL O 137 " (cutoff:3.500A) 1792 hydrogen bonds defined for protein. 4288 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: 13.57 Time building geometry restraints manager: 18.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 9080 1.31 - 1.44: 15088 1.44 - 1.57: 30528 1.57 - 1.69: 72 1.69 - 1.82: 568 Bond restraints: 55336 Sorted by residual: bond pdb=" C7 YNP L 501 " pdb=" C8 YNP L 501 " ideal model delta sigma weight residual 1.555 1.319 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C7 YNP P 501 " pdb=" C8 YNP P 501 " ideal model delta sigma weight residual 1.555 1.319 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C7 YNP H 501 " pdb=" C8 YNP H 501 " ideal model delta sigma weight residual 1.555 1.319 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C7 YNP D 501 " pdb=" C8 YNP D 501 " ideal model delta sigma weight residual 1.555 1.319 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C7 YNP J 501 " pdb=" C8 YNP J 501 " ideal model delta sigma weight residual 1.555 1.319 0.236 2.00e-02 2.50e+03 1.40e+02 ... (remaining 55331 not shown) Histogram of bond angle deviations from ideal: 53.18 - 75.85: 24 75.85 - 98.52: 16 98.52 - 121.18: 61072 121.18 - 143.85: 14176 143.85 - 166.52: 24 Bond angle restraints: 75312 Sorted by residual: angle pdb=" C5 YNP J 501 " pdb=" N2 YNP J 501 " pdb=" C6 YNP J 501 " ideal model delta sigma weight residual 109.57 166.52 -56.95 3.00e+00 1.11e-01 3.60e+02 angle pdb=" C5 YNP N 501 " pdb=" N2 YNP N 501 " pdb=" C6 YNP N 501 " ideal model delta sigma weight residual 109.57 166.52 -56.95 3.00e+00 1.11e-01 3.60e+02 angle pdb=" C5 YNP B 501 " pdb=" N2 YNP B 501 " pdb=" C6 YNP B 501 " ideal model delta sigma weight residual 109.57 166.52 -56.95 3.00e+00 1.11e-01 3.60e+02 angle pdb=" C5 YNP F 501 " pdb=" N2 YNP F 501 " pdb=" C6 YNP F 501 " ideal model delta sigma weight residual 109.57 166.52 -56.95 3.00e+00 1.11e-01 3.60e+02 angle pdb=" C5 YNP L 501 " pdb=" N2 YNP L 501 " pdb=" C6 YNP L 501 " ideal model delta sigma weight residual 109.57 166.51 -56.94 3.00e+00 1.11e-01 3.60e+02 ... (remaining 75307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 32056 35.34 - 70.69: 456 70.69 - 106.03: 64 106.03 - 141.38: 40 141.38 - 176.72: 80 Dihedral angle restraints: 32696 sinusoidal: 12744 harmonic: 19952 Sorted by residual: dihedral pdb=" C8 GTP G 501 " pdb=" C1' GTP G 501 " pdb=" N9 GTP G 501 " pdb=" O4' GTP G 501 " ideal model delta sinusoidal sigma weight residual 104.59 -67.84 172.43 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP O 501 " pdb=" C1' GTP O 501 " pdb=" N9 GTP O 501 " pdb=" O4' GTP O 501 " ideal model delta sinusoidal sigma weight residual 104.59 -67.84 172.43 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -67.84 172.43 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 32693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.027: 8336 1.027 - 2.055: 0 2.055 - 3.082: 0 3.082 - 4.109: 0 4.109 - 5.136: 8 Chirality restraints: 8344 Sorted by residual: chirality pdb=" C18 YNP J 501 " pdb=" C10 YNP J 501 " pdb=" C19 YNP J 501 " pdb=" C20 YNP J 501 " both_signs ideal model delta sigma weight residual False -2.76 2.38 -5.14 2.00e-01 2.50e+01 6.60e+02 chirality pdb=" C18 YNP N 501 " pdb=" C10 YNP N 501 " pdb=" C19 YNP N 501 " pdb=" C20 YNP N 501 " both_signs ideal model delta sigma weight residual False -2.76 2.38 -5.14 2.00e-01 2.50e+01 6.60e+02 chirality pdb=" C18 YNP B 501 " pdb=" C10 YNP B 501 " pdb=" C19 YNP B 501 " pdb=" C20 YNP B 501 " both_signs ideal model delta sigma weight residual False -2.76 2.38 -5.14 2.00e-01 2.50e+01 6.60e+02 ... (remaining 8341 not shown) Planarity restraints: 9792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 YNP L 501 " 0.203 2.00e-02 2.50e+03 1.76e-01 3.87e+02 pdb=" C4 YNP L 501 " -0.051 2.00e-02 2.50e+03 pdb=" C5 YNP L 501 " 0.049 2.00e-02 2.50e+03 pdb=" N1 YNP L 501 " -0.311 2.00e-02 2.50e+03 pdb=" O1 YNP L 501 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 YNP D 501 " -0.203 2.00e-02 2.50e+03 1.76e-01 3.87e+02 pdb=" C4 YNP D 501 " 0.051 2.00e-02 2.50e+03 pdb=" C5 YNP D 501 " -0.049 2.00e-02 2.50e+03 pdb=" N1 YNP D 501 " 0.311 2.00e-02 2.50e+03 pdb=" O1 YNP D 501 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 YNP H 501 " -0.203 2.00e-02 2.50e+03 1.76e-01 3.87e+02 pdb=" C4 YNP H 501 " 0.051 2.00e-02 2.50e+03 pdb=" C5 YNP H 501 " -0.049 2.00e-02 2.50e+03 pdb=" N1 YNP H 501 " 0.311 2.00e-02 2.50e+03 pdb=" O1 YNP H 501 " -0.110 2.00e-02 2.50e+03 ... (remaining 9789 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 320 2.36 - 3.00: 32096 3.00 - 3.63: 87396 3.63 - 4.27: 123404 4.27 - 4.90: 199712 Nonbonded interactions: 442928 Sorted by model distance: nonbonded pdb=" CE1 HIS K 406 " pdb=" O PRO N 259 " model vdw 1.728 3.260 nonbonded pdb=" CE1 HIS C 406 " pdb=" O PRO F 259 " model vdw 1.728 3.260 nonbonded pdb=" O PRO B 259 " pdb=" CE1 HIS O 406 " model vdw 1.728 3.260 nonbonded pdb=" CE1 HIS G 406 " pdb=" O PRO J 259 " model vdw 1.728 3.260 nonbonded pdb=" CE1 HIS I 406 " pdb=" O PRO L 259 " model vdw 1.728 3.260 ... (remaining 442923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = (chain 'B' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'D' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'F' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'H' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'J' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'L' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'N' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'P' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 7.710 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: 0.040 Extract box with map and model: 40.680 Check model and map are aligned: 0.650 Set scattering table: 0.410 Process input model: 120.550 Find NCS groups from input model: 3.420 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 : 0.007 0.236 55336 Z= 0.471 Angle : 1.365 56.950 75312 Z= 0.599 Chirality : 0.168 5.136 8344 Planarity : 0.007 0.176 9792 Dihedral : 18.706 176.719 19912 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 23.77 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.36 % Favored : 89.29 % Rotamer: Outliers : 0.28 % Allowed : 0.99 % Favored : 98.73 % 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: -2.48 (0.10), residues: 6880 helix: -0.34 (0.10), residues: 2784 sheet: -1.80 (0.19), residues: 760 loop : -2.83 (0.11), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 21 HIS 0.004 0.001 HIS G 393 PHE 0.012 0.001 PHE E 244 TYR 0.021 0.002 TYR G 24 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1205 time to evaluate : 4.735 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 SER cc_start: 0.9274 (t) cc_final: 0.8809 (p) REVERT: B 370 ASN cc_start: 0.7967 (t0) cc_final: 0.7737 (t0) REVERT: B 394 PHE cc_start: 0.8060 (m-80) cc_final: 0.7810 (m-80) REVERT: A 108 TYR cc_start: 0.7996 (m-80) cc_final: 0.7784 (m-80) REVERT: A 217 LEU cc_start: 0.8983 (tp) cc_final: 0.8477 (tp) REVERT: A 243 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8337 (mtm-85) REVERT: D 119 VAL cc_start: 0.8007 (t) cc_final: 0.7792 (p) REVERT: D 267 MET cc_start: 0.7710 (ppp) cc_final: 0.7034 (ppp) REVERT: C 36 MET cc_start: 0.7468 (ppp) cc_final: 0.7149 (ppp) REVERT: C 217 LEU cc_start: 0.8836 (tp) cc_final: 0.8306 (tp) REVERT: C 425 MET cc_start: 0.7742 (mmt) cc_final: 0.7407 (mmt) REVERT: F 25 SER cc_start: 0.9273 (t) cc_final: 0.8808 (p) REVERT: F 370 ASN cc_start: 0.7965 (t0) cc_final: 0.7734 (t0) REVERT: F 394 PHE cc_start: 0.8058 (m-80) cc_final: 0.7809 (m-80) REVERT: E 108 TYR cc_start: 0.7996 (m-80) cc_final: 0.7783 (m-80) REVERT: E 217 LEU cc_start: 0.8983 (tp) cc_final: 0.8476 (tp) REVERT: E 243 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8337 (mtm-85) REVERT: H 119 VAL cc_start: 0.8007 (t) cc_final: 0.7792 (p) REVERT: H 267 MET cc_start: 0.7710 (ppp) cc_final: 0.7034 (ppp) REVERT: G 36 MET cc_start: 0.7468 (ppp) cc_final: 0.7149 (ppp) REVERT: G 217 LEU cc_start: 0.8838 (tp) cc_final: 0.8307 (tp) REVERT: G 425 MET cc_start: 0.7744 (mmt) cc_final: 0.7407 (mmt) REVERT: J 25 SER cc_start: 0.9272 (t) cc_final: 0.8807 (p) REVERT: J 370 ASN cc_start: 0.7963 (t0) cc_final: 0.7734 (t0) REVERT: J 394 PHE cc_start: 0.8057 (m-80) cc_final: 0.7807 (m-80) REVERT: I 108 TYR cc_start: 0.7998 (m-80) cc_final: 0.7782 (m-80) REVERT: I 217 LEU cc_start: 0.8983 (tp) cc_final: 0.8477 (tp) REVERT: I 243 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8338 (mtm-85) REVERT: L 119 VAL cc_start: 0.8009 (t) cc_final: 0.7793 (p) REVERT: L 267 MET cc_start: 0.7706 (ppp) cc_final: 0.7032 (ppp) REVERT: K 36 MET cc_start: 0.7469 (ppp) cc_final: 0.7150 (ppp) REVERT: K 217 LEU cc_start: 0.8838 (tp) cc_final: 0.8308 (tp) REVERT: K 425 MET cc_start: 0.7743 (mmt) cc_final: 0.7406 (mmt) REVERT: N 25 SER cc_start: 0.9274 (t) cc_final: 0.8808 (p) REVERT: N 370 ASN cc_start: 0.7963 (t0) cc_final: 0.7733 (t0) REVERT: N 394 PHE cc_start: 0.8058 (m-80) cc_final: 0.7807 (m-80) REVERT: M 108 TYR cc_start: 0.7996 (m-80) cc_final: 0.7782 (m-80) REVERT: M 217 LEU cc_start: 0.8981 (tp) cc_final: 0.8474 (tp) REVERT: M 243 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8338 (mtm-85) REVERT: P 119 VAL cc_start: 0.8009 (t) cc_final: 0.7793 (p) REVERT: P 267 MET cc_start: 0.7706 (ppp) cc_final: 0.7028 (ppp) REVERT: O 36 MET cc_start: 0.7469 (ppp) cc_final: 0.7149 (ppp) REVERT: O 217 LEU cc_start: 0.8836 (tp) cc_final: 0.8306 (tp) REVERT: O 425 MET cc_start: 0.7743 (mmt) cc_final: 0.7406 (mmt) outliers start: 16 outliers final: 0 residues processed: 1221 average time/residue: 0.4532 time to fit residues: 971.1322 Evaluate side-chains 952 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 952 time to evaluate : 4.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 574 optimal weight: 0.6980 chunk 515 optimal weight: 8.9990 chunk 285 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 347 optimal weight: 0.0370 chunk 275 optimal weight: 0.7980 chunk 532 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 324 optimal weight: 0.0870 chunk 396 optimal weight: 3.9990 chunk 617 optimal weight: 1.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN C 256 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN G 256 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN K 256 GLN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 256 GLN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 99 ASN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 206 ASN O 256 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 55336 Z= 0.212 Angle : 0.793 15.313 75312 Z= 0.379 Chirality : 0.046 0.214 8344 Planarity : 0.005 0.058 9792 Dihedral : 17.758 173.808 7840 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.75 % Favored : 90.13 % Rotamer: Outliers : 1.48 % Allowed : 12.64 % Favored : 85.88 % 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: -2.25 (0.10), residues: 6880 helix: -0.18 (0.10), residues: 2728 sheet: -1.90 (0.18), residues: 808 loop : -2.57 (0.11), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 407 HIS 0.011 0.001 HIS E 28 PHE 0.024 0.002 PHE G 296 TYR 0.022 0.002 TYR P 106 ARG 0.006 0.000 ARG K 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1036 time to evaluate : 4.779 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 267 MET cc_start: 0.7941 (ppp) cc_final: 0.7628 (ppp) REVERT: B 370 ASN cc_start: 0.7969 (t0) cc_final: 0.7660 (t0) REVERT: A 76 ASP cc_start: 0.7752 (t0) cc_final: 0.7189 (p0) REVERT: A 217 LEU cc_start: 0.8898 (tp) cc_final: 0.8354 (tp) REVERT: D 119 VAL cc_start: 0.7927 (t) cc_final: 0.7711 (p) REVERT: D 267 MET cc_start: 0.7560 (ppp) cc_final: 0.7251 (ppp) REVERT: C 76 ASP cc_start: 0.7634 (t0) cc_final: 0.7077 (p0) REVERT: C 217 LEU cc_start: 0.8776 (tp) cc_final: 0.8200 (tp) REVERT: C 413 MET cc_start: 0.8113 (mmm) cc_final: 0.7851 (mmm) REVERT: C 425 MET cc_start: 0.7651 (mmt) cc_final: 0.7441 (mmt) REVERT: F 267 MET cc_start: 0.7942 (ppp) cc_final: 0.7629 (ppp) REVERT: F 370 ASN cc_start: 0.7969 (t0) cc_final: 0.7659 (t0) REVERT: E 76 ASP cc_start: 0.7752 (t0) cc_final: 0.7189 (p0) REVERT: E 217 LEU cc_start: 0.8897 (tp) cc_final: 0.8352 (tp) REVERT: H 119 VAL cc_start: 0.7928 (t) cc_final: 0.7712 (p) REVERT: H 267 MET cc_start: 0.7558 (ppp) cc_final: 0.7249 (ppp) REVERT: G 76 ASP cc_start: 0.7637 (t0) cc_final: 0.7078 (p0) REVERT: G 217 LEU cc_start: 0.8776 (tp) cc_final: 0.8200 (tp) REVERT: G 413 MET cc_start: 0.8111 (mmm) cc_final: 0.7849 (mmm) REVERT: G 425 MET cc_start: 0.7652 (mmt) cc_final: 0.7440 (mmt) REVERT: J 267 MET cc_start: 0.7940 (ppp) cc_final: 0.7628 (ppp) REVERT: J 370 ASN cc_start: 0.7969 (t0) cc_final: 0.7658 (t0) REVERT: I 76 ASP cc_start: 0.7752 (t0) cc_final: 0.7189 (p0) REVERT: I 217 LEU cc_start: 0.8899 (tp) cc_final: 0.8354 (tp) REVERT: L 119 VAL cc_start: 0.7929 (t) cc_final: 0.7712 (p) REVERT: L 267 MET cc_start: 0.7560 (ppp) cc_final: 0.7250 (ppp) REVERT: K 76 ASP cc_start: 0.7634 (t0) cc_final: 0.7076 (p0) REVERT: K 217 LEU cc_start: 0.8776 (tp) cc_final: 0.8200 (tp) REVERT: K 413 MET cc_start: 0.8113 (mmm) cc_final: 0.7850 (mmm) REVERT: K 425 MET cc_start: 0.7651 (mmt) cc_final: 0.7440 (mmt) REVERT: N 267 MET cc_start: 0.7941 (ppp) cc_final: 0.7628 (ppp) REVERT: N 370 ASN cc_start: 0.7971 (t0) cc_final: 0.7661 (t0) REVERT: M 76 ASP cc_start: 0.7751 (t0) cc_final: 0.7188 (p0) REVERT: M 217 LEU cc_start: 0.8899 (tp) cc_final: 0.8355 (tp) REVERT: P 119 VAL cc_start: 0.7927 (t) cc_final: 0.7710 (p) REVERT: P 267 MET cc_start: 0.7558 (ppp) cc_final: 0.7250 (ppp) REVERT: O 76 ASP cc_start: 0.7635 (t0) cc_final: 0.7077 (p0) REVERT: O 217 LEU cc_start: 0.8776 (tp) cc_final: 0.8200 (tp) REVERT: O 413 MET cc_start: 0.8112 (mmm) cc_final: 0.7852 (mmm) REVERT: O 425 MET cc_start: 0.7652 (mmt) cc_final: 0.7441 (mmt) outliers start: 84 outliers final: 48 residues processed: 1056 average time/residue: 0.4642 time to fit residues: 860.7359 Evaluate side-chains 1000 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 952 time to evaluate : 4.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain H residue 99 ASN Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 410 GLU Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 189 ILE Chi-restraints excluded: chain L residue 410 GLU Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain P residue 99 ASN Chi-restraints excluded: chain P residue 178 THR Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain P residue 410 GLU Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 253 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 343 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 513 optimal weight: 4.9990 chunk 420 optimal weight: 0.0570 chunk 170 optimal weight: 5.9990 chunk 618 optimal weight: 0.9990 chunk 668 optimal weight: 0.6980 chunk 550 optimal weight: 0.4980 chunk 613 optimal weight: 1.9990 chunk 210 optimal weight: 0.4980 chunk 496 optimal weight: 0.4980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 227 HIS ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN A 258 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN F 227 HIS ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN E 258 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 HIS ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 ASN G 258 ASN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN J 227 HIS ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 ASN I 258 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 227 HIS ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 ASN K 258 ASN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN N 227 HIS ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 249 ASN M 258 ASN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 227 HIS ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 258 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 55336 Z= 0.193 Angle : 0.703 8.169 75312 Z= 0.345 Chirality : 0.044 0.180 8344 Planarity : 0.004 0.053 9792 Dihedral : 16.947 175.142 7840 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.08 % Favored : 90.80 % Rotamer: Outliers : 1.38 % Allowed : 15.85 % Favored : 82.78 % 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: -2.12 (0.10), residues: 6880 helix: -0.16 (0.10), residues: 2712 sheet: -1.70 (0.19), residues: 808 loop : -2.44 (0.11), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 397 HIS 0.006 0.001 HIS A 28 PHE 0.016 0.001 PHE A 296 TYR 0.016 0.001 TYR H 106 ARG 0.009 0.000 ARG I 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1040 time to evaluate : 4.728 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: B 191 GLN cc_start: 0.7358 (pt0) cc_final: 0.7146 (pt0) REVERT: B 267 MET cc_start: 0.7880 (ppp) cc_final: 0.7233 (ppp) REVERT: B 323 MET cc_start: 0.8044 (mtp) cc_final: 0.7734 (tmm) REVERT: B 370 ASN cc_start: 0.7893 (t0) cc_final: 0.7645 (t0) REVERT: A 76 ASP cc_start: 0.7742 (t0) cc_final: 0.7114 (p0) REVERT: A 217 LEU cc_start: 0.8899 (tp) cc_final: 0.8291 (tp) REVERT: D 267 MET cc_start: 0.7474 (ppp) cc_final: 0.6960 (ppp) REVERT: D 330 MET cc_start: 0.8229 (mmp) cc_final: 0.7962 (mmp) REVERT: C 76 ASP cc_start: 0.7647 (t0) cc_final: 0.7418 (t0) REVERT: C 217 LEU cc_start: 0.8754 (tp) cc_final: 0.8159 (tp) REVERT: C 413 MET cc_start: 0.8090 (mmm) cc_final: 0.7777 (mmm) REVERT: F 191 GLN cc_start: 0.7359 (pt0) cc_final: 0.7146 (pt0) REVERT: F 267 MET cc_start: 0.7882 (ppp) cc_final: 0.7235 (ppp) REVERT: F 323 MET cc_start: 0.8045 (mtp) cc_final: 0.7734 (tmm) REVERT: F 370 ASN cc_start: 0.7895 (t0) cc_final: 0.7645 (t0) REVERT: E 76 ASP cc_start: 0.7739 (t0) cc_final: 0.7113 (p0) REVERT: E 217 LEU cc_start: 0.8900 (tp) cc_final: 0.8294 (tp) REVERT: H 267 MET cc_start: 0.7472 (ppp) cc_final: 0.6959 (ppp) REVERT: H 330 MET cc_start: 0.8232 (mmp) cc_final: 0.7963 (mmp) REVERT: G 76 ASP cc_start: 0.7648 (t0) cc_final: 0.7419 (t0) REVERT: G 217 LEU cc_start: 0.8753 (tp) cc_final: 0.8159 (tp) REVERT: G 413 MET cc_start: 0.8089 (mmm) cc_final: 0.7777 (mmm) REVERT: J 191 GLN cc_start: 0.7360 (pt0) cc_final: 0.7148 (pt0) REVERT: J 267 MET cc_start: 0.7877 (ppp) cc_final: 0.7232 (ppp) REVERT: J 323 MET cc_start: 0.8044 (mtp) cc_final: 0.7733 (tmm) REVERT: J 370 ASN cc_start: 0.7897 (t0) cc_final: 0.7647 (t0) REVERT: I 76 ASP cc_start: 0.7740 (t0) cc_final: 0.7113 (p0) REVERT: I 217 LEU cc_start: 0.8901 (tp) cc_final: 0.8295 (tp) REVERT: L 267 MET cc_start: 0.7473 (ppp) cc_final: 0.6960 (ppp) REVERT: L 330 MET cc_start: 0.8231 (mmp) cc_final: 0.7964 (mmp) REVERT: K 76 ASP cc_start: 0.7648 (t0) cc_final: 0.7418 (t0) REVERT: K 217 LEU cc_start: 0.8754 (tp) cc_final: 0.8159 (tp) REVERT: K 413 MET cc_start: 0.8088 (mmm) cc_final: 0.7774 (mmm) REVERT: N 191 GLN cc_start: 0.7358 (pt0) cc_final: 0.7147 (pt0) REVERT: N 267 MET cc_start: 0.7879 (ppp) cc_final: 0.7232 (ppp) REVERT: N 323 MET cc_start: 0.8044 (mtp) cc_final: 0.7733 (tmm) REVERT: N 370 ASN cc_start: 0.7896 (t0) cc_final: 0.7646 (t0) REVERT: M 76 ASP cc_start: 0.7741 (t0) cc_final: 0.7113 (p0) REVERT: M 217 LEU cc_start: 0.8902 (tp) cc_final: 0.8295 (tp) REVERT: P 267 MET cc_start: 0.7470 (ppp) cc_final: 0.6960 (ppp) REVERT: P 330 MET cc_start: 0.8230 (mmp) cc_final: 0.7964 (mmp) REVERT: O 76 ASP cc_start: 0.7648 (t0) cc_final: 0.7418 (t0) REVERT: O 217 LEU cc_start: 0.8754 (tp) cc_final: 0.8160 (tp) REVERT: O 413 MET cc_start: 0.8091 (mmm) cc_final: 0.7777 (mmm) outliers start: 78 outliers final: 56 residues processed: 1066 average time/residue: 0.4516 time to fit residues: 851.8841 Evaluate side-chains 982 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 926 time to evaluate : 4.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain H residue 99 ASN Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 321 MET Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 321 MET Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain N residue 386 THR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain P residue 99 ASN Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 321 MET Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 227 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 611 optimal weight: 3.9990 chunk 465 optimal weight: 2.9990 chunk 321 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 415 optimal weight: 2.9990 chunk 620 optimal weight: 0.7980 chunk 657 optimal weight: 1.9990 chunk 324 optimal weight: 0.4980 chunk 588 optimal weight: 0.0770 chunk 177 optimal weight: 2.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 ASN ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN ** L 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 ASN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 99 ASN ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 184 ASN ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 249 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 55336 Z= 0.223 Angle : 0.709 8.435 75312 Z= 0.349 Chirality : 0.045 0.221 8344 Planarity : 0.004 0.052 9792 Dihedral : 16.645 178.213 7840 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.07 % Favored : 89.81 % Rotamer: Outliers : 1.69 % Allowed : 18.34 % Favored : 79.97 % 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: -2.07 (0.10), residues: 6880 helix: -0.14 (0.10), residues: 2672 sheet: -1.60 (0.20), residues: 752 loop : -2.39 (0.11), residues: 3456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 101 HIS 0.005 0.001 HIS A 8 PHE 0.023 0.001 PHE A 296 TYR 0.020 0.001 TYR E 108 ARG 0.007 0.000 ARG C 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 964 time to evaluate : 4.716 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: symmetry clash REVERT: B 190 HIS cc_start: 0.8539 (OUTLIER) cc_final: 0.8042 (t70) REVERT: B 267 MET cc_start: 0.7943 (ppp) cc_final: 0.7166 (ppp) REVERT: B 370 ASN cc_start: 0.7881 (t0) cc_final: 0.7634 (t0) REVERT: A 76 ASP cc_start: 0.7853 (t0) cc_final: 0.7602 (t0) REVERT: A 203 MET cc_start: 0.7533 (ptp) cc_final: 0.7281 (ptt) REVERT: A 217 LEU cc_start: 0.8905 (tp) cc_final: 0.8270 (tp) REVERT: D 267 MET cc_start: 0.7628 (ppp) cc_final: 0.7094 (ppp) REVERT: D 281 TYR cc_start: 0.3537 (OUTLIER) cc_final: 0.2127 (m-80) REVERT: D 330 MET cc_start: 0.8280 (mmp) cc_final: 0.8048 (mmp) REVERT: C 167 LEU cc_start: 0.7169 (tp) cc_final: 0.6899 (tp) REVERT: C 217 LEU cc_start: 0.8799 (tp) cc_final: 0.8165 (tp) REVERT: C 413 MET cc_start: 0.8134 (mmm) cc_final: 0.7843 (mmm) REVERT: F 190 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.8042 (t70) REVERT: F 267 MET cc_start: 0.7943 (ppp) cc_final: 0.7166 (ppp) REVERT: F 370 ASN cc_start: 0.7881 (t0) cc_final: 0.7634 (t0) REVERT: E 76 ASP cc_start: 0.7853 (t0) cc_final: 0.7602 (t0) REVERT: E 203 MET cc_start: 0.7531 (ptp) cc_final: 0.7280 (ptt) REVERT: E 217 LEU cc_start: 0.8907 (tp) cc_final: 0.8271 (tp) REVERT: H 267 MET cc_start: 0.7626 (ppp) cc_final: 0.7091 (ppp) REVERT: H 281 TYR cc_start: 0.3539 (OUTLIER) cc_final: 0.2126 (m-80) REVERT: H 330 MET cc_start: 0.8280 (mmp) cc_final: 0.8048 (mmp) REVERT: G 167 LEU cc_start: 0.7168 (tp) cc_final: 0.6899 (tp) REVERT: G 217 LEU cc_start: 0.8798 (tp) cc_final: 0.8165 (tp) REVERT: G 413 MET cc_start: 0.8132 (mmm) cc_final: 0.7841 (mmm) REVERT: J 190 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.8041 (t70) REVERT: J 267 MET cc_start: 0.7943 (ppp) cc_final: 0.7167 (ppp) REVERT: J 370 ASN cc_start: 0.7879 (t0) cc_final: 0.7632 (t0) REVERT: I 76 ASP cc_start: 0.7854 (t0) cc_final: 0.7602 (t0) REVERT: I 203 MET cc_start: 0.7533 (ptp) cc_final: 0.7283 (ptt) REVERT: I 217 LEU cc_start: 0.8906 (tp) cc_final: 0.8271 (tp) REVERT: L 267 MET cc_start: 0.7626 (ppp) cc_final: 0.7092 (ppp) REVERT: L 281 TYR cc_start: 0.3538 (OUTLIER) cc_final: 0.2126 (m-80) REVERT: L 330 MET cc_start: 0.8280 (mmp) cc_final: 0.8049 (mmp) REVERT: K 167 LEU cc_start: 0.7168 (tp) cc_final: 0.6899 (tp) REVERT: K 217 LEU cc_start: 0.8800 (tp) cc_final: 0.8166 (tp) REVERT: K 413 MET cc_start: 0.8136 (mmm) cc_final: 0.7845 (mmm) REVERT: N 190 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.8041 (t70) REVERT: N 267 MET cc_start: 0.7943 (ppp) cc_final: 0.7168 (ppp) REVERT: N 370 ASN cc_start: 0.7881 (t0) cc_final: 0.7634 (t0) REVERT: M 76 ASP cc_start: 0.7852 (t0) cc_final: 0.7601 (t0) REVERT: M 203 MET cc_start: 0.7531 (ptp) cc_final: 0.7278 (ptt) REVERT: M 217 LEU cc_start: 0.8905 (tp) cc_final: 0.8270 (tp) REVERT: P 267 MET cc_start: 0.7625 (ppp) cc_final: 0.7091 (ppp) REVERT: P 281 TYR cc_start: 0.3538 (OUTLIER) cc_final: 0.2127 (m-80) REVERT: P 330 MET cc_start: 0.8280 (mmp) cc_final: 0.8048 (mmp) REVERT: O 167 LEU cc_start: 0.7169 (tp) cc_final: 0.6899 (tp) REVERT: O 217 LEU cc_start: 0.8799 (tp) cc_final: 0.8165 (tp) REVERT: O 413 MET cc_start: 0.8134 (mmm) cc_final: 0.7842 (mmm) outliers start: 96 outliers final: 54 residues processed: 1006 average time/residue: 0.4538 time to fit residues: 805.3083 Evaluate side-chains 996 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 934 time to evaluate : 4.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 321 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain J residue 190 HIS Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 321 MET Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain N residue 190 HIS Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 253 LEU Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain P residue 178 THR Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 321 MET Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 253 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.6687 > 50: distance: 93 - 97: 25.709 distance: 97 - 98: 26.265 distance: 98 - 99: 7.686 distance: 98 - 101: 14.133 distance: 99 - 100: 27.961 distance: 99 - 105: 25.547 distance: 101 - 102: 21.151 distance: 102 - 103: 6.934 distance: 102 - 104: 15.555 distance: 105 - 106: 18.921 distance: 106 - 107: 24.924 distance: 106 - 109: 18.661 distance: 107 - 108: 19.605 distance: 107 - 112: 20.230 distance: 109 - 110: 19.560 distance: 109 - 111: 12.541 distance: 112 - 113: 9.640 distance: 113 - 114: 13.267 distance: 113 - 116: 9.215 distance: 114 - 115: 22.187 distance: 114 - 119: 13.053 distance: 115 - 132: 43.115 distance: 116 - 117: 19.634 distance: 116 - 118: 19.482 distance: 119 - 120: 24.733 distance: 120 - 121: 18.959 distance: 120 - 123: 39.008 distance: 121 - 122: 31.505 distance: 121 - 124: 14.407 distance: 124 - 125: 28.375 distance: 125 - 126: 23.599 distance: 125 - 128: 17.215 distance: 126 - 127: 33.433 distance: 126 - 132: 23.777 distance: 127 - 146: 20.354 distance: 128 - 129: 41.523 distance: 128 - 130: 30.174 distance: 129 - 131: 38.824 distance: 132 - 133: 15.538 distance: 133 - 134: 26.734 distance: 133 - 136: 28.799 distance: 134 - 135: 18.057 distance: 134 - 137: 5.598 distance: 135 - 151: 22.907 distance: 137 - 138: 22.070 distance: 138 - 139: 31.494 distance: 138 - 141: 14.035 distance: 139 - 140: 13.728 distance: 139 - 146: 20.842 distance: 140 - 165: 39.221 distance: 141 - 142: 30.002 distance: 142 - 143: 8.130 distance: 143 - 144: 12.571 distance: 143 - 145: 13.720 distance: 146 - 147: 35.603 distance: 147 - 148: 22.329 distance: 147 - 150: 19.477 distance: 148 - 149: 37.751 distance: 148 - 151: 18.224 distance: 149 - 170: 30.783 distance: 151 - 152: 31.629 distance: 152 - 153: 23.201 distance: 152 - 155: 23.583 distance: 153 - 154: 22.715 distance: 153 - 165: 11.673 distance: 154 - 181: 24.135 distance: 155 - 156: 10.430 distance: 156 - 157: 12.527 distance: 156 - 158: 22.699 distance: 157 - 159: 16.897 distance: 158 - 160: 23.699 distance: 158 - 161: 16.907 distance: 159 - 160: 26.171 distance: 160 - 162: 22.491 distance: 161 - 163: 13.425 distance: 162 - 164: 11.128 distance: 163 - 164: 13.626 distance: 165 - 166: 32.054 distance: 166 - 167: 21.248 distance: 166 - 169: 18.771 distance: 167 - 168: 27.941 distance: 167 - 170: 16.598 distance: 168 - 188: 19.263