Starting phenix.real_space_refine on Thu Dec 7 23:09:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2023/7m18_23615_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2023/7m18_23615.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2023/7m18_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_23615/12_2023/7m18_23615_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2023/7m18_23615_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2023/7m18_23615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2023/7m18_23615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2023/7m18_23615_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2023/7m18_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-1.21rc1-5172/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: 32.47, per 1000 atoms: 0.60 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: 16.69 Conformation dependent library (CDL) restraints added in 11.0 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: 7.75 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: 13.02 Time building geometry restraints manager: 18.03 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 1.579 1.319 0.260 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C7 YNP P 501 " pdb=" C8 YNP P 501 " ideal model delta sigma weight residual 1.579 1.319 0.260 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C7 YNP H 501 " pdb=" C8 YNP H 501 " ideal model delta sigma weight residual 1.579 1.319 0.260 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C7 YNP D 501 " pdb=" C8 YNP D 501 " ideal model delta sigma weight residual 1.579 1.319 0.260 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C7 YNP J 501 " pdb=" C8 YNP J 501 " ideal model delta sigma weight residual 1.579 1.319 0.260 2.00e-02 2.50e+03 1.70e+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 109.47 166.52 -57.05 3.00e+00 1.11e-01 3.62e+02 angle pdb=" C5 YNP N 501 " pdb=" N2 YNP N 501 " pdb=" C6 YNP N 501 " ideal model delta sigma weight residual 109.47 166.52 -57.05 3.00e+00 1.11e-01 3.62e+02 angle pdb=" C5 YNP B 501 " pdb=" N2 YNP B 501 " pdb=" C6 YNP B 501 " ideal model delta sigma weight residual 109.47 166.52 -57.05 3.00e+00 1.11e-01 3.62e+02 angle pdb=" C5 YNP F 501 " pdb=" N2 YNP F 501 " pdb=" C6 YNP F 501 " ideal model delta sigma weight residual 109.47 166.52 -57.05 3.00e+00 1.11e-01 3.62e+02 angle pdb=" C5 YNP L 501 " pdb=" N2 YNP L 501 " pdb=" C6 YNP L 501 " ideal model delta sigma weight residual 109.47 166.51 -57.04 3.00e+00 1.11e-01 3.62e+02 ... (remaining 75307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 32148 34.89 - 69.78: 588 69.78 - 104.66: 96 104.66 - 139.55: 48 139.55 - 174.44: 104 Dihedral angle restraints: 32984 sinusoidal: 13032 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 32981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 7216 0.075 - 0.149: 1008 0.149 - 0.224: 56 0.224 - 0.298: 0 0.298 - 0.373: 8 Chirality restraints: 8288 Sorted by residual: chirality pdb=" CA ALA E 273 " pdb=" N ALA E 273 " pdb=" C ALA E 273 " pdb=" CB ALA E 273 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA ALA M 273 " pdb=" N ALA M 273 " pdb=" C ALA M 273 " pdb=" CB ALA M 273 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA ALA I 273 " pdb=" N ALA I 273 " pdb=" C ALA I 273 " pdb=" CB ALA I 273 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 8285 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: 0.000 Normalize map: mean=0, sd=1: 13.610 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: 0.050 Extract box with map and model: 41.490 Check model and map are aligned: 0.590 Set scattering table: 0.370 Process input model: 119.650 Find NCS groups from input model: 3.340 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.090 ------------------------------------------------------------------------------- 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 0.260 55336 Z= 0.484 Angle : 1.332 57.050 75312 Z= 0.591 Chirality : 0.049 0.373 8288 Planarity : 0.007 0.176 9792 Dihedral : 19.798 174.440 20200 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 : 4.613 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 outliers start: 16 outliers final: 0 residues processed: 1221 average time/residue: 0.4600 time to fit residues: 990.8433 Evaluate side-chains 960 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 960 time to evaluate : 4.568 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0886 ------------------------------------------------------------------------------- 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: 0.2980 chunk 176 optimal weight: 2.9990 chunk 347 optimal weight: 0.0370 chunk 275 optimal weight: 0.9990 chunk 532 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 324 optimal weight: 0.0030 chunk 396 optimal weight: 3.9990 chunk 617 optimal weight: 1.9990 overall best weight: 0.3868 ------------------------------------------------------------------------------- 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 ** 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 249 ASN ** 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 ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** 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 249 ASN ** 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 ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** 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 249 ASN ** 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 ** 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 249 ASN ** 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 Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1284 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= 0.207 Angle : 0.813 16.129 75312 Z= 0.385 Chirality : 0.045 0.182 8288 Planarity : 0.005 0.056 9792 Dihedral : 21.583 173.246 8128 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.49 % Favored : 90.40 % Rotamer: Outliers : 1.53 % Allowed : 11.99 % Favored : 86.48 % 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: -0.21 (0.10), residues: 2760 sheet: -1.90 (0.18), residues: 808 loop : -2.56 (0.11), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 407 HIS 0.012 0.001 HIS I 28 PHE 0.025 0.002 PHE M 296 TYR 0.020 0.002 TYR P 106 ARG 0.006 0.000 ARG C 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 1119 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1032 time to evaluate : 4.585 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 outliers start: 87 outliers final: 43 residues processed: 1051 average time/residue: 0.4665 time to fit residues: 865.0048 Evaluate side-chains 999 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 956 time to evaluate : 4.544 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4110 time to fit residues: 39.3586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 343 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 513 optimal weight: 5.9990 chunk 420 optimal weight: 0.0570 chunk 170 optimal weight: 5.9990 chunk 618 optimal weight: 0.7980 chunk 668 optimal weight: 0.2980 chunk 550 optimal weight: 2.9990 chunk 613 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 496 optimal weight: 1.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- 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 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** 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 256 GLN A 258 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** 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 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN C 258 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** 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 256 GLN E 258 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 ASN H 227 HIS ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 256 GLN G 258 ASN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** 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 256 GLN I 258 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN L 227 HIS ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 GLN K 258 ASN ** 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 184 ASN ** 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 256 GLN M 258 ASN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 184 ASN P 227 HIS ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 256 GLN O 258 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 55336 Z= 0.269 Angle : 0.780 11.140 75312 Z= 0.377 Chirality : 0.046 0.199 8288 Planarity : 0.005 0.057 9792 Dihedral : 21.378 178.384 8128 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.41 % Favored : 88.47 % Rotamer: Outliers : 1.39 % Allowed : 16.03 % Favored : 82.58 % 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: -2.40 (0.10), residues: 6880 helix: -0.45 (0.10), residues: 2768 sheet: -1.92 (0.19), residues: 752 loop : -2.54 (0.11), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 407 HIS 0.007 0.001 HIS I 28 PHE 0.016 0.002 PHE J 394 TYR 0.018 0.002 TYR P 106 ARG 0.006 0.000 ARG F 320 *********************** 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 1087 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1008 time to evaluate : 4.680 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 outliers start: 79 outliers final: 44 residues processed: 1035 average time/residue: 0.4645 time to fit residues: 850.3055 Evaluate side-chains 967 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 923 time to evaluate : 4.653 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.3861 time to fit residues: 38.6278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 611 optimal weight: 2.9990 chunk 465 optimal weight: 0.0570 chunk 321 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 295 optimal weight: 0.9980 chunk 415 optimal weight: 3.9990 chunk 620 optimal weight: 1.9990 chunk 657 optimal weight: 3.9990 chunk 324 optimal weight: 0.2980 chunk 588 optimal weight: 0.3980 chunk 177 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 131 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** 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 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** 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 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 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 28 HIS ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN ** 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 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** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN N 131 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN ** 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 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 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 258 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 55336 Z= 0.193 Angle : 0.731 11.119 75312 Z= 0.353 Chirality : 0.045 0.234 8288 Planarity : 0.004 0.062 9792 Dihedral : 21.399 179.326 8128 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.88 % Favored : 91.01 % Rotamer: Outliers : 1.06 % Allowed : 18.04 % Favored : 80.91 % 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: -2.09 (0.10), residues: 6880 helix: -0.11 (0.10), residues: 2664 sheet: -1.69 (0.19), residues: 808 loop : -2.41 (0.11), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 407 HIS 0.005 0.001 HIS I 28 PHE 0.025 0.001 PHE O 296 TYR 0.013 0.001 TYR N 106 ARG 0.004 0.000 ARG K 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 1080 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1020 time to evaluate : 4.579 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 outliers start: 60 outliers final: 33 residues processed: 1039 average time/residue: 0.4737 time to fit residues: 873.6586 Evaluate side-chains 973 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 940 time to evaluate : 4.591 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4165 time to fit residues: 32.2281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 547 optimal weight: 0.9980 chunk 373 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 489 optimal weight: 0.8980 chunk 271 optimal weight: 3.9990 chunk 560 optimal weight: 0.0030 chunk 454 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 335 optimal weight: 0.0050 chunk 589 optimal weight: 3.9990 chunk 165 optimal weight: 0.0980 overall best weight: 0.4004 ------------------------------------------------------------------------------- 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 191 GLN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN A 28 HIS ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN F 191 GLN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN E 28 HIS ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 ASN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN I 28 HIS I 206 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 HIS ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 ASN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN M 28 HIS ** M 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 ASN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS ** O 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 55336 Z= 0.185 Angle : 0.707 10.252 75312 Z= 0.343 Chirality : 0.044 0.189 8288 Planarity : 0.005 0.066 9792 Dihedral : 21.348 179.903 8128 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.12 % Favored : 90.76 % Rotamer: Outliers : 1.09 % Allowed : 20.57 % Favored : 78.33 % 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: -2.05 (0.10), residues: 6880 helix: -0.09 (0.10), residues: 2672 sheet: -1.55 (0.19), residues: 808 loop : -2.42 (0.11), residues: 3400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 407 HIS 0.004 0.001 HIS P 137 PHE 0.020 0.001 PHE C 296 TYR 0.012 0.001 TYR N 106 ARG 0.003 0.000 ARG K 243 *********************** REFINEMENT MACRO_CYCLE 5 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 1063 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1001 time to evaluate : 4.631 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 outliers start: 62 outliers final: 30 residues processed: 1033 average time/residue: 0.4704 time to fit residues: 861.0345 Evaluate side-chains 981 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 951 time to evaluate : 4.549 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4218 time to fit residues: 29.4200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 221 optimal weight: 1.9990 chunk 591 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 385 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 657 optimal weight: 3.9990 chunk 546 optimal weight: 0.0770 chunk 304 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 345 optimal weight: 2.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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 14 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 GLN ** 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 14 ASN ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** 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 14 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 55336 Z= 0.214 Angle : 0.721 10.671 75312 Z= 0.350 Chirality : 0.044 0.182 8288 Planarity : 0.005 0.071 9792 Dihedral : 21.424 179.715 8128 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.58 % Favored : 90.31 % Rotamer: Outliers : 0.78 % Allowed : 21.51 % Favored : 77.72 % 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: -2.00 (0.10), residues: 6880 helix: -0.13 (0.10), residues: 2680 sheet: -1.69 (0.19), residues: 760 loop : -2.26 (0.11), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 388 HIS 0.005 0.001 HIS N 190 PHE 0.021 0.002 PHE O 296 TYR 0.012 0.001 TYR N 106 ARG 0.009 0.000 ARG K 243 *********************** REFINEMENT MACRO_CYCLE 6 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 1036 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 992 time to evaluate : 4.655 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 outliers start: 44 outliers final: 16 residues processed: 1024 average time/residue: 0.4678 time to fit residues: 850.5172 Evaluate side-chains 947 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 931 time to evaluate : 4.626 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3895 time to fit residues: 18.1434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 634 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 374 optimal weight: 0.9980 chunk 480 optimal weight: 2.9990 chunk 372 optimal weight: 0.5980 chunk 553 optimal weight: 0.6980 chunk 367 optimal weight: 0.0020 chunk 655 optimal weight: 0.0770 chunk 410 optimal weight: 0.9990 chunk 399 optimal weight: 2.9990 chunk 302 optimal weight: 8.9990 overall best weight: 0.4346 ------------------------------------------------------------------------------- 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 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 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** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 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** ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 ASN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 55336 Z= 0.188 Angle : 0.727 11.009 75312 Z= 0.349 Chirality : 0.044 0.247 8288 Planarity : 0.005 0.073 9792 Dihedral : 21.184 179.356 8128 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.57 % Favored : 91.31 % Rotamer: Outliers : 0.67 % Allowed : 21.97 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.10), residues: 6880 helix: -0.13 (0.10), residues: 2688 sheet: -1.63 (0.21), residues: 696 loop : -2.19 (0.11), residues: 3496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 407 HIS 0.006 0.001 HIS I 28 PHE 0.019 0.001 PHE C 343 TYR 0.011 0.001 TYR A 108 ARG 0.007 0.000 ARG C 243 *********************** REFINEMENT MACRO_CYCLE 7 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 1032 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 994 time to evaluate : 4.707 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 outliers start: 38 outliers final: 20 residues processed: 1012 average time/residue: 0.4754 time to fit residues: 854.2115 Evaluate side-chains 974 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 954 time to evaluate : 4.606 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4070 time to fit residues: 21.3857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 405 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 391 optimal weight: 0.0770 chunk 197 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 416 optimal weight: 0.0030 chunk 446 optimal weight: 1.9990 chunk 324 optimal weight: 0.2980 chunk 61 optimal weight: 0.4980 chunk 515 optimal weight: 0.9990 overall best weight: 0.2948 ------------------------------------------------------------------------------- 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 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 ASN ** 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 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 55336 Z= 0.174 Angle : 0.717 11.815 75312 Z= 0.345 Chirality : 0.044 0.218 8288 Planarity : 0.005 0.071 9792 Dihedral : 20.765 176.659 8128 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.21 % Favored : 91.68 % Rotamer: Outliers : 0.60 % Allowed : 22.00 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.10), residues: 6880 helix: -0.15 (0.10), residues: 2680 sheet: -1.52 (0.21), residues: 696 loop : -2.21 (0.11), residues: 3504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 21 HIS 0.005 0.001 HIS E 28 PHE 0.018 0.001 PHE M 343 TYR 0.014 0.001 TYR G 108 ARG 0.005 0.000 ARG O 243 *********************** REFINEMENT MACRO_CYCLE 8 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 1075 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1041 time to evaluate : 4.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 8 residues processed: 1071 average time/residue: 0.4719 time to fit residues: 897.9433 Evaluate side-chains 987 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 979 time to evaluate : 4.608 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3820 time to fit residues: 12.1517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 596 optimal weight: 0.8980 chunk 627 optimal weight: 0.6980 chunk 572 optimal weight: 0.7980 chunk 610 optimal weight: 0.0020 chunk 367 optimal weight: 2.9990 chunk 266 optimal weight: 0.6980 chunk 479 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 551 optimal weight: 0.9980 chunk 577 optimal weight: 0.9990 chunk 608 optimal weight: 0.0980 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** 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 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3033 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= 0.188 Angle : 0.736 12.707 75312 Z= 0.353 Chirality : 0.044 0.202 8288 Planarity : 0.005 0.073 9792 Dihedral : 20.551 174.588 8128 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.73 % Favored : 91.15 % Rotamer: Outliers : 0.35 % Allowed : 23.17 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.10), residues: 6880 helix: -0.28 (0.10), residues: 2752 sheet: -1.46 (0.21), residues: 696 loop : -2.19 (0.11), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 21 HIS 0.006 0.001 HIS M 28 PHE 0.018 0.001 PHE K 202 TYR 0.012 0.001 TYR A 108 ARG 0.006 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 9 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 1037 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1017 time to evaluate : 4.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 1025 average time/residue: 0.4673 time to fit residues: 853.9595 Evaluate side-chains 986 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 978 time to evaluate : 4.582 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4039 time to fit residues: 12.2244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 401 optimal weight: 0.0980 chunk 645 optimal weight: 1.9990 chunk 394 optimal weight: 3.9990 chunk 306 optimal weight: 0.9980 chunk 448 optimal weight: 0.0050 chunk 677 optimal weight: 1.9990 chunk 623 optimal weight: 2.9990 chunk 539 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 416 optimal weight: 0.9990 chunk 330 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 55336 Z= 0.203 Angle : 0.741 13.761 75312 Z= 0.358 Chirality : 0.044 0.220 8288 Planarity : 0.005 0.070 9792 Dihedral : 20.416 172.889 8128 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.11 % Favored : 90.77 % Rotamer: Outliers : 0.42 % Allowed : 23.20 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.10), residues: 6880 helix: -0.35 (0.10), residues: 2744 sheet: -1.43 (0.21), residues: 696 loop : -2.14 (0.11), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 21 HIS 0.006 0.001 HIS G 61 PHE 0.017 0.001 PHE M 296 TYR 0.012 0.001 TYR O 108 ARG 0.005 0.000 ARG O 243 ********************** REFINEMENT MACRO_CYCLE 10 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 1020 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 996 time to evaluate : 4.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 1004 average time/residue: 0.4668 time to fit residues: 833.9134 Evaluate side-chains 994 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 978 time to evaluate : 4.913 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4082 time to fit residues: 19.0162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 428 optimal weight: 1.9990 chunk 574 optimal weight: 0.0980 chunk 165 optimal weight: 0.2980 chunk 497 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 540 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 554 optimal weight: 0.5980 chunk 68 optimal weight: 0.0770 chunk 99 optimal weight: 1.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 HIS ** M 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.131964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.110007 restraints weight = 147787.624| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 5.31 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3218 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= 0.183 Angle : 0.751 13.539 75312 Z= 0.362 Chirality : 0.044 0.250 8288 Planarity : 0.005 0.072 9792 Dihedral : 20.177 173.089 8128 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.53 % Favored : 91.36 % Rotamer: Outliers : 0.35 % Allowed : 23.91 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.10), residues: 6880 helix: -0.27 (0.10), residues: 2712 sheet: -1.31 (0.21), residues: 696 loop : -2.07 (0.11), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 21 HIS 0.006 0.001 HIS E 28 PHE 0.020 0.001 PHE M 169 TYR 0.012 0.001 TYR I 108 ARG 0.005 0.000 ARG L 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13777.33 seconds wall clock time: 243 minutes 7.95 seconds (14587.95 seconds total)