Starting phenix.real_space_refine (version: dev) on Sun Dec 11 18:20:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2022/7m18_23615_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2022/7m18_23615.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2022/7m18_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_2022/7m18_23615_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2022/7m18_23615_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2022/7m18_23615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2022/7m18_23615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2022/7m18_23615_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/12_2022/7m18_23615_updated.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B GLU 123": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D GLU 421": "OE1" <-> "OE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 376": "OE1" <-> "OE2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F GLU 421": "OE1" <-> "OE2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "H GLU 376": "OE1" <-> "OE2" Residue "H GLU 383": "OE1" <-> "OE2" Residue "H GLU 421": "OE1" <-> "OE2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G GLU 429": "OE1" <-> "OE2" Residue "J GLU 123": "OE1" <-> "OE2" Residue "J GLU 205": "OE1" <-> "OE2" Residue "J GLU 376": "OE1" <-> "OE2" Residue "J GLU 383": "OE1" <-> "OE2" Residue "J GLU 421": "OE1" <-> "OE2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "I GLU 429": "OE1" <-> "OE2" Residue "L GLU 123": "OE1" <-> "OE2" Residue "L GLU 205": "OE1" <-> "OE2" Residue "L GLU 376": "OE1" <-> "OE2" Residue "L GLU 383": "OE1" <-> "OE2" Residue "L GLU 421": "OE1" <-> "OE2" Residue "K GLU 183": "OE1" <-> "OE2" Residue "K GLU 429": "OE1" <-> "OE2" Residue "N GLU 123": "OE1" <-> "OE2" Residue "N GLU 205": "OE1" <-> "OE2" Residue "N GLU 376": "OE1" <-> "OE2" Residue "N GLU 383": "OE1" <-> "OE2" Residue "N GLU 421": "OE1" <-> "OE2" Residue "M GLU 183": "OE1" <-> "OE2" Residue "M GLU 429": "OE1" <-> "OE2" Residue "P GLU 123": "OE1" <-> "OE2" Residue "P GLU 205": "OE1" <-> "OE2" Residue "P GLU 376": "OE1" <-> "OE2" Residue "P GLU 383": "OE1" <-> "OE2" Residue "P GLU 421": "OE1" <-> "OE2" Residue "O GLU 183": "OE1" <-> "OE2" Residue "O GLU 429": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 36.84, per 1000 atoms: 0.68 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: 20.26 Conformation dependent library (CDL) restraints added in 9.3 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: 3.86 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: 14.61 Time building geometry restraints manager: 21.86 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 1.570 1.319 0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C7 YNP P 501 " pdb=" C8 YNP P 501 " ideal model delta sigma weight residual 1.570 1.319 0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C7 YNP H 501 " pdb=" C8 YNP H 501 " ideal model delta sigma weight residual 1.570 1.319 0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C7 YNP D 501 " pdb=" C8 YNP D 501 " ideal model delta sigma weight residual 1.570 1.319 0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C7 YNP J 501 " pdb=" C8 YNP J 501 " ideal model delta sigma weight residual 1.570 1.319 0.251 2.00e-02 2.50e+03 1.58e+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 109.48 166.52 -57.04 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 109.48 166.52 -57.04 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 109.48 166.52 -57.04 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 109.48 166.52 -57.04 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 109.48 166.51 -57.03 3.00e+00 1.11e-01 3.61e+02 ... (remaining 75307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.57: 31952 34.57 - 69.15: 496 69.15 - 103.72: 80 103.72 - 138.29: 40 138.29 - 172.86: 40 Dihedral angle restraints: 32608 sinusoidal: 12656 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 32605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.032: 8336 1.032 - 2.063: 0 2.063 - 3.095: 0 3.095 - 4.126: 0 4.126 - 5.158: 8 Chirality restraints: 8344 Sorted by residual: chirality pdb=" C18 YNP J 501 " pdb=" C10 YNP J 501 " pdb=" C19 YNP J 501 " pdb=" C20 YNP J 501 " both_signs ideal model delta sigma weight residual False -2.78 2.38 -5.16 2.00e-01 2.50e+01 6.65e+02 chirality pdb=" C18 YNP N 501 " pdb=" C10 YNP N 501 " pdb=" C19 YNP N 501 " pdb=" C20 YNP N 501 " both_signs ideal model delta sigma weight residual False -2.78 2.38 -5.16 2.00e-01 2.50e+01 6.65e+02 chirality pdb=" C18 YNP B 501 " pdb=" C10 YNP B 501 " pdb=" C19 YNP B 501 " pdb=" C20 YNP B 501 " both_signs ideal model delta sigma weight residual False -2.78 2.38 -5.16 2.00e-01 2.50e+01 6.65e+02 ... (remaining 8341 not shown) Planarity restraints: 9792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 YNP L 501 " 0.203 2.00e-02 2.50e+03 1.76e-01 3.87e+02 pdb=" C4 YNP L 501 " -0.051 2.00e-02 2.50e+03 pdb=" C5 YNP L 501 " 0.049 2.00e-02 2.50e+03 pdb=" N1 YNP L 501 " -0.311 2.00e-02 2.50e+03 pdb=" O1 YNP L 501 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 YNP D 501 " -0.203 2.00e-02 2.50e+03 1.76e-01 3.87e+02 pdb=" C4 YNP D 501 " 0.051 2.00e-02 2.50e+03 pdb=" C5 YNP D 501 " -0.049 2.00e-02 2.50e+03 pdb=" N1 YNP D 501 " 0.311 2.00e-02 2.50e+03 pdb=" O1 YNP D 501 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 YNP H 501 " -0.203 2.00e-02 2.50e+03 1.76e-01 3.87e+02 pdb=" C4 YNP H 501 " 0.051 2.00e-02 2.50e+03 pdb=" C5 YNP H 501 " -0.049 2.00e-02 2.50e+03 pdb=" N1 YNP H 501 " 0.311 2.00e-02 2.50e+03 pdb=" O1 YNP H 501 " -0.110 2.00e-02 2.50e+03 ... (remaining 9789 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 320 2.36 - 3.00: 32096 3.00 - 3.63: 87396 3.63 - 4.27: 123404 4.27 - 4.90: 199712 Nonbonded interactions: 442928 Sorted by model distance: nonbonded pdb=" CE1 HIS K 406 " pdb=" O PRO N 259 " model vdw 1.728 3.260 nonbonded pdb=" CE1 HIS C 406 " pdb=" O PRO F 259 " model vdw 1.728 3.260 nonbonded pdb=" O PRO B 259 " pdb=" CE1 HIS O 406 " model vdw 1.728 3.260 nonbonded pdb=" CE1 HIS G 406 " pdb=" O PRO J 259 " model vdw 1.728 3.260 nonbonded pdb=" CE1 HIS I 406 " pdb=" O PRO L 259 " model vdw 1.728 3.260 ... (remaining 442923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = (chain 'B' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'D' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'F' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'H' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'J' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'L' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'N' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'P' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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: 6.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 41.620 Check model and map are aligned: 0.620 Convert atoms to be neutral: 0.360 Process input model: 126.970 Find NCS groups from input model: 3.580 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 0.251 55336 Z= 0.487 Angle : 1.497 57.040 75312 Z= 0.633 Chirality : 0.168 5.158 8344 Planarity : 0.007 0.176 9792 Dihedral : 17.258 172.862 19824 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 23.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.36 % Favored : 89.29 % Rotamer Outliers : 0.28 % 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 *********************** 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 : 4.803 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: 0.4462 time to fit residues: 955.9159 Evaluate side-chains 960 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 960 time to evaluate : 4.881 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4801 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN C 258 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 G 258 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 227 HIS ** 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 I 258 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 O 258 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1382 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= 0.204 Angle : 0.917 30.612 75312 Z= 0.410 Chirality : 0.047 0.379 8344 Planarity : 0.005 0.058 9792 Dihedral : 16.569 175.792 7752 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.49 % Favored : 90.40 % Rotamer Outliers : 1.52 % 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: -2.23 (0.10), residues: 6880 helix: -0.17 (0.10), residues: 2728 sheet: -1.86 (0.18), residues: 808 loop : -2.56 (0.11), residues: 3344 *********************** 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 1134 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1048 time to evaluate : 4.941 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: 86 outliers final: 46 residues processed: 1066 average time/residue: 0.4495 time to fit residues: 843.9806 Evaluate side-chains 994 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 948 time to evaluate : 4.815 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.3663 time to fit residues: 38.6049 ------------------------------------------------------------------------------- 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: 3.9990 chunk 191 optimal weight: 4.9990 chunk 513 optimal weight: 4.9990 chunk 420 optimal weight: 0.2980 chunk 170 optimal weight: 5.9990 chunk 618 optimal weight: 0.9990 chunk 668 optimal weight: 5.9990 chunk 550 optimal weight: 0.8980 chunk 613 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 496 optimal weight: 0.4980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 227 HIS ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN A 256 GLN A 258 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 ASN ** 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 256 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 ASN K 256 GLN K 258 ASN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN N 227 HIS ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 256 GLN M 258 ASN ** P 8 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 256 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 55336 Z= 0.255 Angle : 0.873 30.017 75312 Z= 0.396 Chirality : 0.046 0.176 8344 Planarity : 0.005 0.056 9792 Dihedral : 16.051 177.809 7752 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.27 % Favored : 89.61 % Rotamer Outliers : 1.02 % 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: -2.26 (0.10), residues: 6880 helix: -0.27 (0.10), residues: 2728 sheet: -1.86 (0.19), residues: 752 loop : -2.50 (0.11), residues: 3400 *********************** 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 1054 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 996 time to evaluate : 4.933 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: 58 outliers final: 40 residues processed: 1010 average time/residue: 0.4475 time to fit residues: 794.2189 Evaluate side-chains 970 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 930 time to evaluate : 4.819 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3784 time to fit residues: 34.9215 ------------------------------------------------------------------------------- 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: 1.9990 chunk 321 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 415 optimal weight: 3.9990 chunk 620 optimal weight: 0.6980 chunk 657 optimal weight: 3.9990 chunk 324 optimal weight: 0.0020 chunk 588 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** 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 133 GLN ** 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 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** 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 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 HIS ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 ASN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 ASN ** 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 133 GLN ** 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 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** ** 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 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** 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 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS ** 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 55336 Z= 0.315 Angle : 0.912 30.119 75312 Z= 0.415 Chirality : 0.046 0.207 8344 Planarity : 0.005 0.068 9792 Dihedral : 15.932 178.165 7752 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 23.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.69 % Favored : 88.20 % Rotamer Outliers : 1.23 % 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: -2.39 (0.10), residues: 6880 helix: -0.39 (0.10), residues: 2736 sheet: -1.99 (0.19), residues: 752 loop : -2.56 (0.11), residues: 3392 *********************** 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 1044 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 974 time to evaluate : 5.098 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 outliers start: 70 outliers final: 46 residues processed: 1016 average time/residue: 0.4534 time to fit residues: 812.4320 Evaluate side-chains 954 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 908 time to evaluate : 4.831 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.3739 time to fit residues: 39.1270 ------------------------------------------------------------------------------- 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: 0.5980 chunk 373 optimal weight: 0.0970 chunk 9 optimal weight: 3.9990 chunk 489 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 560 optimal weight: 0.9990 chunk 454 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 335 optimal weight: 0.0040 chunk 589 optimal weight: 1.9990 chunk 165 optimal weight: 0.4980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 131 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 D 227 HIS ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 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** ** 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 28 HIS ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN N 131 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** ** 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 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2147 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= 0.190 Angle : 0.861 30.074 75312 Z= 0.385 Chirality : 0.045 0.240 8344 Planarity : 0.005 0.069 9792 Dihedral : 15.325 173.351 7752 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.63 % Favored : 91.25 % Rotamer Outliers : 0.99 % 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: -2.11 (0.10), residues: 6880 helix: -0.12 (0.10), residues: 2664 sheet: -1.69 (0.19), residues: 808 loop : -2.42 (0.11), residues: 3408 *********************** 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 1072 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1016 time to evaluate : 5.048 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: 56 outliers final: 20 residues processed: 1052 average time/residue: 0.4584 time to fit residues: 850.0902 Evaluate side-chains 972 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 952 time to evaluate : 4.868 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4253 time to fit residues: 21.8405 ------------------------------------------------------------------------------- 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: 3.9990 chunk 591 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 385 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 657 optimal weight: 2.9990 chunk 546 optimal weight: 2.9990 chunk 304 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 345 optimal weight: 0.1980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN A 28 HIS ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN ** 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 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** C 258 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 184 ASN ** 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** G 258 ASN ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN I 28 HIS ** 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 184 ASN ** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN M 28 HIS ** 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 184 ASN ** 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 258 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2313 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= 0.272 Angle : 0.903 30.230 75312 Z= 0.405 Chirality : 0.045 0.209 8344 Planarity : 0.005 0.075 9792 Dihedral : 14.978 173.893 7752 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.26 % Favored : 89.62 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.10), residues: 6880 helix: -0.23 (0.10), residues: 2680 sheet: -1.70 (0.19), residues: 808 loop : -2.37 (0.11), residues: 3392 *********************** 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 1039 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 943 time to evaluate : 4.945 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: 96 outliers final: 42 residues processed: 994 average time/residue: 0.4753 time to fit residues: 836.4163 Evaluate side-chains 926 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 884 time to evaluate : 4.871 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.4060 time to fit residues: 38.4648 ------------------------------------------------------------------------------- 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: 2.9990 chunk 74 optimal weight: 0.5980 chunk 374 optimal weight: 0.2980 chunk 480 optimal weight: 2.9990 chunk 372 optimal weight: 0.3980 chunk 553 optimal weight: 0.6980 chunk 367 optimal weight: 0.9980 chunk 655 optimal weight: 0.9980 chunk 410 optimal weight: 0.0670 chunk 399 optimal weight: 0.0870 chunk 302 optimal weight: 6.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** D 134 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** C 206 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 HIS ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 131 GLN ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 227 HIS ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 131 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 227 HIS ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 206 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2513 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= 0.183 Angle : 0.878 29.717 75312 Z= 0.388 Chirality : 0.044 0.214 8344 Planarity : 0.005 0.075 9792 Dihedral : 14.522 167.987 7752 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.96 % Favored : 91.92 % Rotamer Outliers : 0.72 % 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: -1.95 (0.10), residues: 6880 helix: -0.06 (0.10), residues: 2664 sheet: -1.57 (0.20), residues: 744 loop : -2.28 (0.11), residues: 3472 *********************** 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 1079 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1038 time to evaluate : 5.028 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: 41 outliers final: 23 residues processed: 1064 average time/residue: 0.4512 time to fit residues: 848.6982 Evaluate side-chains 977 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 954 time to evaluate : 4.894 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3811 time to fit residues: 22.9668 ------------------------------------------------------------------------------- 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: 0.9980 chunk 261 optimal weight: 3.9990 chunk 391 optimal weight: 0.0270 chunk 197 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 416 optimal weight: 3.9990 chunk 446 optimal weight: 0.0170 chunk 324 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 515 optimal weight: 8.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 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 ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 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 206 ASN ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 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 206 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2744 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= 0.185 Angle : 0.873 29.835 75312 Z= 0.387 Chirality : 0.044 0.201 8344 Planarity : 0.005 0.073 9792 Dihedral : 14.221 169.237 7752 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.51 % Favored : 91.37 % Rotamer Outliers : 0.56 % 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: -1.93 (0.10), residues: 6880 helix: -0.10 (0.10), residues: 2664 sheet: -1.67 (0.21), residues: 696 loop : -2.18 (0.11), residues: 3520 *********************** 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 1033 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1001 time to evaluate : 5.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 24 residues processed: 1018 average time/residue: 0.4557 time to fit residues: 835.8024 Evaluate side-chains 988 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 964 time to evaluate : 4.857 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3887 time to fit residues: 24.3191 ------------------------------------------------------------------------------- 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: 0.9990 chunk 627 optimal weight: 0.5980 chunk 572 optimal weight: 1.9990 chunk 610 optimal weight: 2.9990 chunk 367 optimal weight: 5.9990 chunk 266 optimal weight: 0.8980 chunk 479 optimal weight: 1.9990 chunk 187 optimal weight: 0.0770 chunk 551 optimal weight: 0.9980 chunk 577 optimal weight: 0.3980 chunk 608 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** 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 134 GLN ** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** 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** ** N 134 GLN ** 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 134 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2892 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= 0.197 Angle : 0.883 29.841 75312 Z= 0.393 Chirality : 0.044 0.220 8344 Planarity : 0.005 0.073 9792 Dihedral : 14.025 170.853 7752 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.85 % Favored : 91.04 % Rotamer Outliers : 0.44 % 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: -1.97 (0.10), residues: 6880 helix: -0.24 (0.10), residues: 2688 sheet: -1.64 (0.20), residues: 696 loop : -2.13 (0.11), residues: 3496 *********************** 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 1029 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1004 time to evaluate : 4.942 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 outliers start: 25 outliers final: 16 residues processed: 1009 average time/residue: 0.4647 time to fit residues: 833.6531 Evaluate side-chains 987 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 971 time to evaluate : 4.828 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4248 time to fit residues: 18.8292 ------------------------------------------------------------------------------- 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: 1.9990 chunk 645 optimal weight: 0.7980 chunk 394 optimal weight: 0.9980 chunk 306 optimal weight: 1.9990 chunk 448 optimal weight: 0.9990 chunk 677 optimal weight: 0.6980 chunk 623 optimal weight: 0.7980 chunk 539 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 416 optimal weight: 0.3980 chunk 330 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 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 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** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** 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** ** 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** ** I 186 ASN ** 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 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 ASN ** 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: 0.7335 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 55336 Z= 0.224 Angle : 0.899 29.989 75312 Z= 0.403 Chirality : 0.045 0.293 8344 Planarity : 0.005 0.072 9792 Dihedral : 13.715 168.229 7752 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.47 % Favored : 90.41 % Rotamer Outliers : 0.32 % 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: -2.03 (0.10), residues: 6880 helix: -0.34 (0.10), residues: 2704 sheet: -1.69 (0.20), residues: 696 loop : -2.13 (0.11), residues: 3480 ********************** 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 989 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 971 time to evaluate : 5.086 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 outliers start: 18 outliers final: 9 residues processed: 977 average time/residue: 0.4556 time to fit residues: 790.5727 Evaluate side-chains 972 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 963 time to evaluate : 4.862 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3729 time to fit residues: 12.8839 ------------------------------------------------------------------------------- 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: 6.9990 chunk 574 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 497 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 540 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 554 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 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 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** 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** ** I 186 ASN ** 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 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.128140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.106235 restraints weight = 149085.650| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 5.21 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4098 r_free = 0.4098 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4098 r_free = 0.4098 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 55336 Z= 0.227 Angle : 0.913 30.623 75312 Z= 0.409 Chirality : 0.045 0.269 8344 Planarity : 0.005 0.072 9792 Dihedral : 13.407 166.092 7752 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.04 % Favored : 89.84 % Rotamer Outliers : 0.41 % 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: -2.08 (0.10), residues: 6880 helix: -0.36 (0.10), residues: 2712 sheet: -1.75 (0.20), residues: 696 loop : -2.16 (0.11), residues: 3472 =============================================================================== Job complete usr+sys time: 13181.63 seconds wall clock time: 232 minutes 30.92 seconds (13950.92 seconds total)