Starting phenix.real_space_refine on Tue Feb 13 10:50:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/02_2024/7m18_23615_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/02_2024/7m18_23615.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/02_2024/7m18_23615_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/02_2024/7m18_23615_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/02_2024/7m18_23615_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/02_2024/7m18_23615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/02_2024/7m18_23615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/02_2024/7m18_23615_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m18_23615/02_2024/7m18_23615_updated.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.484 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 40 5.49 5 S 360 5.16 5 Cl 8 4.86 5 C 34048 2.51 5 N 9200 2.21 5 O 10408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 123": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D GLU 421": "OE1" <-> "OE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 376": "OE1" <-> "OE2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F GLU 421": "OE1" <-> "OE2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "H GLU 376": "OE1" <-> "OE2" Residue "H GLU 383": "OE1" <-> "OE2" Residue "H GLU 421": "OE1" <-> "OE2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G GLU 429": "OE1" <-> "OE2" Residue "J GLU 123": "OE1" <-> "OE2" Residue "J GLU 205": "OE1" <-> "OE2" Residue "J GLU 376": "OE1" <-> "OE2" Residue "J GLU 383": "OE1" <-> "OE2" Residue "J GLU 421": "OE1" <-> "OE2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "I GLU 429": "OE1" <-> "OE2" Residue "L GLU 123": "OE1" <-> "OE2" Residue "L GLU 205": "OE1" <-> "OE2" Residue "L GLU 376": "OE1" <-> "OE2" Residue "L GLU 383": "OE1" <-> "OE2" Residue "L GLU 421": "OE1" <-> "OE2" Residue "K GLU 183": "OE1" <-> "OE2" Residue "K GLU 429": "OE1" <-> "OE2" Residue "N GLU 123": "OE1" <-> "OE2" Residue "N GLU 205": "OE1" <-> "OE2" Residue "N GLU 376": "OE1" <-> "OE2" Residue "N GLU 383": "OE1" <-> "OE2" Residue "N GLU 421": "OE1" <-> "OE2" Residue "M GLU 183": "OE1" <-> "OE2" Residue "M GLU 429": "OE1" <-> "OE2" Residue "P GLU 123": "OE1" <-> "OE2" Residue "P GLU 205": "OE1" <-> "OE2" Residue "P GLU 376": "OE1" <-> "OE2" Residue "P GLU 383": "OE1" <-> "OE2" Residue "P GLU 421": "OE1" <-> "OE2" Residue "O GLU 183": "OE1" <-> "OE2" Residue "O GLU 429": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 29.04, per 1000 atoms: 0.54 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: 15.95 Conformation dependent library (CDL) restraints added in 10.5 seconds 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 264 helices and 32 sheets defined 42.2% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.59 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: 14.62 Time building geometry restraints manager: 17.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 9080 1.31 - 1.44: 15088 1.44 - 1.57: 30528 1.57 - 1.69: 72 1.69 - 1.82: 568 Bond restraints: 55336 Sorted by residual: bond pdb=" C7 YNP L 501 " pdb=" C8 YNP L 501 " ideal model delta sigma weight residual 1.579 1.319 0.260 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C7 YNP P 501 " pdb=" C8 YNP P 501 " ideal model delta sigma weight residual 1.579 1.319 0.260 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C7 YNP H 501 " pdb=" C8 YNP H 501 " ideal model delta sigma weight residual 1.579 1.319 0.260 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C7 YNP D 501 " pdb=" C8 YNP D 501 " ideal model delta sigma weight residual 1.579 1.319 0.260 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C7 YNP J 501 " pdb=" C8 YNP J 501 " ideal model delta sigma weight residual 1.579 1.319 0.260 2.00e-02 2.50e+03 1.70e+02 ... (remaining 55331 not shown) Histogram of bond angle deviations from ideal: 53.18 - 75.85: 24 75.85 - 98.52: 16 98.52 - 121.18: 61072 121.18 - 143.85: 14176 143.85 - 166.52: 24 Bond angle restraints: 75312 Sorted by residual: angle pdb=" C5 YNP J 501 " pdb=" N2 YNP J 501 " pdb=" C6 YNP J 501 " ideal model delta sigma weight residual 109.47 166.52 -57.05 3.00e+00 1.11e-01 3.62e+02 angle pdb=" C5 YNP N 501 " pdb=" N2 YNP N 501 " pdb=" C6 YNP N 501 " ideal model delta sigma weight residual 109.47 166.52 -57.05 3.00e+00 1.11e-01 3.62e+02 angle pdb=" C5 YNP B 501 " pdb=" N2 YNP B 501 " pdb=" C6 YNP B 501 " ideal model delta sigma weight residual 109.47 166.52 -57.05 3.00e+00 1.11e-01 3.62e+02 angle pdb=" C5 YNP F 501 " pdb=" N2 YNP F 501 " pdb=" C6 YNP F 501 " ideal model delta sigma weight residual 109.47 166.52 -57.05 3.00e+00 1.11e-01 3.62e+02 angle pdb=" C5 YNP L 501 " pdb=" N2 YNP L 501 " pdb=" C6 YNP L 501 " ideal model delta sigma weight residual 109.47 166.51 -57.04 3.00e+00 1.11e-01 3.62e+02 ... (remaining 75307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 32148 34.89 - 69.78: 588 69.78 - 104.66: 96 104.66 - 139.55: 48 139.55 - 174.44: 104 Dihedral angle restraints: 32984 sinusoidal: 13032 harmonic: 19952 Sorted by residual: dihedral pdb=" C8 GTP G 501 " pdb=" C1' GTP G 501 " pdb=" N9 GTP G 501 " pdb=" O4' GTP G 501 " ideal model delta sinusoidal sigma weight residual 104.59 -67.84 172.43 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP O 501 " pdb=" C1' GTP O 501 " pdb=" N9 GTP O 501 " pdb=" O4' GTP O 501 " ideal model delta sinusoidal sigma weight residual 104.59 -67.84 172.43 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -67.84 172.43 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 32981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 7216 0.075 - 0.149: 1008 0.149 - 0.224: 56 0.224 - 0.298: 0 0.298 - 0.373: 8 Chirality restraints: 8288 Sorted by residual: chirality pdb=" CA ALA E 273 " pdb=" N ALA E 273 " pdb=" C ALA E 273 " pdb=" CB ALA E 273 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA ALA M 273 " pdb=" N ALA M 273 " pdb=" C ALA M 273 " pdb=" CB ALA M 273 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA ALA I 273 " pdb=" N ALA I 273 " pdb=" C ALA I 273 " pdb=" CB ALA I 273 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 8285 not shown) Planarity restraints: 9792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 YNP L 501 " 0.203 2.00e-02 2.50e+03 1.76e-01 3.87e+02 pdb=" C4 YNP L 501 " -0.051 2.00e-02 2.50e+03 pdb=" C5 YNP L 501 " 0.049 2.00e-02 2.50e+03 pdb=" N1 YNP L 501 " -0.311 2.00e-02 2.50e+03 pdb=" O1 YNP L 501 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 YNP D 501 " -0.203 2.00e-02 2.50e+03 1.76e-01 3.87e+02 pdb=" C4 YNP D 501 " 0.051 2.00e-02 2.50e+03 pdb=" C5 YNP D 501 " -0.049 2.00e-02 2.50e+03 pdb=" N1 YNP D 501 " 0.311 2.00e-02 2.50e+03 pdb=" O1 YNP D 501 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 YNP H 501 " -0.203 2.00e-02 2.50e+03 1.76e-01 3.87e+02 pdb=" C4 YNP H 501 " 0.051 2.00e-02 2.50e+03 pdb=" C5 YNP H 501 " -0.049 2.00e-02 2.50e+03 pdb=" N1 YNP H 501 " 0.311 2.00e-02 2.50e+03 pdb=" O1 YNP H 501 " -0.110 2.00e-02 2.50e+03 ... (remaining 9789 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 320 2.36 - 3.00: 32096 3.00 - 3.63: 87396 3.63 - 4.27: 123404 4.27 - 4.90: 199712 Nonbonded interactions: 442928 Sorted by model distance: nonbonded pdb=" CE1 HIS K 406 " pdb=" O PRO N 259 " model vdw 1.728 3.260 nonbonded pdb=" CE1 HIS C 406 " pdb=" O PRO F 259 " model vdw 1.728 3.260 nonbonded pdb=" O PRO B 259 " pdb=" CE1 HIS O 406 " model vdw 1.728 3.260 nonbonded pdb=" CE1 HIS G 406 " pdb=" O PRO J 259 " model vdw 1.728 3.260 nonbonded pdb=" CE1 HIS I 406 " pdb=" O PRO L 259 " model vdw 1.728 3.260 ... (remaining 442923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = (chain 'B' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'D' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'F' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'H' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'J' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'L' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'N' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) selection = (chain 'P' and (resid 1 through 152 or resid 154 through 427 or resid 501 throug \ h 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 40.640 Check model and map are aligned: 0.580 Set scattering table: 0.380 Process input model: 115.860 Find NCS groups from input model: 3.370 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.260 55336 Z= 0.484 Angle : 1.332 57.050 75312 Z= 0.591 Chirality : 0.049 0.373 8288 Planarity : 0.007 0.176 9792 Dihedral : 19.798 174.440 20200 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 23.77 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.36 % Favored : 89.29 % Rotamer: Outliers : 0.28 % Allowed : 0.99 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.10), residues: 6880 helix: -0.34 (0.10), residues: 2784 sheet: -1.80 (0.19), residues: 760 loop : -2.83 (0.11), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 21 HIS 0.004 0.001 HIS G 393 PHE 0.012 0.001 PHE E 244 TYR 0.021 0.002 TYR G 24 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1205 time to evaluate : 4.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 SER cc_start: 0.9274 (t) cc_final: 0.8809 (p) REVERT: B 370 ASN cc_start: 0.7967 (t0) cc_final: 0.7737 (t0) REVERT: B 394 PHE cc_start: 0.8060 (m-80) cc_final: 0.7810 (m-80) REVERT: A 108 TYR cc_start: 0.7996 (m-80) cc_final: 0.7784 (m-80) REVERT: A 217 LEU cc_start: 0.8983 (tp) cc_final: 0.8477 (tp) REVERT: A 243 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8337 (mtm-85) REVERT: D 119 VAL cc_start: 0.8007 (t) cc_final: 0.7792 (p) REVERT: D 267 MET cc_start: 0.7710 (ppp) cc_final: 0.7034 (ppp) REVERT: C 36 MET cc_start: 0.7468 (ppp) cc_final: 0.7149 (ppp) REVERT: C 217 LEU cc_start: 0.8836 (tp) cc_final: 0.8306 (tp) REVERT: C 425 MET cc_start: 0.7742 (mmt) cc_final: 0.7407 (mmt) REVERT: F 25 SER cc_start: 0.9273 (t) cc_final: 0.8808 (p) REVERT: F 370 ASN cc_start: 0.7965 (t0) cc_final: 0.7734 (t0) REVERT: F 394 PHE cc_start: 0.8058 (m-80) cc_final: 0.7809 (m-80) REVERT: E 108 TYR cc_start: 0.7996 (m-80) cc_final: 0.7783 (m-80) REVERT: E 217 LEU cc_start: 0.8983 (tp) cc_final: 0.8476 (tp) REVERT: E 243 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8337 (mtm-85) REVERT: H 119 VAL cc_start: 0.8007 (t) cc_final: 0.7792 (p) REVERT: H 267 MET cc_start: 0.7710 (ppp) cc_final: 0.7034 (ppp) REVERT: G 36 MET cc_start: 0.7468 (ppp) cc_final: 0.7149 (ppp) REVERT: G 217 LEU cc_start: 0.8838 (tp) cc_final: 0.8307 (tp) REVERT: G 425 MET cc_start: 0.7744 (mmt) cc_final: 0.7407 (mmt) REVERT: J 25 SER cc_start: 0.9272 (t) cc_final: 0.8807 (p) REVERT: J 370 ASN cc_start: 0.7963 (t0) cc_final: 0.7734 (t0) REVERT: J 394 PHE cc_start: 0.8057 (m-80) cc_final: 0.7807 (m-80) REVERT: I 108 TYR cc_start: 0.7998 (m-80) cc_final: 0.7782 (m-80) REVERT: I 217 LEU cc_start: 0.8983 (tp) cc_final: 0.8477 (tp) REVERT: I 243 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8338 (mtm-85) REVERT: L 119 VAL cc_start: 0.8009 (t) cc_final: 0.7793 (p) REVERT: L 267 MET cc_start: 0.7706 (ppp) cc_final: 0.7032 (ppp) REVERT: K 36 MET cc_start: 0.7469 (ppp) cc_final: 0.7150 (ppp) REVERT: K 217 LEU cc_start: 0.8838 (tp) cc_final: 0.8308 (tp) REVERT: K 425 MET cc_start: 0.7743 (mmt) cc_final: 0.7406 (mmt) REVERT: N 25 SER cc_start: 0.9274 (t) cc_final: 0.8808 (p) REVERT: N 370 ASN cc_start: 0.7963 (t0) cc_final: 0.7733 (t0) REVERT: N 394 PHE cc_start: 0.8058 (m-80) cc_final: 0.7807 (m-80) REVERT: M 108 TYR cc_start: 0.7996 (m-80) cc_final: 0.7782 (m-80) REVERT: M 217 LEU cc_start: 0.8981 (tp) cc_final: 0.8474 (tp) REVERT: M 243 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8338 (mtm-85) REVERT: P 119 VAL cc_start: 0.8009 (t) cc_final: 0.7793 (p) REVERT: P 267 MET cc_start: 0.7706 (ppp) cc_final: 0.7028 (ppp) REVERT: O 36 MET cc_start: 0.7469 (ppp) cc_final: 0.7149 (ppp) REVERT: O 217 LEU cc_start: 0.8836 (tp) cc_final: 0.8306 (tp) REVERT: O 425 MET cc_start: 0.7743 (mmt) cc_final: 0.7406 (mmt) outliers start: 16 outliers final: 0 residues processed: 1221 average time/residue: 0.4494 time to fit residues: 967.2582 Evaluate side-chains 952 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 952 time to evaluate : 4.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 574 optimal weight: 0.6980 chunk 515 optimal weight: 8.9990 chunk 285 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 347 optimal weight: 0.0370 chunk 275 optimal weight: 0.7980 chunk 532 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 324 optimal weight: 0.0870 chunk 396 optimal weight: 3.9990 chunk 617 optimal weight: 1.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN K 256 GLN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 256 GLN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 99 ASN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 206 ASN O 256 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1210 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= 0.215 Angle : 0.806 16.409 75312 Z= 0.382 Chirality : 0.045 0.178 8288 Planarity : 0.005 0.057 9792 Dihedral : 21.543 173.275 8128 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.78 % Favored : 90.10 % Rotamer: Outliers : 1.48 % Allowed : 12.22 % Favored : 86.30 % 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: -0.18 (0.10), residues: 2736 sheet: -1.95 (0.18), residues: 808 loop : -2.58 (0.11), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 407 HIS 0.012 0.001 HIS E 28 PHE 0.027 0.002 PHE G 296 TYR 0.020 0.002 TYR P 106 ARG 0.006 0.000 ARG O 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1044 time to evaluate : 4.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 267 MET cc_start: 0.7935 (ppp) cc_final: 0.7626 (ppp) REVERT: B 370 ASN cc_start: 0.7983 (t0) cc_final: 0.7674 (t0) REVERT: A 47 ASP cc_start: 0.7823 (t0) cc_final: 0.7607 (t0) REVERT: A 76 ASP cc_start: 0.7826 (t0) cc_final: 0.7267 (p0) REVERT: A 217 LEU cc_start: 0.8891 (tp) cc_final: 0.8354 (tp) REVERT: D 119 VAL cc_start: 0.7933 (t) cc_final: 0.7714 (p) REVERT: C 76 ASP cc_start: 0.7636 (t0) cc_final: 0.7102 (p0) REVERT: C 217 LEU cc_start: 0.8771 (tp) cc_final: 0.8205 (tp) REVERT: C 413 MET cc_start: 0.8038 (mmm) cc_final: 0.7809 (mmm) REVERT: F 267 MET cc_start: 0.7937 (ppp) cc_final: 0.7629 (ppp) REVERT: F 370 ASN cc_start: 0.7982 (t0) cc_final: 0.7671 (t0) REVERT: E 47 ASP cc_start: 0.7825 (t0) cc_final: 0.7609 (t0) REVERT: E 76 ASP cc_start: 0.7828 (t0) cc_final: 0.7269 (p0) REVERT: E 217 LEU cc_start: 0.8891 (tp) cc_final: 0.8355 (tp) REVERT: H 119 VAL cc_start: 0.7934 (t) cc_final: 0.7715 (p) REVERT: G 76 ASP cc_start: 0.7637 (t0) cc_final: 0.7103 (p0) REVERT: G 217 LEU cc_start: 0.8771 (tp) cc_final: 0.8204 (tp) REVERT: G 413 MET cc_start: 0.8038 (mmm) cc_final: 0.7810 (mmm) REVERT: G 425 MET cc_start: 0.7627 (mmt) cc_final: 0.7426 (mmt) REVERT: J 267 MET cc_start: 0.7936 (ppp) cc_final: 0.7627 (ppp) REVERT: J 370 ASN cc_start: 0.7986 (t0) cc_final: 0.7675 (t0) REVERT: I 47 ASP cc_start: 0.7823 (t0) cc_final: 0.7607 (t0) REVERT: I 76 ASP cc_start: 0.7825 (t0) cc_final: 0.7268 (p0) REVERT: I 217 LEU cc_start: 0.8892 (tp) cc_final: 0.8355 (tp) REVERT: L 119 VAL cc_start: 0.7933 (t) cc_final: 0.7715 (p) REVERT: K 76 ASP cc_start: 0.7637 (t0) cc_final: 0.7103 (p0) REVERT: K 217 LEU cc_start: 0.8770 (tp) cc_final: 0.8204 (tp) REVERT: K 413 MET cc_start: 0.8039 (mmm) cc_final: 0.7811 (mmm) REVERT: K 425 MET cc_start: 0.7628 (mmt) cc_final: 0.7427 (mmt) REVERT: N 267 MET cc_start: 0.7935 (ppp) cc_final: 0.7628 (ppp) REVERT: N 370 ASN cc_start: 0.7983 (t0) cc_final: 0.7674 (t0) REVERT: M 47 ASP cc_start: 0.7824 (t0) cc_final: 0.7606 (t0) REVERT: M 76 ASP cc_start: 0.7826 (t0) cc_final: 0.7268 (p0) REVERT: M 217 LEU cc_start: 0.8891 (tp) cc_final: 0.8354 (tp) REVERT: P 119 VAL cc_start: 0.7932 (t) cc_final: 0.7713 (p) REVERT: O 76 ASP cc_start: 0.7636 (t0) cc_final: 0.7103 (p0) REVERT: O 217 LEU cc_start: 0.8769 (tp) cc_final: 0.8203 (tp) REVERT: O 413 MET cc_start: 0.8038 (mmm) cc_final: 0.7810 (mmm) outliers start: 84 outliers final: 44 residues processed: 1064 average time/residue: 0.4606 time to fit residues: 864.9657 Evaluate side-chains 988 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 944 time to evaluate : 4.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 410 GLU Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 189 ILE Chi-restraints excluded: chain L residue 410 GLU Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain P residue 178 THR Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain P residue 410 GLU Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 253 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 343 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 513 optimal weight: 4.9990 chunk 420 optimal weight: 0.0050 chunk 170 optimal weight: 5.9990 chunk 618 optimal weight: 0.8980 chunk 668 optimal weight: 0.7980 chunk 550 optimal weight: 2.9990 chunk 613 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 496 optimal weight: 0.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 256 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 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 99 ASN ** 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 ** 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 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN J 227 HIS ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 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** ** 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 ** 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 55336 Z= 0.252 Angle : 0.769 12.456 75312 Z= 0.371 Chirality : 0.045 0.220 8288 Planarity : 0.005 0.056 9792 Dihedral : 21.377 179.563 8128 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.81 % Favored : 89.07 % Rotamer: Outliers : 1.76 % Allowed : 16.48 % Favored : 81.75 % 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: -2.34 (0.10), residues: 6880 helix: -0.36 (0.10), residues: 2768 sheet: -1.88 (0.19), residues: 752 loop : -2.56 (0.11), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 407 HIS 0.007 0.001 HIS A 28 PHE 0.013 0.001 PHE C 296 TYR 0.018 0.002 TYR P 106 ARG 0.009 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 992 time to evaluate : 4.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 GLN cc_start: 0.7454 (pt0) cc_final: 0.7224 (pt0) REVERT: B 267 MET cc_start: 0.7959 (ppp) cc_final: 0.7282 (ppp) REVERT: B 323 MET cc_start: 0.8058 (mtp) cc_final: 0.7807 (tmm) REVERT: B 370 ASN cc_start: 0.7958 (t0) cc_final: 0.7716 (t0) REVERT: A 47 ASP cc_start: 0.7749 (t0) cc_final: 0.7504 (t0) REVERT: A 67 PHE cc_start: 0.8344 (m-80) cc_final: 0.8069 (m-80) REVERT: A 76 ASP cc_start: 0.7836 (t0) cc_final: 0.7155 (p0) REVERT: A 217 LEU cc_start: 0.8888 (tp) cc_final: 0.8294 (tp) REVERT: D 119 VAL cc_start: 0.7939 (t) cc_final: 0.7724 (p) REVERT: D 267 MET cc_start: 0.8020 (ppp) cc_final: 0.7249 (ppp) REVERT: D 330 MET cc_start: 0.8232 (mmp) cc_final: 0.7981 (mmp) REVERT: C 76 ASP cc_start: 0.7706 (t0) cc_final: 0.7432 (t0) REVERT: C 217 LEU cc_start: 0.8756 (tp) cc_final: 0.8163 (tp) REVERT: C 413 MET cc_start: 0.8193 (mmm) cc_final: 0.7932 (mmm) REVERT: F 191 GLN cc_start: 0.7454 (pt0) cc_final: 0.7223 (pt0) REVERT: F 267 MET cc_start: 0.7963 (ppp) cc_final: 0.7284 (ppp) REVERT: F 323 MET cc_start: 0.8063 (mtp) cc_final: 0.7807 (tmm) REVERT: F 370 ASN cc_start: 0.7959 (t0) cc_final: 0.7715 (t0) REVERT: E 47 ASP cc_start: 0.7749 (t0) cc_final: 0.7505 (t0) REVERT: E 67 PHE cc_start: 0.8345 (m-80) cc_final: 0.8070 (m-80) REVERT: E 76 ASP cc_start: 0.7835 (t0) cc_final: 0.7154 (p0) REVERT: E 217 LEU cc_start: 0.8888 (tp) cc_final: 0.8294 (tp) REVERT: H 119 VAL cc_start: 0.7939 (t) cc_final: 0.7725 (p) REVERT: H 267 MET cc_start: 0.8019 (ppp) cc_final: 0.7251 (ppp) REVERT: H 330 MET cc_start: 0.8232 (mmp) cc_final: 0.7981 (mmp) REVERT: G 76 ASP cc_start: 0.7705 (t0) cc_final: 0.7432 (t0) REVERT: G 217 LEU cc_start: 0.8760 (tp) cc_final: 0.8166 (tp) REVERT: G 413 MET cc_start: 0.8189 (mmm) cc_final: 0.7928 (mmm) REVERT: J 191 GLN cc_start: 0.7456 (pt0) cc_final: 0.7223 (pt0) REVERT: J 267 MET cc_start: 0.7960 (ppp) cc_final: 0.7284 (ppp) REVERT: J 323 MET cc_start: 0.8060 (mtp) cc_final: 0.7807 (tmm) REVERT: J 370 ASN cc_start: 0.7959 (t0) cc_final: 0.7715 (t0) REVERT: I 47 ASP cc_start: 0.7749 (t0) cc_final: 0.7503 (t0) REVERT: I 67 PHE cc_start: 0.8345 (m-80) cc_final: 0.8069 (m-80) REVERT: I 76 ASP cc_start: 0.7833 (t0) cc_final: 0.7153 (p0) REVERT: I 217 LEU cc_start: 0.8888 (tp) cc_final: 0.8294 (tp) REVERT: L 119 VAL cc_start: 0.7940 (t) cc_final: 0.7726 (p) REVERT: L 267 MET cc_start: 0.8017 (ppp) cc_final: 0.7247 (ppp) REVERT: L 330 MET cc_start: 0.8233 (mmp) cc_final: 0.7980 (mmp) REVERT: K 76 ASP cc_start: 0.7705 (t0) cc_final: 0.7432 (t0) REVERT: K 217 LEU cc_start: 0.8757 (tp) cc_final: 0.8164 (tp) REVERT: K 413 MET cc_start: 0.8188 (mmm) cc_final: 0.7929 (mmm) REVERT: N 191 GLN cc_start: 0.7455 (pt0) cc_final: 0.7224 (pt0) REVERT: N 267 MET cc_start: 0.7961 (ppp) cc_final: 0.7283 (ppp) REVERT: N 323 MET cc_start: 0.8060 (mtp) cc_final: 0.7807 (tmm) REVERT: N 370 ASN cc_start: 0.7962 (t0) cc_final: 0.7718 (t0) REVERT: M 47 ASP cc_start: 0.7748 (t0) cc_final: 0.7504 (t0) REVERT: M 67 PHE cc_start: 0.8345 (m-80) cc_final: 0.8069 (m-80) REVERT: M 76 ASP cc_start: 0.7834 (t0) cc_final: 0.7154 (p0) REVERT: M 217 LEU cc_start: 0.8890 (tp) cc_final: 0.8295 (tp) REVERT: P 119 VAL cc_start: 0.7939 (t) cc_final: 0.7725 (p) REVERT: P 267 MET cc_start: 0.8017 (ppp) cc_final: 0.7248 (ppp) REVERT: P 330 MET cc_start: 0.8234 (mmp) cc_final: 0.7981 (mmp) REVERT: O 76 ASP cc_start: 0.7704 (t0) cc_final: 0.7430 (t0) REVERT: O 217 LEU cc_start: 0.8757 (tp) cc_final: 0.8164 (tp) REVERT: O 413 MET cc_start: 0.8191 (mmm) cc_final: 0.7932 (mmm) outliers start: 100 outliers final: 64 residues processed: 1016 average time/residue: 0.4472 time to fit residues: 805.8818 Evaluate side-chains 1000 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 936 time to evaluate : 4.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 321 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 321 MET Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain P residue 178 THR Chi-restraints excluded: chain P residue 194 GLU Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 321 MET Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 253 THR Rotamers are restrained with sigma=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: 3.9990 chunk 68 optimal weight: 0.7980 chunk 295 optimal weight: 1.9990 chunk 415 optimal weight: 5.9990 chunk 620 optimal weight: 2.9990 chunk 657 optimal weight: 3.9990 chunk 324 optimal weight: 0.6980 chunk 588 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 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 ** 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** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 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 28 HIS ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 ASN ** I 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 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 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 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 ** M 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 258 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 28 HIS ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 55336 Z= 0.303 Angle : 0.775 11.139 75312 Z= 0.379 Chirality : 0.046 0.180 8288 Planarity : 0.005 0.056 9792 Dihedral : 21.600 178.125 8128 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.61 % Favored : 88.27 % Rotamer: Outliers : 2.12 % Allowed : 18.09 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.10), residues: 6880 helix: -0.44 (0.10), residues: 2752 sheet: -1.95 (0.19), residues: 752 loop : -2.55 (0.11), residues: 3376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 407 HIS 0.006 0.001 HIS I 28 PHE 0.024 0.002 PHE O 296 TYR 0.021 0.002 TYR A 108 ARG 0.004 0.000 ARG F 156 *********************** 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 1103 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 983 time to evaluate : 4.625 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: B 267 MET cc_start: 0.8009 (ppp) cc_final: 0.7330 (ppp) REVERT: B 370 ASN cc_start: 0.8039 (t0) cc_final: 0.7810 (t0) REVERT: A 47 ASP cc_start: 0.7825 (t0) cc_final: 0.7602 (t0) REVERT: A 67 PHE cc_start: 0.8344 (m-80) cc_final: 0.8070 (m-80) REVERT: A 76 ASP cc_start: 0.7868 (t0) cc_final: 0.7591 (t0) REVERT: A 203 MET cc_start: 0.7306 (ptt) cc_final: 0.7095 (ptp) REVERT: A 217 LEU cc_start: 0.8936 (tp) cc_final: 0.8309 (tp) REVERT: D 267 MET cc_start: 0.7996 (ppp) cc_final: 0.7506 (ppp) REVERT: D 281 TYR cc_start: 0.3597 (OUTLIER) cc_final: 0.2062 (m-80) REVERT: D 323 MET cc_start: 0.8037 (tmm) cc_final: 0.7770 (mtp) REVERT: D 330 MET cc_start: 0.8300 (mmp) cc_final: 0.8087 (mmp) REVERT: C 76 ASP cc_start: 0.7677 (t0) cc_final: 0.7390 (t0) REVERT: C 217 LEU cc_start: 0.8814 (tp) cc_final: 0.8180 (tp) REVERT: C 413 MET cc_start: 0.8152 (mmm) cc_final: 0.7921 (mmm) REVERT: F 267 MET cc_start: 0.8011 (ppp) cc_final: 0.7333 (ppp) REVERT: F 370 ASN cc_start: 0.8038 (t0) cc_final: 0.7809 (t0) REVERT: E 47 ASP cc_start: 0.7827 (t0) cc_final: 0.7604 (t0) REVERT: E 67 PHE cc_start: 0.8344 (m-80) cc_final: 0.8070 (m-80) REVERT: E 76 ASP cc_start: 0.7868 (t0) cc_final: 0.7591 (t0) REVERT: E 203 MET cc_start: 0.7305 (ptt) cc_final: 0.7093 (ptp) REVERT: E 217 LEU cc_start: 0.8937 (tp) cc_final: 0.8308 (tp) REVERT: H 267 MET cc_start: 0.7997 (ppp) cc_final: 0.7505 (ppp) REVERT: H 281 TYR cc_start: 0.3598 (OUTLIER) cc_final: 0.2063 (m-80) REVERT: H 323 MET cc_start: 0.8037 (tmm) cc_final: 0.7771 (mtp) REVERT: H 330 MET cc_start: 0.8298 (mmp) cc_final: 0.8086 (mmp) REVERT: G 76 ASP cc_start: 0.7676 (t0) cc_final: 0.7389 (t0) REVERT: G 217 LEU cc_start: 0.8815 (tp) cc_final: 0.8180 (tp) REVERT: G 413 MET cc_start: 0.8146 (mmm) cc_final: 0.7918 (mmm) REVERT: J 267 MET cc_start: 0.8010 (ppp) cc_final: 0.7335 (ppp) REVERT: J 370 ASN cc_start: 0.8041 (t0) cc_final: 0.7809 (t0) REVERT: I 47 ASP cc_start: 0.7826 (t0) cc_final: 0.7603 (t0) REVERT: I 67 PHE cc_start: 0.8344 (m-80) cc_final: 0.8071 (m-80) REVERT: I 76 ASP cc_start: 0.7869 (t0) cc_final: 0.7591 (t0) REVERT: I 203 MET cc_start: 0.7307 (ptt) cc_final: 0.7093 (ptp) REVERT: I 217 LEU cc_start: 0.8937 (tp) cc_final: 0.8308 (tp) REVERT: L 267 MET cc_start: 0.7994 (ppp) cc_final: 0.7504 (ppp) REVERT: L 281 TYR cc_start: 0.3595 (OUTLIER) cc_final: 0.2060 (m-80) REVERT: L 323 MET cc_start: 0.8037 (tmm) cc_final: 0.7770 (mtp) REVERT: L 330 MET cc_start: 0.8298 (mmp) cc_final: 0.8085 (mmp) REVERT: K 76 ASP cc_start: 0.7674 (t0) cc_final: 0.7387 (t0) REVERT: K 217 LEU cc_start: 0.8814 (tp) cc_final: 0.8179 (tp) REVERT: K 413 MET cc_start: 0.8150 (mmm) cc_final: 0.7918 (mmm) REVERT: N 267 MET cc_start: 0.8010 (ppp) cc_final: 0.7333 (ppp) REVERT: N 370 ASN cc_start: 0.8041 (t0) cc_final: 0.7811 (t0) REVERT: M 47 ASP cc_start: 0.7824 (t0) cc_final: 0.7602 (t0) REVERT: M 67 PHE cc_start: 0.8343 (m-80) cc_final: 0.8069 (m-80) REVERT: M 76 ASP cc_start: 0.7867 (t0) cc_final: 0.7589 (t0) REVERT: M 203 MET cc_start: 0.7307 (ptt) cc_final: 0.7096 (ptp) REVERT: M 217 LEU cc_start: 0.8938 (tp) cc_final: 0.8310 (tp) REVERT: P 267 MET cc_start: 0.7992 (ppp) cc_final: 0.7502 (ppp) REVERT: P 281 TYR cc_start: 0.3597 (OUTLIER) cc_final: 0.2062 (m-80) REVERT: P 323 MET cc_start: 0.8036 (tmm) cc_final: 0.7770 (mtp) REVERT: P 330 MET cc_start: 0.8300 (mmp) cc_final: 0.8086 (mmp) REVERT: O 76 ASP cc_start: 0.7677 (t0) cc_final: 0.7390 (t0) REVERT: O 217 LEU cc_start: 0.8815 (tp) cc_final: 0.8181 (tp) REVERT: O 413 MET cc_start: 0.8154 (mmm) cc_final: 0.7924 (mmm) outliers start: 120 outliers final: 88 residues processed: 1039 average time/residue: 0.4755 time to fit residues: 878.5457 Evaluate side-chains 996 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 904 time to evaluate : 4.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 321 MET Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain J residue 194 GLU Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 321 MET Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain N residue 194 GLU Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain N residue 386 THR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain P residue 178 THR Chi-restraints excluded: chain P residue 194 GLU Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 321 MET Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 157 LEU Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 253 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 547 optimal weight: 0.0870 chunk 373 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 489 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 560 optimal weight: 0.7980 chunk 454 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 335 optimal weight: 0.0370 chunk 589 optimal weight: 0.8980 chunk 165 optimal weight: 0.0470 overall best weight: 0.3734 ------------------------------------------------------------------------------- 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 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN A 258 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN C 249 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN F 131 GLN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN E 258 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN 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** I 249 ASN I 258 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 227 HIS ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 HIS ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 ASN ** K 258 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** M 206 ASN M 249 ASN M 258 ASN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 227 HIS ** 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** O 258 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2120 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= 0.184 Angle : 0.713 11.945 75312 Z= 0.347 Chirality : 0.045 0.235 8288 Planarity : 0.004 0.053 9792 Dihedral : 21.432 179.300 8128 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.51 % Favored : 91.37 % Rotamer: Outliers : 2.10 % Allowed : 20.19 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.10), residues: 6880 helix: -0.17 (0.10), residues: 2664 sheet: -1.62 (0.19), residues: 808 loop : -2.44 (0.11), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 21 HIS 0.004 0.001 HIS I 28 PHE 0.019 0.001 PHE O 296 TYR 0.013 0.001 TYR A 108 ARG 0.003 0.000 ARG D 156 *********************** 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 1163 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1044 time to evaluate : 4.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASN cc_start: 0.8706 (m-40) cc_final: 0.8506 (m110) REVERT: B 25 SER cc_start: 0.8939 (t) cc_final: 0.8336 (p) REVERT: B 190 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.8016 (t70) REVERT: B 267 MET cc_start: 0.7929 (ppp) cc_final: 0.7652 (ppp) REVERT: B 370 ASN cc_start: 0.8085 (t0) cc_final: 0.7806 (t0) REVERT: A 36 MET cc_start: 0.8006 (ppp) cc_final: 0.7678 (ppp) REVERT: A 47 ASP cc_start: 0.7799 (t0) cc_final: 0.7597 (t0) REVERT: A 76 ASP cc_start: 0.7863 (t0) cc_final: 0.7650 (t0) REVERT: A 217 LEU cc_start: 0.8870 (tp) cc_final: 0.8230 (tp) REVERT: A 338 LYS cc_start: 0.7816 (mmtt) cc_final: 0.7166 (tmtt) REVERT: D 14 ASN cc_start: 0.8278 (m-40) cc_final: 0.7769 (m110) REVERT: D 267 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7396 (ppp) REVERT: D 281 TYR cc_start: 0.3695 (OUTLIER) cc_final: 0.2237 (m-80) REVERT: D 330 MET cc_start: 0.8382 (mmp) cc_final: 0.8176 (mmp) REVERT: C 217 LEU cc_start: 0.8798 (tp) cc_final: 0.8136 (tp) REVERT: C 413 MET cc_start: 0.8002 (mmm) cc_final: 0.7708 (mmm) REVERT: F 14 ASN cc_start: 0.8707 (m-40) cc_final: 0.8506 (m110) REVERT: F 25 SER cc_start: 0.8939 (t) cc_final: 0.8336 (p) REVERT: F 190 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.8019 (t70) REVERT: F 267 MET cc_start: 0.7928 (ppp) cc_final: 0.7653 (ppp) REVERT: F 370 ASN cc_start: 0.8085 (t0) cc_final: 0.7805 (t0) REVERT: E 36 MET cc_start: 0.8005 (ppp) cc_final: 0.7678 (ppp) REVERT: E 47 ASP cc_start: 0.7800 (t0) cc_final: 0.7597 (t0) REVERT: E 76 ASP cc_start: 0.7862 (t0) cc_final: 0.7650 (t0) REVERT: E 217 LEU cc_start: 0.8871 (tp) cc_final: 0.8230 (tp) REVERT: E 338 LYS cc_start: 0.7815 (mmtt) cc_final: 0.7166 (tmtt) REVERT: H 14 ASN cc_start: 0.8278 (m-40) cc_final: 0.7770 (m110) REVERT: H 267 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7420 (ppp) REVERT: H 281 TYR cc_start: 0.3694 (OUTLIER) cc_final: 0.2237 (m-80) REVERT: H 330 MET cc_start: 0.8381 (mmp) cc_final: 0.8176 (mmp) REVERT: G 217 LEU cc_start: 0.8800 (tp) cc_final: 0.8138 (tp) REVERT: G 413 MET cc_start: 0.8001 (mmm) cc_final: 0.7707 (mmm) REVERT: J 14 ASN cc_start: 0.8708 (m-40) cc_final: 0.8507 (m110) REVERT: J 25 SER cc_start: 0.8938 (t) cc_final: 0.8335 (p) REVERT: J 190 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.8018 (t70) REVERT: J 267 MET cc_start: 0.7926 (ppp) cc_final: 0.7650 (ppp) REVERT: J 370 ASN cc_start: 0.8085 (t0) cc_final: 0.7805 (t0) REVERT: I 36 MET cc_start: 0.8004 (ppp) cc_final: 0.7677 (ppp) REVERT: I 47 ASP cc_start: 0.7797 (t0) cc_final: 0.7596 (t0) REVERT: I 76 ASP cc_start: 0.7863 (t0) cc_final: 0.7651 (t0) REVERT: I 217 LEU cc_start: 0.8871 (tp) cc_final: 0.8230 (tp) REVERT: I 338 LYS cc_start: 0.7816 (mmtt) cc_final: 0.7189 (tmtt) REVERT: L 14 ASN cc_start: 0.8275 (m-40) cc_final: 0.7765 (m110) REVERT: L 267 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7396 (ppp) REVERT: L 281 TYR cc_start: 0.3694 (OUTLIER) cc_final: 0.2236 (m-80) REVERT: L 330 MET cc_start: 0.8381 (mmp) cc_final: 0.8175 (mmp) REVERT: K 217 LEU cc_start: 0.8798 (tp) cc_final: 0.8136 (tp) REVERT: K 413 MET cc_start: 0.8002 (mmm) cc_final: 0.7707 (mmm) REVERT: N 14 ASN cc_start: 0.8708 (m-40) cc_final: 0.8507 (m110) REVERT: N 25 SER cc_start: 0.8940 (t) cc_final: 0.8337 (p) REVERT: N 190 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.8018 (t70) REVERT: N 267 MET cc_start: 0.7927 (ppp) cc_final: 0.7651 (ppp) REVERT: N 370 ASN cc_start: 0.8084 (t0) cc_final: 0.7806 (t0) REVERT: M 36 MET cc_start: 0.8004 (ppp) cc_final: 0.7675 (ppp) REVERT: M 47 ASP cc_start: 0.7799 (t0) cc_final: 0.7596 (t0) REVERT: M 76 ASP cc_start: 0.7863 (t0) cc_final: 0.7651 (t0) REVERT: M 217 LEU cc_start: 0.8870 (tp) cc_final: 0.8229 (tp) REVERT: M 338 LYS cc_start: 0.7815 (mmtt) cc_final: 0.7189 (tmtt) REVERT: P 14 ASN cc_start: 0.8274 (m-40) cc_final: 0.7764 (m110) REVERT: P 267 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7393 (ppp) REVERT: P 281 TYR cc_start: 0.3694 (OUTLIER) cc_final: 0.2237 (m-80) REVERT: P 330 MET cc_start: 0.8382 (mmp) cc_final: 0.8177 (mmp) REVERT: O 217 LEU cc_start: 0.8799 (tp) cc_final: 0.8137 (tp) REVERT: O 413 MET cc_start: 0.8001 (mmm) cc_final: 0.7706 (mmm) outliers start: 119 outliers final: 73 residues processed: 1104 average time/residue: 0.5005 time to fit residues: 984.9882 Evaluate side-chains 1053 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 968 time to evaluate : 4.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 321 MET Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 190 HIS Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 318 LEU Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 190 HIS Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 321 MET Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 190 HIS Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain P residue 178 THR Chi-restraints excluded: chain P residue 190 HIS Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 267 MET Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 321 MET Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 227 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 221 optimal weight: 0.0970 chunk 591 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 385 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 657 optimal weight: 2.9990 chunk 546 optimal weight: 3.9990 chunk 304 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 345 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 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 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 206 ASN ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 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 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 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** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 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 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 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 55336 Z= 0.279 Angle : 0.757 10.173 75312 Z= 0.372 Chirality : 0.046 0.192 8288 Planarity : 0.005 0.054 9792 Dihedral : 21.636 179.851 8128 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.70 % Favored : 89.19 % Rotamer: Outliers : 2.34 % Allowed : 21.17 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.10), residues: 6880 helix: -0.26 (0.10), residues: 2680 sheet: -1.72 (0.18), residues: 808 loop : -2.37 (0.11), residues: 3392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 407 HIS 0.006 0.001 HIS F 190 PHE 0.022 0.002 PHE O 296 TYR 0.015 0.002 TYR N 106 ARG 0.006 0.000 ARG K 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 951 time to evaluate : 4.465 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: B 14 ASN cc_start: 0.8672 (m-40) cc_final: 0.8444 (m110) REVERT: B 150 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8726 (tt) REVERT: B 267 MET cc_start: 0.8006 (ppp) cc_final: 0.7039 (ppp) REVERT: B 370 ASN cc_start: 0.8049 (t0) cc_final: 0.7812 (t0) REVERT: B 388 MET cc_start: 0.8298 (tmm) cc_final: 0.7845 (tmm) REVERT: A 36 MET cc_start: 0.8096 (ppp) cc_final: 0.7573 (ppp) REVERT: A 47 ASP cc_start: 0.7886 (t0) cc_final: 0.7645 (t0) REVERT: A 76 ASP cc_start: 0.7929 (t0) cc_final: 0.7654 (t0) REVERT: A 244 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.7082 (m-10) REVERT: A 338 LYS cc_start: 0.7877 (mmtt) cc_final: 0.7289 (tmtt) REVERT: D 267 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7722 (ppp) REVERT: D 281 TYR cc_start: 0.3647 (OUTLIER) cc_final: 0.2115 (m-80) REVERT: C 207 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8856 (pm20) REVERT: C 318 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8112 (tt) REVERT: C 413 MET cc_start: 0.8244 (mmm) cc_final: 0.7980 (mmm) REVERT: F 14 ASN cc_start: 0.8672 (m-40) cc_final: 0.8445 (m110) REVERT: F 150 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8726 (tt) REVERT: F 267 MET cc_start: 0.8005 (ppp) cc_final: 0.7039 (ppp) REVERT: F 370 ASN cc_start: 0.8049 (t0) cc_final: 0.7811 (t0) REVERT: F 388 MET cc_start: 0.8300 (tmm) cc_final: 0.7847 (tmm) REVERT: E 36 MET cc_start: 0.8093 (ppp) cc_final: 0.7570 (ppp) REVERT: E 47 ASP cc_start: 0.7888 (t0) cc_final: 0.7647 (t0) REVERT: E 76 ASP cc_start: 0.7927 (t0) cc_final: 0.7651 (t0) REVERT: E 244 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.7083 (m-10) REVERT: E 338 LYS cc_start: 0.7877 (mmtt) cc_final: 0.7289 (tmtt) REVERT: H 267 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7716 (ppp) REVERT: H 281 TYR cc_start: 0.3648 (OUTLIER) cc_final: 0.2116 (m-80) REVERT: G 318 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8110 (tt) REVERT: G 413 MET cc_start: 0.8244 (mmm) cc_final: 0.7979 (mmm) REVERT: J 14 ASN cc_start: 0.8671 (m-40) cc_final: 0.8444 (m110) REVERT: J 150 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8725 (tt) REVERT: J 267 MET cc_start: 0.8007 (ppp) cc_final: 0.7041 (ppp) REVERT: J 370 ASN cc_start: 0.8052 (t0) cc_final: 0.7814 (t0) REVERT: J 388 MET cc_start: 0.8298 (tmm) cc_final: 0.7845 (tmm) REVERT: I 36 MET cc_start: 0.8091 (ppp) cc_final: 0.7569 (ppp) REVERT: I 47 ASP cc_start: 0.7885 (t0) cc_final: 0.7644 (t0) REVERT: I 76 ASP cc_start: 0.7926 (t0) cc_final: 0.7651 (t0) REVERT: I 244 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.7080 (m-10) REVERT: I 338 LYS cc_start: 0.7877 (mmtt) cc_final: 0.7289 (tmtt) REVERT: L 267 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7723 (ppp) REVERT: L 281 TYR cc_start: 0.3647 (OUTLIER) cc_final: 0.2116 (m-80) REVERT: K 318 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8110 (tt) REVERT: K 413 MET cc_start: 0.8243 (mmm) cc_final: 0.7981 (mmm) REVERT: N 14 ASN cc_start: 0.8672 (m-40) cc_final: 0.8445 (m110) REVERT: N 150 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8723 (tt) REVERT: N 267 MET cc_start: 0.8002 (ppp) cc_final: 0.7038 (ppp) REVERT: N 370 ASN cc_start: 0.8051 (t0) cc_final: 0.7814 (t0) REVERT: N 388 MET cc_start: 0.8298 (tmm) cc_final: 0.7845 (tmm) REVERT: M 36 MET cc_start: 0.8094 (ppp) cc_final: 0.7571 (ppp) REVERT: M 47 ASP cc_start: 0.7882 (t0) cc_final: 0.7643 (t0) REVERT: M 76 ASP cc_start: 0.7928 (t0) cc_final: 0.7653 (t0) REVERT: M 244 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.7082 (m-10) REVERT: M 338 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7290 (tmtt) REVERT: P 267 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7722 (ppp) REVERT: P 281 TYR cc_start: 0.3646 (OUTLIER) cc_final: 0.2115 (m-80) REVERT: O 318 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8112 (tt) REVERT: O 413 MET cc_start: 0.8247 (mmm) cc_final: 0.7981 (mmm) outliers start: 133 outliers final: 77 residues processed: 1023 average time/residue: 0.4470 time to fit residues: 807.7013 Evaluate side-chains 1004 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 906 time to evaluate : 4.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 191 GLN Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 321 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 190 HIS Chi-restraints excluded: chain J residue 191 GLN Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 244 PHE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 190 HIS Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 321 MET Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 318 LEU Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 190 HIS Chi-restraints excluded: chain N residue 191 GLN Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 244 PHE Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain P residue 178 THR Chi-restraints excluded: chain P residue 190 HIS Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 267 MET Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 321 MET Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 634 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 374 optimal weight: 0.8980 chunk 480 optimal weight: 2.9990 chunk 372 optimal weight: 0.9990 chunk 553 optimal weight: 0.9980 chunk 367 optimal weight: 0.2980 chunk 655 optimal weight: 0.6980 chunk 410 optimal weight: 0.0870 chunk 399 optimal weight: 0.1980 chunk 302 optimal weight: 5.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 HIS ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN F 99 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN J 99 ASN ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 206 ASN N 99 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 HIS ** 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 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 206 ASN ** O 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 55336 Z= 0.185 Angle : 0.729 12.778 75312 Z= 0.353 Chirality : 0.045 0.211 8288 Planarity : 0.004 0.053 9792 Dihedral : 21.233 179.220 8128 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.37 % Favored : 91.52 % Rotamer: Outliers : 2.26 % Allowed : 22.09 % Favored : 75.65 % 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: -2.02 (0.10), residues: 6880 helix: -0.12 (0.10), residues: 2656 sheet: -1.58 (0.18), residues: 856 loop : -2.32 (0.11), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 21 HIS 0.015 0.001 HIS B 190 PHE 0.025 0.001 PHE G 202 TYR 0.011 0.001 TYR N 200 ARG 0.002 0.000 ARG L 318 *********************** 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 1141 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1013 time to evaluate : 4.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.7616 (tt0) cc_final: 0.7397 (tt0) REVERT: B 150 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8627 (tt) REVERT: B 191 GLN cc_start: 0.6836 (pt0) cc_final: 0.6634 (pp30) REVERT: B 267 MET cc_start: 0.7887 (ppp) cc_final: 0.6901 (ppp) REVERT: B 370 ASN cc_start: 0.8001 (t0) cc_final: 0.7731 (t0) REVERT: A 36 MET cc_start: 0.7921 (ppp) cc_final: 0.7428 (ppp) REVERT: A 47 ASP cc_start: 0.7908 (t0) cc_final: 0.7601 (t0) REVERT: A 76 ASP cc_start: 0.7857 (t0) cc_final: 0.7637 (t0) REVERT: A 207 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8954 (pm20) REVERT: A 230 LEU cc_start: 0.9492 (tt) cc_final: 0.9263 (tt) REVERT: A 244 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6917 (m-10) REVERT: A 338 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7132 (tmtt) REVERT: D 14 ASN cc_start: 0.8291 (m-40) cc_final: 0.7817 (m110) REVERT: D 267 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7475 (ppp) REVERT: D 281 TYR cc_start: 0.3774 (OUTLIER) cc_final: 0.2346 (m-80) REVERT: C 167 LEU cc_start: 0.7052 (tp) cc_final: 0.6731 (tp) REVERT: C 207 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8912 (pm20) REVERT: C 390 ARG cc_start: 0.7853 (mtm110) cc_final: 0.6833 (mmm-85) REVERT: C 413 MET cc_start: 0.8035 (mmm) cc_final: 0.7733 (mmm) REVERT: F 8 GLN cc_start: 0.7614 (tt0) cc_final: 0.7395 (tt0) REVERT: F 150 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8629 (tt) REVERT: F 191 GLN cc_start: 0.6837 (pt0) cc_final: 0.6635 (pp30) REVERT: F 267 MET cc_start: 0.7886 (ppp) cc_final: 0.6902 (ppp) REVERT: F 370 ASN cc_start: 0.7998 (t0) cc_final: 0.7729 (t0) REVERT: E 36 MET cc_start: 0.7919 (ppp) cc_final: 0.7426 (ppp) REVERT: E 47 ASP cc_start: 0.7902 (t0) cc_final: 0.7620 (t0) REVERT: E 76 ASP cc_start: 0.7857 (t0) cc_final: 0.7636 (t0) REVERT: E 207 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8954 (pm20) REVERT: E 230 LEU cc_start: 0.9492 (tt) cc_final: 0.9263 (tt) REVERT: E 244 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6946 (m-10) REVERT: E 338 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7132 (tmtt) REVERT: H 14 ASN cc_start: 0.8293 (m-40) cc_final: 0.7818 (m110) REVERT: H 267 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7492 (ppp) REVERT: H 281 TYR cc_start: 0.3770 (OUTLIER) cc_final: 0.2345 (m-80) REVERT: G 167 LEU cc_start: 0.7006 (tp) cc_final: 0.6791 (tp) REVERT: G 390 ARG cc_start: 0.7853 (mtm110) cc_final: 0.6827 (mmm-85) REVERT: G 413 MET cc_start: 0.8034 (mmm) cc_final: 0.7734 (mmm) REVERT: J 8 GLN cc_start: 0.7615 (tt0) cc_final: 0.7394 (tt0) REVERT: J 150 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8628 (tt) REVERT: J 191 GLN cc_start: 0.6838 (pt0) cc_final: 0.6636 (pp30) REVERT: J 267 MET cc_start: 0.7885 (ppp) cc_final: 0.6900 (ppp) REVERT: J 370 ASN cc_start: 0.8000 (t0) cc_final: 0.7731 (t0) REVERT: I 36 MET cc_start: 0.7920 (ppp) cc_final: 0.7427 (ppp) REVERT: I 47 ASP cc_start: 0.7899 (t0) cc_final: 0.7617 (t0) REVERT: I 76 ASP cc_start: 0.7857 (t0) cc_final: 0.7636 (t0) REVERT: I 207 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8954 (pm20) REVERT: I 230 LEU cc_start: 0.9492 (tt) cc_final: 0.9262 (tt) REVERT: I 244 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6946 (m-10) REVERT: I 338 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7130 (tmtt) REVERT: L 14 ASN cc_start: 0.8291 (m-40) cc_final: 0.7817 (m110) REVERT: L 267 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7477 (ppp) REVERT: L 281 TYR cc_start: 0.3772 (OUTLIER) cc_final: 0.2345 (m-80) REVERT: K 167 LEU cc_start: 0.7009 (tp) cc_final: 0.6792 (tp) REVERT: K 390 ARG cc_start: 0.7852 (mtm110) cc_final: 0.6826 (mmm-85) REVERT: K 413 MET cc_start: 0.8034 (mmm) cc_final: 0.7735 (mmm) REVERT: N 8 GLN cc_start: 0.7617 (tt0) cc_final: 0.7397 (tt0) REVERT: N 150 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8628 (tt) REVERT: N 191 GLN cc_start: 0.6838 (pt0) cc_final: 0.6636 (pp30) REVERT: N 267 MET cc_start: 0.7886 (ppp) cc_final: 0.6900 (ppp) REVERT: N 370 ASN cc_start: 0.8000 (t0) cc_final: 0.7731 (t0) REVERT: M 36 MET cc_start: 0.7919 (ppp) cc_final: 0.7426 (ppp) REVERT: M 47 ASP cc_start: 0.7907 (t0) cc_final: 0.7599 (t0) REVERT: M 76 ASP cc_start: 0.7857 (t0) cc_final: 0.7636 (t0) REVERT: M 207 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8988 (pm20) REVERT: M 244 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6915 (m-10) REVERT: M 338 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7132 (tmtt) REVERT: P 14 ASN cc_start: 0.8292 (m-40) cc_final: 0.7816 (m110) REVERT: P 267 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7473 (ppp) REVERT: P 281 TYR cc_start: 0.3773 (OUTLIER) cc_final: 0.2347 (m-80) REVERT: O 390 ARG cc_start: 0.7851 (mtm110) cc_final: 0.6825 (mmm-85) REVERT: O 413 MET cc_start: 0.8036 (mmm) cc_final: 0.7736 (mmm) outliers start: 128 outliers final: 93 residues processed: 1084 average time/residue: 0.4836 time to fit residues: 928.0546 Evaluate side-chains 1082 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 968 time to evaluate : 4.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 321 MET Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 190 HIS Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 207 GLU Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 244 PHE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 318 LEU Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 190 HIS Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 321 MET Chi-restraints excluded: chain K residue 61 HIS Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 206 ASN Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 190 HIS Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 207 GLU Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 244 PHE Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 178 THR Chi-restraints excluded: chain P residue 190 HIS Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 267 MET Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 321 MET Chi-restraints excluded: chain O residue 61 HIS Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 227 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 405 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 391 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 416 optimal weight: 0.9990 chunk 446 optimal weight: 2.9990 chunk 324 optimal weight: 0.0010 chunk 61 optimal weight: 0.6980 chunk 515 optimal weight: 7.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** 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** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN ** 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** ** 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 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2573 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= 0.204 Angle : 0.732 11.354 75312 Z= 0.354 Chirality : 0.045 0.213 8288 Planarity : 0.005 0.059 9792 Dihedral : 21.093 176.361 8128 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.15 % Favored : 90.73 % Rotamer: Outliers : 2.40 % Allowed : 22.60 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.10), residues: 6880 helix: -0.18 (0.10), residues: 2672 sheet: -1.74 (0.19), residues: 744 loop : -2.18 (0.11), residues: 3464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 21 HIS 0.007 0.001 HIS M 28 PHE 0.016 0.001 PHE D 394 TYR 0.011 0.001 TYR O 108 ARG 0.005 0.000 ARG K 243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13760 Ramachandran restraints generated. 6880 Oldfield, 0 Emsley, 6880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 991 time to evaluate : 4.479 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: B 8 GLN cc_start: 0.7646 (tt0) cc_final: 0.7348 (tt0) REVERT: B 267 MET cc_start: 0.7951 (ppp) cc_final: 0.6978 (ppp) REVERT: B 370 ASN cc_start: 0.7995 (t0) cc_final: 0.7755 (t0) REVERT: B 388 MET cc_start: 0.8289 (tmm) cc_final: 0.7866 (tmm) REVERT: A 36 MET cc_start: 0.7914 (ppp) cc_final: 0.7520 (ppp) REVERT: A 47 ASP cc_start: 0.7896 (t0) cc_final: 0.7631 (t0) REVERT: A 76 ASP cc_start: 0.7769 (t0) cc_final: 0.7556 (t0) REVERT: A 259 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8399 (mm) REVERT: D 14 ASN cc_start: 0.8346 (m-40) cc_final: 0.7862 (m110) REVERT: D 267 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7586 (ppp) REVERT: D 281 TYR cc_start: 0.3694 (OUTLIER) cc_final: 0.2270 (m-80) REVERT: D 331 LEU cc_start: 0.9490 (pp) cc_final: 0.9209 (mt) REVERT: C 167 LEU cc_start: 0.6901 (tp) cc_final: 0.6669 (tp) REVERT: C 390 ARG cc_start: 0.7857 (mtm110) cc_final: 0.6832 (mmm-85) REVERT: C 413 MET cc_start: 0.8139 (mmm) cc_final: 0.7833 (mmm) REVERT: C 425 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7172 (mmt) REVERT: F 8 GLN cc_start: 0.7645 (tt0) cc_final: 0.7346 (tt0) REVERT: F 267 MET cc_start: 0.7951 (ppp) cc_final: 0.6980 (ppp) REVERT: F 370 ASN cc_start: 0.7997 (t0) cc_final: 0.7755 (t0) REVERT: F 388 MET cc_start: 0.8289 (tmm) cc_final: 0.7867 (tmm) REVERT: E 36 MET cc_start: 0.7915 (ppp) cc_final: 0.7520 (ppp) REVERT: E 47 ASP cc_start: 0.7843 (t0) cc_final: 0.7558 (t0) REVERT: E 76 ASP cc_start: 0.7765 (t0) cc_final: 0.7552 (t0) REVERT: E 244 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.7009 (m-10) REVERT: E 259 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8400 (mm) REVERT: H 14 ASN cc_start: 0.8347 (m-40) cc_final: 0.7863 (m110) REVERT: H 267 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7580 (ppp) REVERT: H 281 TYR cc_start: 0.3698 (OUTLIER) cc_final: 0.2272 (m-80) REVERT: H 331 LEU cc_start: 0.9490 (pp) cc_final: 0.9210 (mt) REVERT: G 167 LEU cc_start: 0.7070 (tp) cc_final: 0.6810 (tp) REVERT: G 390 ARG cc_start: 0.7855 (mtm110) cc_final: 0.6824 (mmm-85) REVERT: G 413 MET cc_start: 0.8138 (mmm) cc_final: 0.7831 (mmm) REVERT: J 8 GLN cc_start: 0.7645 (tt0) cc_final: 0.7345 (tt0) REVERT: J 267 MET cc_start: 0.7948 (ppp) cc_final: 0.6976 (ppp) REVERT: J 370 ASN cc_start: 0.8001 (t0) cc_final: 0.7758 (t0) REVERT: J 388 MET cc_start: 0.8290 (tmm) cc_final: 0.7867 (tmm) REVERT: I 36 MET cc_start: 0.7914 (ppp) cc_final: 0.7518 (ppp) REVERT: I 47 ASP cc_start: 0.7848 (t0) cc_final: 0.7545 (t0) REVERT: I 76 ASP cc_start: 0.7767 (t0) cc_final: 0.7554 (t0) REVERT: I 244 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6974 (m-10) REVERT: I 259 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8394 (mm) REVERT: L 14 ASN cc_start: 0.8345 (m-40) cc_final: 0.7861 (m110) REVERT: L 267 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7586 (ppp) REVERT: L 281 TYR cc_start: 0.3694 (OUTLIER) cc_final: 0.2269 (m-80) REVERT: L 331 LEU cc_start: 0.9489 (pp) cc_final: 0.9209 (mt) REVERT: K 167 LEU cc_start: 0.7072 (tp) cc_final: 0.6811 (tp) REVERT: K 390 ARG cc_start: 0.7854 (mtm110) cc_final: 0.6826 (mmm-85) REVERT: K 413 MET cc_start: 0.8135 (mmm) cc_final: 0.7830 (mmm) REVERT: N 8 GLN cc_start: 0.7651 (tt0) cc_final: 0.7351 (tt0) REVERT: N 267 MET cc_start: 0.7950 (ppp) cc_final: 0.6976 (ppp) REVERT: N 370 ASN cc_start: 0.7996 (t0) cc_final: 0.7756 (t0) REVERT: N 388 MET cc_start: 0.8291 (tmm) cc_final: 0.7870 (tmm) REVERT: M 36 MET cc_start: 0.7914 (ppp) cc_final: 0.7521 (ppp) REVERT: M 47 ASP cc_start: 0.7896 (t0) cc_final: 0.7631 (t0) REVERT: M 76 ASP cc_start: 0.7769 (t0) cc_final: 0.7556 (t0) REVERT: M 259 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8395 (mm) REVERT: P 14 ASN cc_start: 0.8345 (m-40) cc_final: 0.7863 (m110) REVERT: P 267 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7587 (ppp) REVERT: P 281 TYR cc_start: 0.3698 (OUTLIER) cc_final: 0.2272 (m-80) REVERT: P 331 LEU cc_start: 0.9489 (pp) cc_final: 0.9209 (mt) REVERT: O 167 LEU cc_start: 0.7067 (tp) cc_final: 0.6864 (tp) REVERT: O 390 ARG cc_start: 0.7855 (mtm110) cc_final: 0.6825 (mmm-85) REVERT: O 413 MET cc_start: 0.8138 (mmm) cc_final: 0.7832 (mmm) REVERT: O 425 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7170 (mmt) outliers start: 136 outliers final: 92 residues processed: 1069 average time/residue: 0.4857 time to fit residues: 919.6762 Evaluate side-chains 1061 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 953 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 425 MET Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 321 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 190 HIS Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 244 PHE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 318 LEU Chi-restraints excluded: chain L residue 190 HIS Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 321 MET Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 190 HIS Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 273 LEU Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain P residue 190 HIS Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 267 MET Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 321 MET Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 425 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 596 optimal weight: 2.9990 chunk 627 optimal weight: 0.5980 chunk 572 optimal weight: 3.9990 chunk 610 optimal weight: 0.6980 chunk 367 optimal weight: 0.0870 chunk 266 optimal weight: 2.9990 chunk 479 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 551 optimal weight: 0.7980 chunk 577 optimal weight: 0.8980 chunk 608 optimal weight: 0.0030 overall best weight: 0.4368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** 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** ** 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** F 99 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 ** 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 99 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 55336 Z= 0.185 Angle : 0.726 11.678 75312 Z= 0.351 Chirality : 0.045 0.227 8288 Planarity : 0.005 0.052 9792 Dihedral : 20.807 175.666 8128 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.44 % Favored : 91.44 % Rotamer: Outliers : 2.33 % Allowed : 22.94 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.10), residues: 6880 helix: -0.21 (0.10), residues: 2672 sheet: -1.65 (0.19), residues: 744 loop : -2.15 (0.11), residues: 3464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 21 HIS 0.008 0.001 HIS M 28 PHE 0.019 0.001 PHE A 343 TYR 0.011 0.001 TYR B 200 ARG 0.004 0.000 ARG G 243 *********************** 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 1122 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 990 time to evaluate : 4.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.7591 (tt0) cc_final: 0.7389 (tt0) REVERT: B 267 MET cc_start: 0.7937 (ppp) cc_final: 0.6986 (ppp) REVERT: B 323 MET cc_start: 0.8119 (mtp) cc_final: 0.7752 (tmm) REVERT: B 370 ASN cc_start: 0.7960 (t0) cc_final: 0.7738 (t0) REVERT: A 36 MET cc_start: 0.7720 (ppp) cc_final: 0.6962 (ppp) REVERT: A 47 ASP cc_start: 0.7820 (t0) cc_final: 0.7557 (t0) REVERT: A 67 PHE cc_start: 0.8068 (m-80) cc_final: 0.7847 (m-80) REVERT: A 76 ASP cc_start: 0.7683 (t0) cc_final: 0.7468 (t0) REVERT: A 207 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8996 (pm20) REVERT: A 230 LEU cc_start: 0.9464 (tt) cc_final: 0.9180 (tt) REVERT: A 259 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8358 (mm) REVERT: D 14 ASN cc_start: 0.8263 (m-40) cc_final: 0.7884 (m110) REVERT: D 267 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7292 (ppp) REVERT: D 281 TYR cc_start: 0.3801 (OUTLIER) cc_final: 0.2254 (m-80) REVERT: D 331 LEU cc_start: 0.9481 (pp) cc_final: 0.9201 (mt) REVERT: C 167 LEU cc_start: 0.6904 (tp) cc_final: 0.6695 (tp) REVERT: C 390 ARG cc_start: 0.7823 (mtm110) cc_final: 0.6764 (mmm-85) REVERT: C 413 MET cc_start: 0.8088 (mmm) cc_final: 0.7771 (mmm) REVERT: C 425 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7131 (mmt) REVERT: F 8 GLN cc_start: 0.7590 (tt0) cc_final: 0.7387 (tt0) REVERT: F 267 MET cc_start: 0.7935 (ppp) cc_final: 0.6984 (ppp) REVERT: F 323 MET cc_start: 0.8120 (mtp) cc_final: 0.7753 (tmm) REVERT: F 370 ASN cc_start: 0.7959 (t0) cc_final: 0.7737 (t0) REVERT: E 36 MET cc_start: 0.7717 (ppp) cc_final: 0.6963 (ppp) REVERT: E 47 ASP cc_start: 0.7907 (t0) cc_final: 0.7631 (t70) REVERT: E 67 PHE cc_start: 0.8070 (m-80) cc_final: 0.7849 (m-80) REVERT: E 76 ASP cc_start: 0.7682 (t0) cc_final: 0.7467 (t0) REVERT: E 207 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8994 (pm20) REVERT: E 230 LEU cc_start: 0.9465 (tt) cc_final: 0.9180 (tt) REVERT: E 244 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6912 (m-10) REVERT: E 259 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8361 (mm) REVERT: H 14 ASN cc_start: 0.8262 (m-40) cc_final: 0.7883 (m110) REVERT: H 267 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7280 (ppp) REVERT: H 281 TYR cc_start: 0.3798 (OUTLIER) cc_final: 0.2252 (m-80) REVERT: H 331 LEU cc_start: 0.9482 (pp) cc_final: 0.9202 (mt) REVERT: G 167 LEU cc_start: 0.6909 (tp) cc_final: 0.6705 (tp) REVERT: G 390 ARG cc_start: 0.7820 (mtm110) cc_final: 0.6758 (mmm-85) REVERT: G 413 MET cc_start: 0.8088 (mmm) cc_final: 0.7771 (mmm) REVERT: G 425 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7114 (mmt) REVERT: J 8 GLN cc_start: 0.7589 (tt0) cc_final: 0.7386 (tt0) REVERT: J 267 MET cc_start: 0.7934 (ppp) cc_final: 0.6984 (ppp) REVERT: J 323 MET cc_start: 0.8120 (mtp) cc_final: 0.7753 (tmm) REVERT: J 370 ASN cc_start: 0.7961 (t0) cc_final: 0.7738 (t0) REVERT: I 36 MET cc_start: 0.7718 (ppp) cc_final: 0.6963 (ppp) REVERT: I 47 ASP cc_start: 0.7778 (t0) cc_final: 0.7504 (t70) REVERT: I 67 PHE cc_start: 0.8069 (m-80) cc_final: 0.7849 (m-80) REVERT: I 76 ASP cc_start: 0.7684 (t0) cc_final: 0.7468 (t0) REVERT: I 207 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8994 (pm20) REVERT: I 230 LEU cc_start: 0.9464 (tt) cc_final: 0.9180 (tt) REVERT: I 244 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6934 (m-10) REVERT: I 259 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8353 (mm) REVERT: L 14 ASN cc_start: 0.8259 (m-40) cc_final: 0.7881 (m110) REVERT: L 267 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7290 (ppp) REVERT: L 281 TYR cc_start: 0.3797 (OUTLIER) cc_final: 0.2253 (m-80) REVERT: L 331 LEU cc_start: 0.9481 (pp) cc_final: 0.9202 (mt) REVERT: K 167 LEU cc_start: 0.6912 (tp) cc_final: 0.6708 (tp) REVERT: K 390 ARG cc_start: 0.7820 (mtm110) cc_final: 0.6759 (mmm-85) REVERT: K 413 MET cc_start: 0.8087 (mmm) cc_final: 0.7770 (mmm) REVERT: K 425 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7117 (mmt) REVERT: N 8 GLN cc_start: 0.7592 (tt0) cc_final: 0.7389 (tt0) REVERT: N 267 MET cc_start: 0.7935 (ppp) cc_final: 0.6985 (ppp) REVERT: N 323 MET cc_start: 0.8121 (mtp) cc_final: 0.7753 (tmm) REVERT: N 370 ASN cc_start: 0.7958 (t0) cc_final: 0.7738 (t0) REVERT: M 36 MET cc_start: 0.7716 (ppp) cc_final: 0.6961 (ppp) REVERT: M 47 ASP cc_start: 0.7819 (t0) cc_final: 0.7555 (t0) REVERT: M 67 PHE cc_start: 0.8069 (m-80) cc_final: 0.7789 (m-80) REVERT: M 76 ASP cc_start: 0.7683 (t0) cc_final: 0.7466 (t0) REVERT: M 207 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.8993 (pm20) REVERT: M 230 LEU cc_start: 0.9465 (tt) cc_final: 0.9180 (tt) REVERT: M 259 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8352 (mm) REVERT: P 14 ASN cc_start: 0.8263 (m-40) cc_final: 0.7884 (m110) REVERT: P 267 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7292 (ppp) REVERT: P 281 TYR cc_start: 0.3801 (OUTLIER) cc_final: 0.2256 (m-80) REVERT: P 331 LEU cc_start: 0.9481 (pp) cc_final: 0.9202 (mt) REVERT: O 167 LEU cc_start: 0.7046 (tp) cc_final: 0.6811 (tp) REVERT: O 390 ARG cc_start: 0.7869 (mtm110) cc_final: 0.6823 (mmm-85) REVERT: O 413 MET cc_start: 0.8088 (mmm) cc_final: 0.7771 (mmm) REVERT: O 425 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7132 (mmt) outliers start: 132 outliers final: 89 residues processed: 1061 average time/residue: 0.4636 time to fit residues: 866.9951 Evaluate side-chains 1071 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 960 time to evaluate : 4.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 425 MET Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 321 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 190 HIS Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 207 GLU Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 244 PHE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 318 LEU Chi-restraints excluded: chain L residue 190 HIS Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 321 MET Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 425 MET Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 190 HIS Chi-restraints excluded: chain N residue 233 MET Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 273 LEU Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 207 GLU Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain P residue 190 HIS Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 267 MET Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 321 MET Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 401 optimal weight: 3.9990 chunk 645 optimal weight: 0.9990 chunk 394 optimal weight: 3.9990 chunk 306 optimal weight: 0.7980 chunk 448 optimal weight: 0.2980 chunk 677 optimal weight: 1.9990 chunk 623 optimal weight: 0.8980 chunk 539 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 416 optimal weight: 0.9980 chunk 330 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** 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 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN ** 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 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 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 55336 Z= 0.225 Angle : 0.740 10.669 75312 Z= 0.360 Chirality : 0.046 0.288 8288 Planarity : 0.005 0.051 9792 Dihedral : 20.767 173.158 8128 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.30 % Favored : 90.58 % Rotamer: Outliers : 2.06 % Allowed : 23.27 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.10), residues: 6880 helix: -0.26 (0.10), residues: 2672 sheet: -1.66 (0.19), residues: 744 loop : -2.13 (0.11), residues: 3464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 21 HIS 0.009 0.001 HIS M 28 PHE 0.019 0.002 PHE H 367 TYR 0.022 0.001 TYR O 24 ARG 0.003 0.000 ARG N 86 ********************** 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 1091 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 974 time to evaluate : 4.612 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: B 14 ASN cc_start: 0.8633 (m-40) cc_final: 0.8310 (m110) REVERT: B 323 MET cc_start: 0.8207 (mtp) cc_final: 0.7816 (tmm) REVERT: B 370 ASN cc_start: 0.7998 (t0) cc_final: 0.7766 (t0) REVERT: B 388 MET cc_start: 0.8279 (tmm) cc_final: 0.7868 (tmm) REVERT: A 36 MET cc_start: 0.7740 (ppp) cc_final: 0.6995 (ppp) REVERT: A 47 ASP cc_start: 0.7809 (t0) cc_final: 0.7519 (t0) REVERT: A 67 PHE cc_start: 0.8129 (m-80) cc_final: 0.7912 (m-80) REVERT: A 76 ASP cc_start: 0.7709 (t0) cc_final: 0.7476 (t0) REVERT: D 14 ASN cc_start: 0.8340 (m-40) cc_final: 0.7854 (m110) REVERT: D 281 TYR cc_start: 0.3816 (OUTLIER) cc_final: 0.2286 (m-80) REVERT: D 363 MET cc_start: 0.3582 (pmm) cc_final: 0.3344 (pmm) REVERT: C 167 LEU cc_start: 0.6981 (tp) cc_final: 0.6751 (tp) REVERT: C 390 ARG cc_start: 0.7891 (mtm110) cc_final: 0.6830 (mmm-85) REVERT: C 413 MET cc_start: 0.8112 (mmm) cc_final: 0.7797 (mmm) REVERT: C 425 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7127 (mmt) REVERT: F 14 ASN cc_start: 0.8631 (m-40) cc_final: 0.8309 (m110) REVERT: F 323 MET cc_start: 0.8206 (mtp) cc_final: 0.7817 (tmm) REVERT: F 370 ASN cc_start: 0.7999 (t0) cc_final: 0.7765 (t0) REVERT: F 388 MET cc_start: 0.8280 (tmm) cc_final: 0.7869 (tmm) REVERT: E 36 MET cc_start: 0.7742 (ppp) cc_final: 0.6997 (ppp) REVERT: E 47 ASP cc_start: 0.7835 (t0) cc_final: 0.7526 (t0) REVERT: E 67 PHE cc_start: 0.8146 (m-80) cc_final: 0.7910 (m-80) REVERT: E 76 ASP cc_start: 0.7680 (t0) cc_final: 0.7455 (t0) REVERT: E 244 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.6996 (m-10) REVERT: H 14 ASN cc_start: 0.8340 (m-40) cc_final: 0.7853 (m110) REVERT: H 267 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7683 (ppp) REVERT: H 281 TYR cc_start: 0.3814 (OUTLIER) cc_final: 0.2285 (m-80) REVERT: H 363 MET cc_start: 0.3579 (pmm) cc_final: 0.3341 (pmm) REVERT: G 167 LEU cc_start: 0.6959 (tp) cc_final: 0.6729 (tp) REVERT: G 390 ARG cc_start: 0.7888 (mtm110) cc_final: 0.6874 (mmm-85) REVERT: G 413 MET cc_start: 0.8108 (mmm) cc_final: 0.7795 (mmm) REVERT: G 425 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7086 (mmt) REVERT: J 14 ASN cc_start: 0.8629 (m-40) cc_final: 0.8307 (m110) REVERT: J 323 MET cc_start: 0.8206 (mtp) cc_final: 0.7817 (tmm) REVERT: J 370 ASN cc_start: 0.7997 (t0) cc_final: 0.7763 (t0) REVERT: J 388 MET cc_start: 0.8278 (tmm) cc_final: 0.7868 (tmm) REVERT: I 36 MET cc_start: 0.7742 (ppp) cc_final: 0.6998 (ppp) REVERT: I 47 ASP cc_start: 0.7828 (t0) cc_final: 0.7555 (t70) REVERT: I 67 PHE cc_start: 0.8131 (m-80) cc_final: 0.7912 (m-80) REVERT: I 76 ASP cc_start: 0.7678 (t0) cc_final: 0.7453 (t0) REVERT: I 244 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6984 (m-10) REVERT: I 259 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8429 (mm) REVERT: L 14 ASN cc_start: 0.8337 (m-40) cc_final: 0.7851 (m110) REVERT: L 281 TYR cc_start: 0.3815 (OUTLIER) cc_final: 0.2287 (m-80) REVERT: L 363 MET cc_start: 0.3575 (pmm) cc_final: 0.3342 (pmm) REVERT: K 167 LEU cc_start: 0.6959 (tp) cc_final: 0.6728 (tp) REVERT: K 390 ARG cc_start: 0.7889 (mtm110) cc_final: 0.6875 (mmm-85) REVERT: K 413 MET cc_start: 0.8110 (mmm) cc_final: 0.7795 (mmm) REVERT: K 425 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7087 (mmt) REVERT: N 14 ASN cc_start: 0.8631 (m-40) cc_final: 0.8307 (m110) REVERT: N 323 MET cc_start: 0.8207 (mtp) cc_final: 0.7817 (tmm) REVERT: N 370 ASN cc_start: 0.7997 (t0) cc_final: 0.7763 (t0) REVERT: N 388 MET cc_start: 0.8279 (tmm) cc_final: 0.7868 (tmm) REVERT: M 36 MET cc_start: 0.7738 (ppp) cc_final: 0.6994 (ppp) REVERT: M 47 ASP cc_start: 0.7810 (t0) cc_final: 0.7520 (t0) REVERT: M 76 ASP cc_start: 0.7708 (t0) cc_final: 0.7474 (t0) REVERT: M 259 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8429 (mm) REVERT: P 14 ASN cc_start: 0.8339 (m-40) cc_final: 0.7851 (m110) REVERT: P 281 TYR cc_start: 0.3816 (OUTLIER) cc_final: 0.2286 (m-80) REVERT: P 363 MET cc_start: 0.3573 (pmm) cc_final: 0.3339 (pmm) REVERT: O 167 LEU cc_start: 0.7017 (tp) cc_final: 0.6801 (tp) REVERT: O 390 ARG cc_start: 0.7886 (mtm110) cc_final: 0.6874 (mmm-85) REVERT: O 413 MET cc_start: 0.8110 (mmm) cc_final: 0.7797 (mmm) REVERT: O 425 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7125 (mmt) outliers start: 117 outliers final: 85 residues processed: 1033 average time/residue: 0.4662 time to fit residues: 848.7244 Evaluate side-chains 1057 residues out of total 5872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 959 time to evaluate : 4.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 425 MET Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 321 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 190 HIS Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 244 PHE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 318 LEU Chi-restraints excluded: chain L residue 190 HIS Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 321 MET Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 425 MET Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 190 HIS Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 273 LEU Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain P residue 190 HIS Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 321 MET Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 428 optimal weight: 2.9990 chunk 574 optimal weight: 0.8980 chunk 165 optimal weight: 0.4980 chunk 497 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 540 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 554 optimal weight: 0.0980 chunk 68 optimal weight: 0.0980 chunk 99 optimal weight: 3.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 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 ** 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 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.130543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.108765 restraints weight = 146322.907| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 5.25 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2952 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= 0.185 Angle : 0.742 12.273 75312 Z= 0.358 Chirality : 0.046 0.284 8288 Planarity : 0.005 0.052 9792 Dihedral : 20.530 173.906 8128 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.92 % Favored : 91.97 % Rotamer: Outliers : 1.99 % Allowed : 22.97 % Favored : 75.04 % 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: -0.27 (0.10), residues: 2672 sheet: -1.40 (0.20), residues: 744 loop : -2.14 (0.11), residues: 3464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 101 HIS 0.008 0.001 HIS M 28 PHE 0.018 0.001 PHE L 367 TYR 0.013 0.001 TYR B 200 ARG 0.009 0.000 ARG C 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13899.68 seconds wall clock time: 245 minutes 10.25 seconds (14710.25 seconds total)