Starting phenix.real_space_refine on Tue Feb 13 12:44:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2024/7lxb_23569_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2024/7lxb_23569.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2024/7lxb_23569_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2024/7lxb_23569_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2024/7lxb_23569_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2024/7lxb_23569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2024/7lxb_23569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2024/7lxb_23569_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2024/7lxb_23569_neut_updated.pdb" } resolution = 3.26 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= 0.034 sd= 0.521 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 368 5.16 5 Cl 8 4.86 5 C 34152 2.51 5 N 9256 2.21 5 O 10456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D ARG 391": "NH1" <-> "NH2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E GLU 417": "OE1" <-> "OE2" Residue "E GLU 423": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "F ARG 391": "NH1" <-> "NH2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G GLU 417": "OE1" <-> "OE2" Residue "G GLU 423": "OE1" <-> "OE2" Residue "H GLU 158": "OE1" <-> "OE2" Residue "H GLU 198": "OE1" <-> "OE2" Residue "H GLU 325": "OE1" <-> "OE2" Residue "H ARG 391": "NH1" <-> "NH2" Residue "H GLU 405": "OE1" <-> "OE2" Residue "I GLU 97": "OE1" <-> "OE2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "I GLU 417": "OE1" <-> "OE2" Residue "I GLU 423": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J GLU 198": "OE1" <-> "OE2" Residue "J GLU 325": "OE1" <-> "OE2" Residue "J ARG 391": "NH1" <-> "NH2" Residue "J GLU 405": "OE1" <-> "OE2" Residue "K GLU 97": "OE1" <-> "OE2" Residue "K GLU 183": "OE1" <-> "OE2" Residue "K GLU 417": "OE1" <-> "OE2" Residue "K GLU 423": "OE1" <-> "OE2" Residue "L GLU 158": "OE1" <-> "OE2" Residue "L GLU 198": "OE1" <-> "OE2" Residue "L GLU 325": "OE1" <-> "OE2" Residue "L ARG 391": "NH1" <-> "NH2" Residue "L GLU 405": "OE1" <-> "OE2" Residue "M GLU 97": "OE1" <-> "OE2" Residue "M GLU 183": "OE1" <-> "OE2" Residue "M GLU 417": "OE1" <-> "OE2" Residue "M GLU 423": "OE1" <-> "OE2" Residue "N GLU 158": "OE1" <-> "OE2" Residue "N GLU 198": "OE1" <-> "OE2" Residue "N GLU 325": "OE1" <-> "OE2" Residue "N ARG 391": "NH1" <-> "NH2" Residue "N GLU 405": "OE1" <-> "OE2" Residue "O GLU 97": "OE1" <-> "OE2" Residue "O GLU 183": "OE1" <-> "OE2" Residue "O GLU 417": "OE1" <-> "OE2" Residue "O GLU 423": "OE1" <-> "OE2" Residue "P GLU 158": "OE1" <-> "OE2" Residue "P GLU 198": "OE1" <-> "OE2" Residue "P GLU 325": "OE1" <-> "OE2" Residue "P ARG 391": "NH1" <-> "NH2" Residue "P GLU 405": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 54280 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3349 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3329 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 410} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3349 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3329 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 410} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3349 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "F" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3329 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 410} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3349 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "H" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3329 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 410} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "I" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3349 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "J" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3329 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 410} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "K" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3349 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "L" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3329 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 410} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "M" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3349 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "N" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3329 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 410} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "O" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3349 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "P" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3329 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 410} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 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: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'GDP': 1, 'YGY': 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: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'GDP': 1, 'YGY': 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: "F" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'GDP': 1, 'YGY': 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: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'GDP': 1, 'YGY': 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: "J" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'GDP': 1, 'YGY': 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: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'GDP': 1, 'YGY': 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: "N" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'GDP': 1, 'YGY': 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} Chain: "P" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'GDP': 1, 'YGY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.95, per 1000 atoms: 0.39 Number of scatterers: 54280 At special positions: 0 Unit cell: (310.58, 310.58, 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 368 16.00 P 40 15.00 O 10456 8.00 N 9256 7.00 C 34152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.70 Conformation dependent library (CDL) restraints added in 7.6 seconds 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 312 helices and 32 sheets defined 44.0% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.19 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.850A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 103 through 107 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 removed outlier: 3.950A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.741A 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 191 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 226 through 243 removed outlier: 4.738A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.507A 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: 4.413A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' 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 337 removed outlier: 4.184A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.678A pdb=" N ALA A 387 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 5.189A pdb=" N GLY A 410 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 434 Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' 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 70 through 78 removed outlier: 3.922A pdb=" N MET B 73 " --> pdb=" O PRO B 70 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP B 74 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 78 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 142 through 158 removed outlier: 6.365A pdb=" N MET B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.869A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 224 through 241 removed outlier: 4.353A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 4.784A 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 323 through 335 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 373 through 390 removed outlier: 3.931A 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 'C' and resid 10 through 27 removed outlier: 3.850A pdb=" N GLU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 103 through 107 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 removed outlier: 3.951A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 160 removed outlier: 4.741A 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 191 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 226 through 243 removed outlier: 4.738A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.507A 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: 4.413A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' 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 337 removed outlier: 4.184A pdb=" N THR C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.678A pdb=" N ALA C 387 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 5.190A pdb=" N GLY C 410 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 434 Processing helix chain 'D' and resid 10 through 27 Processing helix chain 'D' and resid 41 through 43 No H-bonds generated for 'chain 'D' and resid 41 through 43' 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 70 through 78 removed outlier: 3.922A pdb=" N MET D 73 " --> pdb=" O PRO D 70 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP D 74 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 78 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 142 through 158 removed outlier: 6.365A pdb=" N MET D 147 " --> pdb=" O THR D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.869A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 224 through 241 removed outlier: 4.353A pdb=" N SER D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 4.784A 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 323 through 335 Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 373 through 390 removed outlier: 3.931A 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 'E' and resid 10 through 27 removed outlier: 3.850A pdb=" N GLU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 79 Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing helix chain 'E' and resid 103 through 107 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 removed outlier: 3.950A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 160 removed outlier: 4.741A 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 191 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 226 through 243 removed outlier: 4.738A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.507A 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: 4.413A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' 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 337 removed outlier: 4.184A pdb=" N THR E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.678A pdb=" N ALA E 387 " --> pdb=" O ILE E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 removed outlier: 5.189A pdb=" N GLY E 410 " --> pdb=" O TRP E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 434 Processing helix chain 'F' and resid 10 through 27 Processing helix chain 'F' and resid 41 through 43 No H-bonds generated for 'chain 'F' and resid 41 through 43' 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 70 through 78 removed outlier: 3.922A pdb=" N MET F 73 " --> pdb=" O PRO F 70 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP F 74 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER F 78 " --> pdb=" O SER F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 84 No H-bonds generated for 'chain 'F' and resid 82 through 84' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 142 through 158 removed outlier: 6.365A pdb=" N MET F 147 " --> pdb=" O THR F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'F' and resid 181 through 195 removed outlier: 3.869A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 213 Processing helix chain 'F' and resid 224 through 241 removed outlier: 4.353A pdb=" N SER F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 4.784A 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 323 through 335 Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 373 through 390 removed outlier: 3.931A 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 'G' and resid 10 through 27 removed outlier: 3.850A pdb=" N GLU G 22 " --> pdb=" O ASN G 18 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU G 23 " --> pdb=" O ALA G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 79 Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 103 through 107 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 removed outlier: 3.951A pdb=" N GLN G 128 " --> pdb=" O LYS G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 160 removed outlier: 4.741A 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 191 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 206 through 216 Processing helix chain 'G' and resid 226 through 243 removed outlier: 4.738A pdb=" N SER G 241 " --> pdb=" O SER G 237 " (cutoff:3.500A) removed outlier: 5.507A 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: 4.413A pdb=" N PHE G 296 " --> pdb=" O THR G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 300 No H-bonds generated for 'chain 'G' and resid 298 through 300' 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 337 removed outlier: 4.184A pdb=" N THR G 337 " --> pdb=" O ALA G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 400 removed outlier: 3.678A pdb=" N ALA G 387 " --> pdb=" O ILE G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 411 removed outlier: 5.190A pdb=" N GLY G 410 " --> pdb=" O TRP G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 434 Processing helix chain 'H' and resid 10 through 27 Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' 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 70 through 78 removed outlier: 3.922A pdb=" N MET H 73 " --> pdb=" O PRO H 70 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP H 74 " --> pdb=" O GLY H 71 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER H 78 " --> pdb=" O SER H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 142 through 158 removed outlier: 6.365A pdb=" N MET H 147 " --> pdb=" O THR H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 175 No H-bonds generated for 'chain 'H' and resid 173 through 175' Processing helix chain 'H' and resid 181 through 195 removed outlier: 3.869A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU H 194 " --> pdb=" O HIS H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 224 through 241 removed outlier: 4.353A pdb=" N SER H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 4.784A 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 323 through 335 Processing helix chain 'H' and resid 338 through 340 No H-bonds generated for 'chain 'H' and resid 338 through 340' Processing helix chain 'H' and resid 373 through 390 removed outlier: 3.931A 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 'I' and resid 10 through 27 removed outlier: 3.850A pdb=" N GLU I 22 " --> pdb=" O ASN I 18 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU I 23 " --> pdb=" O ALA I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 79 Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'I' and resid 103 through 107 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 removed outlier: 3.950A pdb=" N GLN I 128 " --> pdb=" O LYS I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 160 removed outlier: 4.741A 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 191 Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 226 through 243 removed outlier: 4.738A pdb=" N SER I 241 " --> pdb=" O SER I 237 " (cutoff:3.500A) removed outlier: 5.507A 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: 4.413A pdb=" N PHE I 296 " --> pdb=" O THR I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' 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 337 removed outlier: 4.184A pdb=" N THR I 337 " --> pdb=" O ALA I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 400 removed outlier: 3.678A pdb=" N ALA I 387 " --> pdb=" O ILE I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 411 removed outlier: 5.189A pdb=" N GLY I 410 " --> pdb=" O TRP I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 434 Processing helix chain 'J' and resid 10 through 27 Processing helix chain 'J' and resid 41 through 43 No H-bonds generated for 'chain 'J' and resid 41 through 43' 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 70 through 78 removed outlier: 3.922A pdb=" N MET J 73 " --> pdb=" O PRO J 70 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP J 74 " --> pdb=" O GLY J 71 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER J 78 " --> pdb=" O SER J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 84 No H-bonds generated for 'chain 'J' and resid 82 through 84' Processing helix chain 'J' and resid 113 through 125 Processing helix chain 'J' and resid 142 through 158 removed outlier: 6.365A pdb=" N MET J 147 " --> pdb=" O THR J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 175 No H-bonds generated for 'chain 'J' and resid 173 through 175' Processing helix chain 'J' and resid 181 through 195 removed outlier: 3.869A pdb=" N GLN J 191 " --> pdb=" O LEU J 187 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU J 194 " --> pdb=" O HIS J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 213 Processing helix chain 'J' and resid 224 through 241 removed outlier: 4.353A pdb=" N SER J 239 " --> pdb=" O GLY J 235 " (cutoff:3.500A) removed outlier: 4.784A 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 323 through 335 Processing helix chain 'J' and resid 338 through 340 No H-bonds generated for 'chain 'J' and resid 338 through 340' Processing helix chain 'J' and resid 373 through 390 removed outlier: 3.931A 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 'K' and resid 10 through 27 removed outlier: 3.850A pdb=" N GLU K 22 " --> pdb=" O ASN K 18 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU K 23 " --> pdb=" O ALA K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 79 Processing helix chain 'K' and resid 84 through 86 No H-bonds generated for 'chain 'K' and resid 84 through 86' Processing helix chain 'K' and resid 103 through 107 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 removed outlier: 3.951A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 160 removed outlier: 4.741A 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 191 Processing helix chain 'K' and resid 195 through 197 No H-bonds generated for 'chain 'K' and resid 195 through 197' Processing helix chain 'K' and resid 206 through 216 Processing helix chain 'K' and resid 226 through 243 removed outlier: 4.738A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.507A 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: 4.413A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' 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 337 removed outlier: 4.184A pdb=" N THR K 337 " --> pdb=" O ALA K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 400 removed outlier: 3.678A pdb=" N ALA K 387 " --> pdb=" O ILE K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 411 removed outlier: 5.190A pdb=" N GLY K 410 " --> pdb=" O TRP K 407 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 434 Processing helix chain 'L' and resid 10 through 27 Processing helix chain 'L' and resid 41 through 43 No H-bonds generated for 'chain 'L' and resid 41 through 43' 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 70 through 78 removed outlier: 3.922A pdb=" N MET L 73 " --> pdb=" O PRO L 70 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP L 74 " --> pdb=" O GLY L 71 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER L 78 " --> pdb=" O SER L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 84 No H-bonds generated for 'chain 'L' and resid 82 through 84' Processing helix chain 'L' and resid 113 through 125 Processing helix chain 'L' and resid 142 through 158 removed outlier: 6.365A pdb=" N MET L 147 " --> pdb=" O THR L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 175 No H-bonds generated for 'chain 'L' and resid 173 through 175' Processing helix chain 'L' and resid 181 through 195 removed outlier: 3.869A pdb=" N GLN L 191 " --> pdb=" O LEU L 187 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU L 194 " --> pdb=" O HIS L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 213 Processing helix chain 'L' and resid 224 through 241 removed outlier: 4.353A pdb=" N SER L 239 " --> pdb=" O GLY L 235 " (cutoff:3.500A) removed outlier: 4.784A 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 323 through 335 Processing helix chain 'L' and resid 338 through 340 No H-bonds generated for 'chain 'L' and resid 338 through 340' Processing helix chain 'L' and resid 373 through 390 removed outlier: 3.931A 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 'M' and resid 10 through 27 removed outlier: 3.850A pdb=" N GLU M 22 " --> pdb=" O ASN M 18 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU M 23 " --> pdb=" O ALA M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 79 Processing helix chain 'M' and resid 84 through 86 No H-bonds generated for 'chain 'M' and resid 84 through 86' Processing helix chain 'M' and resid 103 through 107 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 removed outlier: 3.950A pdb=" N GLN M 128 " --> pdb=" O LYS M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 160 removed outlier: 4.741A 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 191 Processing helix chain 'M' and resid 195 through 197 No H-bonds generated for 'chain 'M' and resid 195 through 197' Processing helix chain 'M' and resid 206 through 216 Processing helix chain 'M' and resid 226 through 243 removed outlier: 4.738A pdb=" N SER M 241 " --> pdb=" O SER M 237 " (cutoff:3.500A) removed outlier: 5.507A 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: 4.413A pdb=" N PHE M 296 " --> pdb=" O THR M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 300 No H-bonds generated for 'chain 'M' and resid 298 through 300' 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 337 removed outlier: 4.184A pdb=" N THR M 337 " --> pdb=" O ALA M 333 " (cutoff:3.500A) Processing helix chain 'M' and resid 383 through 400 removed outlier: 3.678A pdb=" N ALA M 387 " --> pdb=" O ILE M 384 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 411 removed outlier: 5.189A pdb=" N GLY M 410 " --> pdb=" O TRP M 407 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 434 Processing helix chain 'N' and resid 10 through 27 Processing helix chain 'N' and resid 41 through 43 No H-bonds generated for 'chain 'N' and resid 41 through 43' 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 70 through 78 removed outlier: 3.922A pdb=" N MET N 73 " --> pdb=" O PRO N 70 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP N 74 " --> pdb=" O GLY N 71 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER N 78 " --> pdb=" O SER N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 84 No H-bonds generated for 'chain 'N' and resid 82 through 84' Processing helix chain 'N' and resid 113 through 125 Processing helix chain 'N' and resid 142 through 158 removed outlier: 6.365A pdb=" N MET N 147 " --> pdb=" O THR N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 173 through 175 No H-bonds generated for 'chain 'N' and resid 173 through 175' Processing helix chain 'N' and resid 181 through 195 removed outlier: 3.869A pdb=" N GLN N 191 " --> pdb=" O LEU N 187 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU N 194 " --> pdb=" O HIS N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 213 Processing helix chain 'N' and resid 224 through 241 removed outlier: 4.353A pdb=" N SER N 239 " --> pdb=" O GLY N 235 " (cutoff:3.500A) removed outlier: 4.784A 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 323 through 335 Processing helix chain 'N' and resid 338 through 340 No H-bonds generated for 'chain 'N' and resid 338 through 340' Processing helix chain 'N' and resid 373 through 390 removed outlier: 3.931A 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 'O' and resid 10 through 27 removed outlier: 3.850A pdb=" N GLU O 22 " --> pdb=" O ASN O 18 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU O 23 " --> pdb=" O ALA O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 79 Processing helix chain 'O' and resid 84 through 86 No H-bonds generated for 'chain 'O' and resid 84 through 86' Processing helix chain 'O' and resid 103 through 107 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 removed outlier: 3.951A pdb=" N GLN O 128 " --> pdb=" O LYS O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 160 removed outlier: 4.741A 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 191 Processing helix chain 'O' and resid 195 through 197 No H-bonds generated for 'chain 'O' and resid 195 through 197' Processing helix chain 'O' and resid 206 through 216 Processing helix chain 'O' and resid 226 through 243 removed outlier: 4.738A pdb=" N SER O 241 " --> pdb=" O SER O 237 " (cutoff:3.500A) removed outlier: 5.507A 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: 4.413A pdb=" N PHE O 296 " --> pdb=" O THR O 292 " (cutoff:3.500A) Processing helix chain 'O' and resid 298 through 300 No H-bonds generated for 'chain 'O' and resid 298 through 300' 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 337 removed outlier: 4.184A pdb=" N THR O 337 " --> pdb=" O ALA O 333 " (cutoff:3.500A) Processing helix chain 'O' and resid 383 through 400 removed outlier: 3.678A pdb=" N ALA O 387 " --> pdb=" O ILE O 384 " (cutoff:3.500A) Processing helix chain 'O' and resid 405 through 411 removed outlier: 5.190A pdb=" N GLY O 410 " --> pdb=" O TRP O 407 " (cutoff:3.500A) Processing helix chain 'O' and resid 416 through 434 Processing helix chain 'P' and resid 10 through 27 Processing helix chain 'P' and resid 41 through 43 No H-bonds generated for 'chain 'P' and resid 41 through 43' 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 70 through 78 removed outlier: 3.922A pdb=" N MET P 73 " --> pdb=" O PRO P 70 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP P 74 " --> pdb=" O GLY P 71 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER P 78 " --> pdb=" O SER P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 84 No H-bonds generated for 'chain 'P' and resid 82 through 84' Processing helix chain 'P' and resid 113 through 125 Processing helix chain 'P' and resid 142 through 158 removed outlier: 6.365A pdb=" N MET P 147 " --> pdb=" O THR P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 175 No H-bonds generated for 'chain 'P' and resid 173 through 175' Processing helix chain 'P' and resid 181 through 195 removed outlier: 3.869A pdb=" N GLN P 191 " --> pdb=" O LEU P 187 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU P 194 " --> pdb=" O HIS P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 205 through 213 Processing helix chain 'P' and resid 224 through 241 removed outlier: 4.353A pdb=" N SER P 239 " --> pdb=" O GLY P 235 " (cutoff:3.500A) removed outlier: 4.784A 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 323 through 335 Processing helix chain 'P' and resid 338 through 340 No H-bonds generated for 'chain 'P' and resid 338 through 340' Processing helix chain 'P' and resid 373 through 390 removed outlier: 3.931A 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 sheet with id= A, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.248A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 5 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 317 through 320 removed outlier: 3.792A pdb=" N GLY A 354 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 63 through 66 removed outlier: 8.122A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL B 5 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE B 133 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE B 7 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 135 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ALA B 9 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU B 198 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER B 168 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR B 200 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 170 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE B 202 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 267 through 269 removed outlier: 3.517A pdb=" N MET B 267 " --> pdb=" O GLY B 369 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY B 369 " --> pdb=" O MET B 267 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 65 through 68 removed outlier: 7.248A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 5 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N VAL C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N SER C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 317 through 320 removed outlier: 3.791A pdb=" N GLY C 354 " --> pdb=" O LEU C 317 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 63 through 66 removed outlier: 8.122A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL D 5 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE D 133 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE D 7 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU D 135 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA D 9 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN D 165 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU D 198 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER D 168 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR D 200 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL D 170 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE D 202 " --> pdb=" O VAL D 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 267 through 269 removed outlier: 3.517A pdb=" N MET D 267 " --> pdb=" O GLY D 369 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY D 369 " --> pdb=" O MET D 267 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 65 through 68 removed outlier: 7.248A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE E 5 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 317 through 320 removed outlier: 3.792A pdb=" N GLY E 354 " --> pdb=" O LEU E 317 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 63 through 66 removed outlier: 8.122A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL F 5 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE F 133 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE F 7 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU F 135 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ALA F 9 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN F 165 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU F 198 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER F 168 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR F 200 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL F 170 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE F 202 " --> pdb=" O VAL F 170 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 267 through 269 removed outlier: 3.517A pdb=" N MET F 267 " --> pdb=" O GLY F 369 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY F 369 " --> pdb=" O MET F 267 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 65 through 68 removed outlier: 7.248A pdb=" N SER G 6 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N VAL G 68 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE G 5 " --> pdb=" O GLY G 134 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER G 165 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N VAL G 137 " --> pdb=" O SER G 165 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU G 167 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS G 200 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N SER G 170 " --> pdb=" O CYS G 200 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE G 202 " --> pdb=" O SER G 170 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 317 through 320 removed outlier: 3.791A pdb=" N GLY G 354 " --> pdb=" O LEU G 317 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 63 through 66 removed outlier: 8.122A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL H 5 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE H 133 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE H 7 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU H 135 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA H 9 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN H 165 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU H 198 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER H 168 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR H 200 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL H 170 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE H 202 " --> pdb=" O VAL H 170 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 267 through 269 removed outlier: 3.517A pdb=" N MET H 267 " --> pdb=" O GLY H 369 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY H 369 " --> pdb=" O MET H 267 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 65 through 68 removed outlier: 7.248A pdb=" N SER I 6 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N VAL I 68 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE I 5 " --> pdb=" O GLY I 134 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER I 165 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N VAL I 137 " --> pdb=" O SER I 165 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU I 167 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS I 200 " --> pdb=" O GLU I 168 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N SER I 170 " --> pdb=" O CYS I 200 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE I 202 " --> pdb=" O SER I 170 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 317 through 320 removed outlier: 3.792A pdb=" N GLY I 354 " --> pdb=" O LEU I 317 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 63 through 66 removed outlier: 8.122A pdb=" N ILE J 64 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS J 6 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL J 66 " --> pdb=" O HIS J 6 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN J 8 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL J 5 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE J 133 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE J 7 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU J 135 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ALA J 9 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN J 165 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU J 198 " --> pdb=" O THR J 166 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER J 168 " --> pdb=" O GLU J 198 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR J 200 " --> pdb=" O SER J 168 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL J 170 " --> pdb=" O TYR J 200 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE J 202 " --> pdb=" O VAL J 170 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 267 through 269 removed outlier: 3.517A pdb=" N MET J 267 " --> pdb=" O GLY J 369 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY J 369 " --> pdb=" O MET J 267 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 65 through 68 removed outlier: 7.248A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE K 5 " --> pdb=" O GLY K 134 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER K 165 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N VAL K 137 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N SER K 170 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE K 202 " --> pdb=" O SER K 170 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 317 through 320 removed outlier: 3.791A pdb=" N GLY K 354 " --> pdb=" O LEU K 317 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 63 through 66 removed outlier: 8.122A pdb=" N ILE L 64 " --> pdb=" O ILE L 4 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS L 6 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL L 66 " --> pdb=" O HIS L 6 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN L 8 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL L 5 " --> pdb=" O GLN L 131 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE L 133 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE L 7 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU L 135 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA L 9 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN L 165 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU L 198 " --> pdb=" O THR L 166 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER L 168 " --> pdb=" O GLU L 198 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR L 200 " --> pdb=" O SER L 168 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL L 170 " --> pdb=" O TYR L 200 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE L 202 " --> pdb=" O VAL L 170 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 267 through 269 removed outlier: 3.517A pdb=" N MET L 267 " --> pdb=" O GLY L 369 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY L 369 " --> pdb=" O MET L 267 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 65 through 68 removed outlier: 7.248A pdb=" N SER M 6 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N VAL M 68 " --> pdb=" O SER M 6 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS M 8 " --> pdb=" O VAL M 68 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE M 5 " --> pdb=" O GLY M 134 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER M 165 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N VAL M 137 " --> pdb=" O SER M 165 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU M 167 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS M 200 " --> pdb=" O GLU M 168 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N SER M 170 " --> pdb=" O CYS M 200 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE M 202 " --> pdb=" O SER M 170 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 317 through 320 removed outlier: 3.792A pdb=" N GLY M 354 " --> pdb=" O LEU M 317 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'N' and resid 63 through 66 removed outlier: 8.122A pdb=" N ILE N 64 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS N 6 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL N 66 " --> pdb=" O HIS N 6 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN N 8 " --> pdb=" O VAL N 66 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL N 5 " --> pdb=" O GLN N 131 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE N 133 " --> pdb=" O VAL N 5 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE N 7 " --> pdb=" O PHE N 133 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU N 135 " --> pdb=" O ILE N 7 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ALA N 9 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN N 165 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU N 198 " --> pdb=" O THR N 166 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER N 168 " --> pdb=" O GLU N 198 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR N 200 " --> pdb=" O SER N 168 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL N 170 " --> pdb=" O TYR N 200 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE N 202 " --> pdb=" O VAL N 170 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'N' and resid 267 through 269 removed outlier: 3.517A pdb=" N MET N 267 " --> pdb=" O GLY N 369 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY N 369 " --> pdb=" O MET N 267 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 65 through 68 removed outlier: 7.248A pdb=" N SER O 6 " --> pdb=" O VAL O 66 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N VAL O 68 " --> pdb=" O SER O 6 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS O 8 " --> pdb=" O VAL O 68 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE O 5 " --> pdb=" O GLY O 134 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER O 165 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N VAL O 137 " --> pdb=" O SER O 165 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU O 167 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS O 200 " --> pdb=" O GLU O 168 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N SER O 170 " --> pdb=" O CYS O 200 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE O 202 " --> pdb=" O SER O 170 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 317 through 320 removed outlier: 3.791A pdb=" N GLY O 354 " --> pdb=" O LEU O 317 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'P' and resid 63 through 66 removed outlier: 8.122A pdb=" N ILE P 64 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS P 6 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL P 66 " --> pdb=" O HIS P 6 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN P 8 " --> pdb=" O VAL P 66 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL P 5 " --> pdb=" O GLN P 131 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE P 133 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE P 7 " --> pdb=" O PHE P 133 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU P 135 " --> pdb=" O ILE P 7 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA P 9 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN P 165 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU P 198 " --> pdb=" O THR P 166 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER P 168 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR P 200 " --> pdb=" O SER P 168 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL P 170 " --> pdb=" O TYR P 200 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE P 202 " --> pdb=" O VAL P 170 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'P' and resid 267 through 269 removed outlier: 3.517A pdb=" N MET P 267 " --> pdb=" O GLY P 369 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY P 369 " --> pdb=" O MET P 267 " (cutoff:3.500A) 1848 hydrogen bonds defined for protein. 4704 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: 16.98 Time building geometry restraints manager: 18.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 9088 1.28 - 1.41: 14112 1.41 - 1.54: 31628 1.54 - 1.68: 116 1.68 - 1.81: 584 Bond restraints: 55528 Sorted by residual: bond pdb=" C7 YGY D1201 " pdb=" C8 YGY D1201 " ideal model delta sigma weight residual 1.575 1.324 0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C7 YGY P1201 " pdb=" C8 YGY P1201 " ideal model delta sigma weight residual 1.575 1.324 0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C7 YGY H1201 " pdb=" C8 YGY H1201 " ideal model delta sigma weight residual 1.575 1.324 0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C7 YGY L1201 " pdb=" C8 YGY L1201 " ideal model delta sigma weight residual 1.575 1.324 0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C7 YGY N1201 " pdb=" C8 YGY N1201 " ideal model delta sigma weight residual 1.575 1.324 0.251 2.00e-02 2.50e+03 1.58e+02 ... (remaining 55523 not shown) Histogram of bond angle deviations from ideal: 53.08 - 76.57: 24 76.57 - 100.06: 48 100.06 - 123.54: 73716 123.54 - 147.03: 1740 147.03 - 170.51: 24 Bond angle restraints: 75552 Sorted by residual: angle pdb=" C3 YGY N1201 " pdb=" N1 YGY N1201 " pdb=" C4 YGY N1201 " ideal model delta sigma weight residual 109.51 170.51 -61.00 3.00e+00 1.11e-01 4.13e+02 angle pdb=" C3 YGY J1201 " pdb=" N1 YGY J1201 " pdb=" C4 YGY J1201 " ideal model delta sigma weight residual 109.51 170.51 -61.00 3.00e+00 1.11e-01 4.13e+02 angle pdb=" C3 YGY B1201 " pdb=" N1 YGY B1201 " pdb=" C4 YGY B1201 " ideal model delta sigma weight residual 109.51 170.51 -61.00 3.00e+00 1.11e-01 4.13e+02 angle pdb=" C3 YGY F1201 " pdb=" N1 YGY F1201 " pdb=" C4 YGY F1201 " ideal model delta sigma weight residual 109.51 170.51 -61.00 3.00e+00 1.11e-01 4.13e+02 angle pdb=" C3 YGY P1201 " pdb=" N1 YGY P1201 " pdb=" C4 YGY P1201 " ideal model delta sigma weight residual 109.51 170.45 -60.94 3.00e+00 1.11e-01 4.13e+02 ... (remaining 75547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 32024 35.97 - 71.94: 840 71.94 - 107.91: 200 107.91 - 143.87: 32 143.87 - 179.84: 56 Dihedral angle restraints: 33152 sinusoidal: 13160 harmonic: 19992 Sorted by residual: dihedral pdb=" C4' GTP O 601 " pdb=" C5' GTP O 601 " pdb=" O5' GTP O 601 " pdb=" PA GTP O 601 " ideal model delta sinusoidal sigma weight residual -99.13 76.30 -175.43 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C4' GTP G 601 " pdb=" C5' GTP G 601 " pdb=" O5' GTP G 601 " pdb=" PA GTP G 601 " ideal model delta sinusoidal sigma weight residual -99.13 76.30 -175.43 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C4' GTP K 601 " pdb=" C5' GTP K 601 " pdb=" O5' GTP K 601 " pdb=" PA GTP K 601 " ideal model delta sinusoidal sigma weight residual -99.13 76.30 -175.43 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 33149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 5451 0.047 - 0.094: 2118 0.094 - 0.141: 579 0.141 - 0.188: 112 0.188 - 0.235: 52 Chirality restraints: 8312 Sorted by residual: chirality pdb=" CB ILE O 42 " pdb=" CA ILE O 42 " pdb=" CG1 ILE O 42 " pdb=" CG2 ILE O 42 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE C 42 " pdb=" CA ILE C 42 " pdb=" CG1 ILE C 42 " pdb=" CG2 ILE C 42 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE K 42 " pdb=" CA ILE K 42 " pdb=" CG1 ILE K 42 " pdb=" CG2 ILE K 42 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 8309 not shown) Planarity restraints: 9816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 YGY B1201 " 0.078 2.00e-02 2.50e+03 6.89e-02 5.93e+01 pdb=" C6 YGY B1201 " -0.023 2.00e-02 2.50e+03 pdb=" C7 YGY B1201 " 0.034 2.00e-02 2.50e+03 pdb=" N2 YGY B1201 " -0.122 2.00e-02 2.50e+03 pdb=" O2 YGY B1201 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 YGY F1201 " 0.078 2.00e-02 2.50e+03 6.89e-02 5.93e+01 pdb=" C6 YGY F1201 " -0.023 2.00e-02 2.50e+03 pdb=" C7 YGY F1201 " 0.034 2.00e-02 2.50e+03 pdb=" N2 YGY F1201 " -0.122 2.00e-02 2.50e+03 pdb=" O2 YGY F1201 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 YGY N1201 " -0.078 2.00e-02 2.50e+03 6.89e-02 5.93e+01 pdb=" C6 YGY N1201 " 0.023 2.00e-02 2.50e+03 pdb=" C7 YGY N1201 " -0.034 2.00e-02 2.50e+03 pdb=" N2 YGY N1201 " 0.122 2.00e-02 2.50e+03 pdb=" O2 YGY N1201 " -0.032 2.00e-02 2.50e+03 ... (remaining 9813 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 7449 2.74 - 3.28: 59155 3.28 - 3.82: 91884 3.82 - 4.36: 108818 4.36 - 4.90: 177070 Nonbonded interactions: 444376 Sorted by model distance: nonbonded pdb=" O GLY H 235 " pdb=" OG1 THR H 238 " model vdw 2.203 2.440 nonbonded pdb=" O GLY L 235 " pdb=" OG1 THR L 238 " model vdw 2.203 2.440 nonbonded pdb=" O GLY D 235 " pdb=" OG1 THR D 238 " model vdw 2.203 2.440 nonbonded pdb=" O GLY P 235 " pdb=" OG1 THR P 238 " model vdw 2.203 2.440 nonbonded pdb=" O GLY F 235 " pdb=" OG1 THR F 238 " model vdw 2.203 2.440 ... (remaining 444371 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' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } 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=1.00 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: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 18.760 Check model and map are aligned: 0.680 Set scattering table: 0.390 Process input model: 108.770 Find NCS groups from input model: 3.630 Set up NCS constraints: 0.530 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: 0.020 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 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 : 0.009 0.251 55528 Z= 0.568 Angle : 1.427 61.002 75552 Z= 0.610 Chirality : 0.055 0.235 8312 Planarity : 0.005 0.069 9816 Dihedral : 20.273 179.842 20336 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.57 % Allowed : 13.89 % Favored : 85.54 % Rotamer: Outliers : 0.58 % Allowed : 1.30 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.10), residues: 6896 helix: 0.64 (0.10), residues: 2768 sheet: -1.92 (0.16), residues: 1008 loop : -3.11 (0.10), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 346 HIS 0.005 0.002 HIS P 190 PHE 0.023 0.002 PHE I 53 TYR 0.028 0.003 TYR C 185 ARG 0.005 0.001 ARG K 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1112 time to evaluate : 4.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8486 (mmt) cc_final: 0.8282 (mmt) REVERT: A 167 LEU cc_start: 0.8469 (tp) cc_final: 0.8186 (tp) REVERT: A 211 ASP cc_start: 0.7137 (t0) cc_final: 0.6245 (t0) REVERT: A 346 TRP cc_start: 0.8506 (OUTLIER) cc_final: 0.7477 (p-90) REVERT: A 394 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7794 (mmtt) REVERT: A 417 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7596 (mp0) REVERT: B 44 LEU cc_start: 0.8428 (mp) cc_final: 0.7766 (mp) REVERT: B 101 TRP cc_start: 0.5378 (m100) cc_final: 0.4645 (m-10) REVERT: B 200 TYR cc_start: 0.7722 (m-80) cc_final: 0.7416 (m-80) REVERT: B 203 ASP cc_start: 0.6865 (t0) cc_final: 0.6613 (t0) REVERT: B 253 LEU cc_start: 0.8500 (mt) cc_final: 0.8175 (mt) REVERT: B 299 MET cc_start: 0.7909 (ptp) cc_final: 0.7365 (ptp) REVERT: B 423 GLN cc_start: 0.8185 (tp40) cc_final: 0.7860 (tp40) REVERT: C 138 PHE cc_start: 0.7093 (m-80) cc_final: 0.6876 (m-80) REVERT: C 153 LEU cc_start: 0.9136 (tp) cc_final: 0.8892 (tp) REVERT: C 233 GLN cc_start: 0.7367 (tm130) cc_final: 0.6903 (tp40) REVERT: C 346 TRP cc_start: 0.8492 (OUTLIER) cc_final: 0.7626 (p-90) REVERT: D 101 TRP cc_start: 0.5591 (m100) cc_final: 0.4703 (m-10) REVERT: D 257 MET cc_start: 0.7945 (mmp) cc_final: 0.7666 (mmp) REVERT: D 299 MET cc_start: 0.7666 (ptp) cc_final: 0.7302 (ptp) REVERT: D 330 MET cc_start: 0.8726 (mmp) cc_final: 0.8342 (mmm) REVERT: E 154 MET cc_start: 0.8484 (mmt) cc_final: 0.8281 (mmt) REVERT: E 167 LEU cc_start: 0.8439 (tp) cc_final: 0.8180 (tp) REVERT: E 211 ASP cc_start: 0.7143 (t0) cc_final: 0.6248 (t0) REVERT: E 346 TRP cc_start: 0.8506 (OUTLIER) cc_final: 0.7477 (p-90) REVERT: E 394 LYS cc_start: 0.8203 (mtmt) cc_final: 0.7793 (mmtt) REVERT: E 417 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7596 (mp0) REVERT: F 44 LEU cc_start: 0.8426 (mp) cc_final: 0.7764 (mp) REVERT: F 101 TRP cc_start: 0.5378 (m100) cc_final: 0.4642 (m-10) REVERT: F 200 TYR cc_start: 0.7725 (m-80) cc_final: 0.7419 (m-80) REVERT: F 203 ASP cc_start: 0.6865 (t0) cc_final: 0.6613 (t0) REVERT: F 253 LEU cc_start: 0.8496 (mt) cc_final: 0.8176 (mt) REVERT: F 299 MET cc_start: 0.7910 (ptp) cc_final: 0.7368 (ptp) REVERT: F 423 GLN cc_start: 0.8184 (tp40) cc_final: 0.7859 (tp40) REVERT: G 138 PHE cc_start: 0.7086 (m-80) cc_final: 0.6868 (m-80) REVERT: G 153 LEU cc_start: 0.9136 (tp) cc_final: 0.8892 (tp) REVERT: G 233 GLN cc_start: 0.7367 (tm130) cc_final: 0.6904 (tp40) REVERT: G 346 TRP cc_start: 0.8493 (OUTLIER) cc_final: 0.7626 (p-90) REVERT: H 101 TRP cc_start: 0.5592 (m100) cc_final: 0.4704 (m-10) REVERT: H 257 MET cc_start: 0.7942 (mmp) cc_final: 0.7659 (mmp) REVERT: H 299 MET cc_start: 0.7667 (ptp) cc_final: 0.7302 (ptp) REVERT: H 330 MET cc_start: 0.8724 (mmp) cc_final: 0.8335 (mmm) REVERT: I 154 MET cc_start: 0.8483 (mmt) cc_final: 0.8281 (mmt) REVERT: I 167 LEU cc_start: 0.8479 (tp) cc_final: 0.8198 (tp) REVERT: I 211 ASP cc_start: 0.7142 (t0) cc_final: 0.6247 (t0) REVERT: I 346 TRP cc_start: 0.8506 (OUTLIER) cc_final: 0.7477 (p-90) REVERT: I 394 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7793 (mmtt) REVERT: I 417 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7559 (mp0) REVERT: J 44 LEU cc_start: 0.8426 (mp) cc_final: 0.7764 (mp) REVERT: J 101 TRP cc_start: 0.5382 (m100) cc_final: 0.4643 (m-10) REVERT: J 200 TYR cc_start: 0.7725 (m-80) cc_final: 0.7420 (m-80) REVERT: J 253 LEU cc_start: 0.8496 (mt) cc_final: 0.8176 (mt) REVERT: J 299 MET cc_start: 0.7909 (ptp) cc_final: 0.7363 (ptp) REVERT: J 423 GLN cc_start: 0.8185 (tp40) cc_final: 0.7859 (tp40) REVERT: K 138 PHE cc_start: 0.7086 (m-80) cc_final: 0.6867 (m-80) REVERT: K 153 LEU cc_start: 0.9135 (tp) cc_final: 0.8891 (tp) REVERT: K 233 GLN cc_start: 0.7380 (tm130) cc_final: 0.6813 (tp40) REVERT: K 346 TRP cc_start: 0.8493 (OUTLIER) cc_final: 0.7627 (p-90) REVERT: L 101 TRP cc_start: 0.5591 (m100) cc_final: 0.4701 (m-10) REVERT: L 257 MET cc_start: 0.7944 (mmp) cc_final: 0.7666 (mmp) REVERT: L 299 MET cc_start: 0.7665 (ptp) cc_final: 0.7301 (ptp) REVERT: L 330 MET cc_start: 0.8724 (mmp) cc_final: 0.8337 (mmm) REVERT: M 154 MET cc_start: 0.8484 (mmt) cc_final: 0.8281 (mmt) REVERT: M 167 LEU cc_start: 0.8437 (tp) cc_final: 0.8188 (tp) REVERT: M 211 ASP cc_start: 0.7141 (t0) cc_final: 0.6245 (t0) REVERT: M 346 TRP cc_start: 0.8505 (OUTLIER) cc_final: 0.7477 (p-90) REVERT: M 394 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7794 (mmtt) REVERT: M 417 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7558 (mp0) REVERT: N 44 LEU cc_start: 0.8426 (mp) cc_final: 0.7765 (mp) REVERT: N 101 TRP cc_start: 0.5380 (m100) cc_final: 0.4642 (m-10) REVERT: N 200 TYR cc_start: 0.7725 (m-80) cc_final: 0.7419 (m-80) REVERT: N 253 LEU cc_start: 0.8500 (mt) cc_final: 0.8176 (mt) REVERT: N 299 MET cc_start: 0.7909 (ptp) cc_final: 0.7364 (ptp) REVERT: N 423 GLN cc_start: 0.8184 (tp40) cc_final: 0.7859 (tp40) REVERT: O 138 PHE cc_start: 0.7092 (m-80) cc_final: 0.6875 (m-80) REVERT: O 153 LEU cc_start: 0.9135 (tp) cc_final: 0.8891 (tp) REVERT: O 233 GLN cc_start: 0.7375 (tm130) cc_final: 0.6809 (tp40) REVERT: O 346 TRP cc_start: 0.8493 (OUTLIER) cc_final: 0.7626 (p-90) REVERT: P 101 TRP cc_start: 0.5593 (m100) cc_final: 0.4704 (m-10) REVERT: P 257 MET cc_start: 0.7944 (mmp) cc_final: 0.7665 (mmp) REVERT: P 299 MET cc_start: 0.7666 (ptp) cc_final: 0.7302 (ptp) REVERT: P 330 MET cc_start: 0.8724 (mmp) cc_final: 0.8340 (mmm) outliers start: 33 outliers final: 8 residues processed: 1128 average time/residue: 0.4694 time to fit residues: 919.3394 Evaluate side-chains 855 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 839 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain C residue 346 TRP Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain E residue 346 TRP Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain G residue 346 TRP Chi-restraints excluded: chain G residue 347 CYS Chi-restraints excluded: chain I residue 346 TRP Chi-restraints excluded: chain I residue 347 CYS Chi-restraints excluded: chain K residue 346 TRP Chi-restraints excluded: chain K residue 347 CYS Chi-restraints excluded: chain M residue 346 TRP Chi-restraints excluded: chain M residue 347 CYS Chi-restraints excluded: chain O residue 346 TRP Chi-restraints excluded: chain O residue 347 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 580 optimal weight: 10.0000 chunk 521 optimal weight: 4.9990 chunk 289 optimal weight: 0.8980 chunk 178 optimal weight: 0.8980 chunk 351 optimal weight: 0.7980 chunk 278 optimal weight: 0.6980 chunk 539 optimal weight: 0.0980 chunk 208 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 chunk 401 optimal weight: 3.9990 chunk 624 optimal weight: 0.0170 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 11 GLN B 256 ASN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 100 ASN D 256 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN F 256 ASN ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 100 ASN H 256 ASN ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN J 256 ASN ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 100 ASN L 256 ASN ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN N 256 ASN ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN P 100 ASN P 256 ASN ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 55528 Z= 0.191 Angle : 0.708 12.969 75552 Z= 0.339 Chirality : 0.046 0.183 8312 Planarity : 0.005 0.061 9816 Dihedral : 22.003 169.014 8192 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.48 % Favored : 90.41 % Rotamer: Outliers : 1.09 % Allowed : 13.01 % Favored : 85.90 % 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: -1.75 (0.10), residues: 6896 helix: 0.71 (0.10), residues: 2872 sheet: -1.69 (0.16), residues: 1000 loop : -2.94 (0.10), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 346 HIS 0.003 0.001 HIS M 8 PHE 0.011 0.001 PHE K 202 TYR 0.017 0.002 TYR O 103 ARG 0.002 0.000 ARG L 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 981 time to evaluate : 4.977 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: A 167 LEU cc_start: 0.8603 (tp) cc_final: 0.8194 (tp) REVERT: A 211 ASP cc_start: 0.6763 (t0) cc_final: 0.6116 (t0) REVERT: A 292 THR cc_start: 0.8353 (t) cc_final: 0.8148 (t) REVERT: A 417 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7522 (mp0) REVERT: B 101 TRP cc_start: 0.5029 (m100) cc_final: 0.4277 (m-10) REVERT: B 195 ASN cc_start: 0.8590 (m-40) cc_final: 0.8285 (m-40) REVERT: B 203 ASP cc_start: 0.6795 (t0) cc_final: 0.6559 (t0) REVERT: B 299 MET cc_start: 0.7952 (ptp) cc_final: 0.7477 (ptp) REVERT: C 97 GLU cc_start: 0.6758 (tt0) cc_final: 0.6471 (tt0) REVERT: C 153 LEU cc_start: 0.9133 (tp) cc_final: 0.8862 (tp) REVERT: C 233 GLN cc_start: 0.7267 (tm-30) cc_final: 0.6989 (tp40) REVERT: C 346 TRP cc_start: 0.8520 (p-90) cc_final: 0.8280 (p-90) REVERT: D 86 ARG cc_start: 0.7758 (ttt90) cc_final: 0.7444 (ttt-90) REVERT: D 101 TRP cc_start: 0.4910 (m100) cc_final: 0.4003 (m-10) REVERT: D 159 TYR cc_start: 0.8396 (m-10) cc_final: 0.8194 (m-10) REVERT: D 330 MET cc_start: 0.8719 (mmp) cc_final: 0.8392 (mmm) REVERT: E 97 GLU cc_start: 0.7108 (tt0) cc_final: 0.6819 (pp20) REVERT: E 211 ASP cc_start: 0.6767 (t0) cc_final: 0.6117 (t0) REVERT: E 292 THR cc_start: 0.8380 (t) cc_final: 0.8175 (t) REVERT: E 417 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7518 (mp0) REVERT: F 101 TRP cc_start: 0.5032 (m100) cc_final: 0.4278 (m-10) REVERT: F 195 ASN cc_start: 0.8590 (m-40) cc_final: 0.8285 (m-40) REVERT: F 203 ASP cc_start: 0.6796 (t0) cc_final: 0.6559 (t0) REVERT: F 299 MET cc_start: 0.7954 (ptp) cc_final: 0.7477 (ptp) REVERT: G 97 GLU cc_start: 0.6759 (tt0) cc_final: 0.6486 (tt0) REVERT: G 153 LEU cc_start: 0.9134 (tp) cc_final: 0.8861 (tp) REVERT: G 233 GLN cc_start: 0.7409 (tm130) cc_final: 0.7045 (tp40) REVERT: G 346 TRP cc_start: 0.8520 (p-90) cc_final: 0.8281 (p-90) REVERT: H 86 ARG cc_start: 0.7760 (ttt90) cc_final: 0.7446 (ttt-90) REVERT: H 101 TRP cc_start: 0.4908 (m100) cc_final: 0.4003 (m-10) REVERT: H 159 TYR cc_start: 0.8396 (m-10) cc_final: 0.8193 (m-10) REVERT: H 330 MET cc_start: 0.8716 (mmp) cc_final: 0.8386 (mmm) REVERT: I 167 LEU cc_start: 0.8617 (tp) cc_final: 0.8209 (tp) REVERT: I 211 ASP cc_start: 0.6768 (t0) cc_final: 0.6116 (t0) REVERT: I 292 THR cc_start: 0.8380 (t) cc_final: 0.8175 (t) REVERT: I 417 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7482 (mp0) REVERT: J 101 TRP cc_start: 0.5032 (m100) cc_final: 0.4278 (m-10) REVERT: J 195 ASN cc_start: 0.8589 (m-40) cc_final: 0.8285 (m-40) REVERT: J 299 MET cc_start: 0.7954 (ptp) cc_final: 0.7474 (ptp) REVERT: K 153 LEU cc_start: 0.9134 (tp) cc_final: 0.8859 (tp) REVERT: K 233 GLN cc_start: 0.7429 (tm130) cc_final: 0.6955 (tp40) REVERT: K 346 TRP cc_start: 0.8519 (p-90) cc_final: 0.8280 (p-90) REVERT: L 101 TRP cc_start: 0.4908 (m100) cc_final: 0.4002 (m-10) REVERT: L 159 TYR cc_start: 0.8395 (m-10) cc_final: 0.8192 (m-10) REVERT: L 330 MET cc_start: 0.8718 (mmp) cc_final: 0.8385 (mmm) REVERT: M 211 ASP cc_start: 0.6770 (t0) cc_final: 0.6121 (t0) REVERT: M 292 THR cc_start: 0.8381 (t) cc_final: 0.8177 (t) REVERT: M 417 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7482 (mp0) REVERT: N 101 TRP cc_start: 0.5030 (m100) cc_final: 0.4276 (m-10) REVERT: N 195 ASN cc_start: 0.8589 (m-40) cc_final: 0.8284 (m-40) REVERT: N 299 MET cc_start: 0.7955 (ptp) cc_final: 0.7474 (ptp) REVERT: O 153 LEU cc_start: 0.9133 (tp) cc_final: 0.8859 (tp) REVERT: O 233 GLN cc_start: 0.7426 (tm130) cc_final: 0.6950 (tp40) REVERT: O 346 TRP cc_start: 0.8520 (p-90) cc_final: 0.8281 (p-90) REVERT: P 101 TRP cc_start: 0.4908 (m100) cc_final: 0.4002 (m-10) REVERT: P 159 TYR cc_start: 0.8393 (m-10) cc_final: 0.8192 (m-10) REVERT: P 330 MET cc_start: 0.8718 (mmp) cc_final: 0.8390 (mmm) outliers start: 62 outliers final: 36 residues processed: 1001 average time/residue: 0.4780 time to fit residues: 829.7219 Evaluate side-chains 888 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 852 time to evaluate : 4.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 347 CYS Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 347 CYS Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 347 CYS Chi-restraints excluded: chain K residue 368 LEU Chi-restraints excluded: chain M residue 194 THR Chi-restraints excluded: chain M residue 347 CYS Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 347 CYS Chi-restraints excluded: chain O residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 347 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 519 optimal weight: 3.9990 chunk 425 optimal weight: 0.6980 chunk 172 optimal weight: 8.9990 chunk 625 optimal weight: 1.9990 chunk 676 optimal weight: 2.9990 chunk 557 optimal weight: 0.6980 chunk 620 optimal weight: 0.7980 chunk 213 optimal weight: 0.0970 chunk 502 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 ASN ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN L 256 ASN ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN ** N 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 256 ASN ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 55528 Z= 0.174 Angle : 0.659 12.331 75552 Z= 0.313 Chirality : 0.044 0.175 8312 Planarity : 0.004 0.043 9816 Dihedral : 21.388 171.476 8176 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.18 % Favored : 90.72 % Rotamer: Outliers : 2.00 % Allowed : 15.73 % Favored : 82.27 % 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: -1.56 (0.10), residues: 6896 helix: 0.72 (0.10), residues: 2952 sheet: -1.52 (0.16), residues: 968 loop : -2.76 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 346 HIS 0.003 0.001 HIS J 396 PHE 0.011 0.001 PHE C 169 TYR 0.018 0.001 TYR C 312 ARG 0.002 0.000 ARG H 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 915 time to evaluate : 4.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8604 (tp) cc_final: 0.8203 (tp) REVERT: A 211 ASP cc_start: 0.6631 (t0) cc_final: 0.6102 (t0) REVERT: A 254 GLU cc_start: 0.8453 (tt0) cc_final: 0.8102 (tt0) REVERT: A 398 MET cc_start: 0.7788 (mtt) cc_final: 0.7456 (mtt) REVERT: A 417 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7618 (mp0) REVERT: B 101 TRP cc_start: 0.5092 (m100) cc_final: 0.4311 (m-10) REVERT: B 158 GLU cc_start: 0.7890 (tt0) cc_final: 0.7456 (tt0) REVERT: B 195 ASN cc_start: 0.8577 (m-40) cc_final: 0.8294 (m-40) REVERT: B 299 MET cc_start: 0.7713 (ptp) cc_final: 0.7377 (ptp) REVERT: B 363 MET cc_start: 0.6859 (mpp) cc_final: 0.6228 (mtt) REVERT: C 97 GLU cc_start: 0.6763 (tt0) cc_final: 0.6521 (tt0) REVERT: C 153 LEU cc_start: 0.9039 (tp) cc_final: 0.8702 (tp) REVERT: C 346 TRP cc_start: 0.8503 (p-90) cc_final: 0.8288 (p-90) REVERT: D 101 TRP cc_start: 0.4734 (m100) cc_final: 0.4025 (m-10) REVERT: D 300 MET cc_start: 0.6247 (mtt) cc_final: 0.5798 (mtt) REVERT: D 363 MET cc_start: 0.6700 (mpp) cc_final: 0.6274 (mtt) REVERT: D 401 GLU cc_start: 0.6518 (tp30) cc_final: 0.6310 (tp30) REVERT: D 426 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7195 (tm-30) REVERT: E 211 ASP cc_start: 0.6626 (t0) cc_final: 0.6096 (t0) REVERT: E 254 GLU cc_start: 0.8456 (tt0) cc_final: 0.8102 (tt0) REVERT: E 398 MET cc_start: 0.7787 (mtt) cc_final: 0.7456 (mtt) REVERT: E 417 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7615 (mp0) REVERT: F 101 TRP cc_start: 0.5096 (m100) cc_final: 0.4313 (m-10) REVERT: F 158 GLU cc_start: 0.7890 (tt0) cc_final: 0.7456 (tt0) REVERT: F 195 ASN cc_start: 0.8574 (m-40) cc_final: 0.8292 (m-40) REVERT: F 299 MET cc_start: 0.7715 (ptp) cc_final: 0.7379 (ptp) REVERT: F 363 MET cc_start: 0.6859 (mpp) cc_final: 0.6230 (mtt) REVERT: G 97 GLU cc_start: 0.6762 (tt0) cc_final: 0.6477 (tt0) REVERT: G 153 LEU cc_start: 0.9039 (tp) cc_final: 0.8702 (tp) REVERT: G 346 TRP cc_start: 0.8503 (p-90) cc_final: 0.8289 (p-90) REVERT: H 101 TRP cc_start: 0.4738 (m100) cc_final: 0.4027 (m-10) REVERT: H 257 MET cc_start: 0.7881 (mmp) cc_final: 0.7681 (mmp) REVERT: H 300 MET cc_start: 0.6249 (mtt) cc_final: 0.5801 (mtt) REVERT: H 363 MET cc_start: 0.6877 (mpp) cc_final: 0.6415 (mtt) REVERT: H 401 GLU cc_start: 0.6518 (tp30) cc_final: 0.6309 (tp30) REVERT: H 426 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7195 (tm-30) REVERT: I 167 LEU cc_start: 0.8616 (tp) cc_final: 0.8212 (tp) REVERT: I 211 ASP cc_start: 0.6630 (t0) cc_final: 0.6097 (t0) REVERT: I 254 GLU cc_start: 0.8457 (tt0) cc_final: 0.8104 (tt0) REVERT: I 398 MET cc_start: 0.7789 (mtt) cc_final: 0.7458 (mtt) REVERT: I 417 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7574 (mp0) REVERT: J 101 TRP cc_start: 0.5096 (m100) cc_final: 0.4314 (m-10) REVERT: J 158 GLU cc_start: 0.7891 (tt0) cc_final: 0.7457 (tt0) REVERT: J 195 ASN cc_start: 0.8575 (m-40) cc_final: 0.8293 (m-40) REVERT: J 299 MET cc_start: 0.7714 (ptp) cc_final: 0.7378 (ptp) REVERT: J 363 MET cc_start: 0.6862 (mpp) cc_final: 0.6231 (mtt) REVERT: K 153 LEU cc_start: 0.9116 (tp) cc_final: 0.8853 (tp) REVERT: K 346 TRP cc_start: 0.8501 (p-90) cc_final: 0.8288 (p-90) REVERT: L 101 TRP cc_start: 0.4734 (m100) cc_final: 0.4026 (m-10) REVERT: L 257 MET cc_start: 0.7887 (mmp) cc_final: 0.7685 (mmp) REVERT: L 300 MET cc_start: 0.6248 (mtt) cc_final: 0.5800 (mtt) REVERT: L 363 MET cc_start: 0.6875 (mpp) cc_final: 0.6413 (mtt) REVERT: L 401 GLU cc_start: 0.6514 (tp30) cc_final: 0.6308 (tp30) REVERT: L 426 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7195 (tm-30) REVERT: M 154 MET cc_start: 0.8490 (mmm) cc_final: 0.8252 (mmt) REVERT: M 211 ASP cc_start: 0.6633 (t0) cc_final: 0.6100 (t0) REVERT: M 254 GLU cc_start: 0.8454 (tt0) cc_final: 0.8100 (tt0) REVERT: M 398 MET cc_start: 0.7785 (mtt) cc_final: 0.7453 (mtt) REVERT: M 417 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7574 (mp0) REVERT: N 101 TRP cc_start: 0.5095 (m100) cc_final: 0.4325 (m-10) REVERT: N 158 GLU cc_start: 0.7889 (tt0) cc_final: 0.7454 (tt0) REVERT: N 195 ASN cc_start: 0.8574 (m-40) cc_final: 0.8293 (m-40) REVERT: N 299 MET cc_start: 0.7713 (ptp) cc_final: 0.7379 (ptp) REVERT: N 363 MET cc_start: 0.6831 (mpp) cc_final: 0.6150 (mtt) REVERT: O 153 LEU cc_start: 0.9116 (tp) cc_final: 0.8853 (tp) REVERT: O 346 TRP cc_start: 0.8503 (p-90) cc_final: 0.8289 (p-90) REVERT: P 101 TRP cc_start: 0.4735 (m100) cc_final: 0.4027 (m-10) REVERT: P 300 MET cc_start: 0.6247 (mtt) cc_final: 0.5795 (mtt) REVERT: P 363 MET cc_start: 0.6877 (mpp) cc_final: 0.6418 (mtt) REVERT: P 401 GLU cc_start: 0.6518 (tp30) cc_final: 0.6308 (tp30) REVERT: P 426 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7197 (tm-30) outliers start: 114 outliers final: 76 residues processed: 985 average time/residue: 0.4696 time to fit residues: 805.1807 Evaluate side-chains 902 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 826 time to evaluate : 5.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 347 CYS Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 386 THR Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 347 CYS Chi-restraints excluded: chain L residue 100 ASN Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 270 PHE Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 386 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 194 THR Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain N residue 374 ILE Chi-restraints excluded: chain N residue 386 THR Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 347 CYS Chi-restraints excluded: chain P residue 100 ASN Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 386 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 618 optimal weight: 2.9990 chunk 470 optimal weight: 3.9990 chunk 324 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 chunk 420 optimal weight: 9.9990 chunk 628 optimal weight: 0.0040 chunk 665 optimal weight: 4.9990 chunk 328 optimal weight: 3.9990 chunk 595 optimal weight: 6.9990 chunk 179 optimal weight: 0.7980 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 334 GLN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 334 GLN ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 334 GLN ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 GLN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN P 334 GLN ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 55528 Z= 0.232 Angle : 0.678 12.046 75552 Z= 0.323 Chirality : 0.045 0.273 8312 Planarity : 0.004 0.043 9816 Dihedral : 21.367 171.677 8172 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.08 % Favored : 89.82 % Rotamer: Outliers : 2.46 % Allowed : 18.42 % Favored : 79.13 % 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: -1.47 (0.10), residues: 6896 helix: 0.75 (0.10), residues: 2952 sheet: -1.41 (0.17), residues: 960 loop : -2.70 (0.10), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 346 HIS 0.005 0.001 HIS L 396 PHE 0.012 0.002 PHE G 255 TYR 0.027 0.002 TYR C 312 ARG 0.006 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 867 time to evaluate : 4.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8771 (tp) cc_final: 0.8417 (tp) REVERT: A 313 MET cc_start: 0.7699 (mmp) cc_final: 0.7475 (mmp) REVERT: A 417 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7670 (mp0) REVERT: B 101 TRP cc_start: 0.5232 (m100) cc_final: 0.4544 (m-10) REVERT: B 195 ASN cc_start: 0.8612 (m-40) cc_final: 0.8319 (m-40) REVERT: B 293 MET cc_start: 0.5405 (tpp) cc_final: 0.4913 (tpt) REVERT: B 299 MET cc_start: 0.7754 (ptp) cc_final: 0.7476 (ptp) REVERT: C 97 GLU cc_start: 0.6904 (tt0) cc_final: 0.6654 (tt0) REVERT: C 153 LEU cc_start: 0.9060 (tp) cc_final: 0.8711 (tp) REVERT: D 101 TRP cc_start: 0.4991 (m100) cc_final: 0.4255 (m-10) REVERT: D 280 GLN cc_start: 0.2452 (OUTLIER) cc_final: 0.2239 (pp30) REVERT: D 300 MET cc_start: 0.6309 (mtt) cc_final: 0.5798 (mtt) REVERT: E 167 LEU cc_start: 0.8586 (tp) cc_final: 0.8261 (tp) REVERT: E 313 MET cc_start: 0.7714 (mmp) cc_final: 0.7507 (mmp) REVERT: E 417 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7667 (mp0) REVERT: F 101 TRP cc_start: 0.5240 (m100) cc_final: 0.4555 (m-10) REVERT: F 195 ASN cc_start: 0.8609 (m-40) cc_final: 0.8315 (m-40) REVERT: F 299 MET cc_start: 0.7765 (ptp) cc_final: 0.7483 (ptp) REVERT: G 97 GLU cc_start: 0.6905 (tt0) cc_final: 0.6625 (tt0) REVERT: G 153 LEU cc_start: 0.9061 (tp) cc_final: 0.8711 (tp) REVERT: H 101 TRP cc_start: 0.4992 (m100) cc_final: 0.4254 (m-10) REVERT: H 280 GLN cc_start: 0.2455 (OUTLIER) cc_final: 0.2241 (pp30) REVERT: H 300 MET cc_start: 0.6311 (mtt) cc_final: 0.5799 (mtt) REVERT: I 167 LEU cc_start: 0.8765 (tp) cc_final: 0.8386 (tp) REVERT: I 313 MET cc_start: 0.7722 (mmp) cc_final: 0.7506 (mmp) REVERT: I 417 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7634 (mp0) REVERT: J 101 TRP cc_start: 0.5236 (m100) cc_final: 0.4552 (m-10) REVERT: J 195 ASN cc_start: 0.8610 (m-40) cc_final: 0.8315 (m-40) REVERT: J 299 MET cc_start: 0.7763 (ptp) cc_final: 0.7481 (ptp) REVERT: K 153 LEU cc_start: 0.9108 (tp) cc_final: 0.8847 (tp) REVERT: L 101 TRP cc_start: 0.4991 (m100) cc_final: 0.4253 (m-10) REVERT: L 280 GLN cc_start: 0.2454 (OUTLIER) cc_final: 0.2240 (pp30) REVERT: L 300 MET cc_start: 0.6310 (mtt) cc_final: 0.5796 (mtt) REVERT: M 167 LEU cc_start: 0.8531 (tp) cc_final: 0.8198 (tp) REVERT: M 313 MET cc_start: 0.7706 (mmp) cc_final: 0.7476 (mmp) REVERT: M 417 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7633 (mp0) REVERT: N 101 TRP cc_start: 0.5232 (m100) cc_final: 0.4541 (m-10) REVERT: N 195 ASN cc_start: 0.8609 (m-40) cc_final: 0.8317 (m-40) REVERT: N 293 MET cc_start: 0.5299 (tpp) cc_final: 0.4806 (tpt) REVERT: N 299 MET cc_start: 0.7761 (ptp) cc_final: 0.7481 (ptp) REVERT: O 153 LEU cc_start: 0.9108 (tp) cc_final: 0.8846 (tp) REVERT: P 101 TRP cc_start: 0.4991 (m100) cc_final: 0.4251 (m-10) REVERT: P 280 GLN cc_start: 0.2458 (OUTLIER) cc_final: 0.2245 (pp30) REVERT: P 300 MET cc_start: 0.6309 (mtt) cc_final: 0.5792 (mtt) outliers start: 140 outliers final: 96 residues processed: 960 average time/residue: 0.4621 time to fit residues: 778.1736 Evaluate side-chains 904 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 804 time to evaluate : 4.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 347 CYS Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 280 GLN Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 386 THR Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 137 HIS Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain J residue 399 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 347 CYS Chi-restraints excluded: chain L residue 100 ASN Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 270 PHE Chi-restraints excluded: chain L residue 280 GLN Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 386 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 194 THR Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 137 HIS Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 280 GLN Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 374 ILE Chi-restraints excluded: chain N residue 386 THR Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 194 THR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 347 CYS Chi-restraints excluded: chain P residue 100 ASN Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain P residue 280 GLN Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 323 MET Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 386 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 553 optimal weight: 1.9990 chunk 377 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 495 optimal weight: 0.9990 chunk 274 optimal weight: 4.9990 chunk 567 optimal weight: 5.9990 chunk 459 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 339 optimal weight: 0.9990 chunk 596 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 GLN I 11 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 423 GLN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN P 226 ASN ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 423 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 55528 Z= 0.200 Angle : 0.668 11.885 75552 Z= 0.318 Chirality : 0.044 0.224 8312 Planarity : 0.004 0.041 9816 Dihedral : 21.014 168.577 8172 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.25 % Favored : 90.65 % Rotamer: Outliers : 2.95 % Allowed : 19.82 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.10), residues: 6896 helix: 0.79 (0.10), residues: 2952 sheet: -1.32 (0.17), residues: 952 loop : -2.59 (0.11), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 346 HIS 0.004 0.001 HIS C 406 PHE 0.012 0.001 PHE C 169 TYR 0.024 0.001 TYR G 312 ARG 0.005 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 871 time to evaluate : 4.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8622 (mmm) cc_final: 0.8361 (mmt) REVERT: A 254 GLU cc_start: 0.8522 (tt0) cc_final: 0.7995 (tt0) REVERT: A 337 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7613 (m) REVERT: A 417 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7698 (mp0) REVERT: B 101 TRP cc_start: 0.5243 (m100) cc_final: 0.4696 (m100) REVERT: B 195 ASN cc_start: 0.8634 (m-40) cc_final: 0.8358 (m-40) REVERT: B 293 MET cc_start: 0.5308 (tpp) cc_final: 0.4881 (tpt) REVERT: B 299 MET cc_start: 0.7787 (ptp) cc_final: 0.7497 (ptp) REVERT: B 363 MET cc_start: 0.6646 (mpp) cc_final: 0.6038 (mtt) REVERT: C 97 GLU cc_start: 0.6869 (tt0) cc_final: 0.6588 (tt0) REVERT: C 153 LEU cc_start: 0.9031 (tp) cc_final: 0.8674 (tp) REVERT: C 337 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7348 (m) REVERT: C 429 GLU cc_start: 0.7109 (pp20) cc_final: 0.6888 (pp20) REVERT: D 101 TRP cc_start: 0.5182 (m100) cc_final: 0.4200 (m-10) REVERT: D 300 MET cc_start: 0.6467 (mtt) cc_final: 0.5915 (mtt) REVERT: D 388 MET cc_start: 0.7691 (tpp) cc_final: 0.7456 (tpp) REVERT: E 154 MET cc_start: 0.8650 (mmm) cc_final: 0.8382 (mmt) REVERT: E 167 LEU cc_start: 0.8574 (tp) cc_final: 0.8226 (tp) REVERT: E 254 GLU cc_start: 0.8527 (tt0) cc_final: 0.7988 (tt0) REVERT: E 337 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7612 (m) REVERT: E 417 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7696 (mp0) REVERT: F 101 TRP cc_start: 0.5245 (m100) cc_final: 0.4696 (m100) REVERT: F 195 ASN cc_start: 0.8633 (m-40) cc_final: 0.8356 (m-40) REVERT: F 293 MET cc_start: 0.5114 (tpp) cc_final: 0.4710 (tpt) REVERT: F 299 MET cc_start: 0.7796 (ptp) cc_final: 0.7507 (ptp) REVERT: F 363 MET cc_start: 0.6600 (mpp) cc_final: 0.6023 (mtt) REVERT: G 97 GLU cc_start: 0.6883 (tt0) cc_final: 0.6643 (tt0) REVERT: G 153 LEU cc_start: 0.9032 (tp) cc_final: 0.8676 (tp) REVERT: G 337 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7349 (m) REVERT: G 429 GLU cc_start: 0.7110 (pp20) cc_final: 0.6890 (pp20) REVERT: H 101 TRP cc_start: 0.5191 (m100) cc_final: 0.4221 (m-10) REVERT: H 299 MET cc_start: 0.7498 (ptp) cc_final: 0.7132 (ptp) REVERT: H 300 MET cc_start: 0.6448 (mtt) cc_final: 0.5898 (mtt) REVERT: H 363 MET cc_start: 0.6883 (mpp) cc_final: 0.5934 (mtt) REVERT: H 388 MET cc_start: 0.7690 (tpp) cc_final: 0.7455 (tpp) REVERT: I 154 MET cc_start: 0.8633 (mmm) cc_final: 0.8351 (mmt) REVERT: I 254 GLU cc_start: 0.8532 (tt0) cc_final: 0.7993 (tt0) REVERT: I 337 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7613 (m) REVERT: I 417 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7623 (mp0) REVERT: J 101 TRP cc_start: 0.5242 (m100) cc_final: 0.4694 (m100) REVERT: J 195 ASN cc_start: 0.8634 (m-40) cc_final: 0.8356 (m-40) REVERT: J 293 MET cc_start: 0.5114 (tpp) cc_final: 0.4711 (tpt) REVERT: J 299 MET cc_start: 0.7789 (ptp) cc_final: 0.7500 (ptp) REVERT: J 363 MET cc_start: 0.6612 (mpp) cc_final: 0.6026 (mtt) REVERT: K 153 LEU cc_start: 0.9080 (tp) cc_final: 0.8828 (tp) REVERT: K 337 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7347 (m) REVERT: K 429 GLU cc_start: 0.7109 (pp20) cc_final: 0.6889 (pp20) REVERT: L 101 TRP cc_start: 0.5193 (m100) cc_final: 0.4220 (m-10) REVERT: L 299 MET cc_start: 0.7496 (ptp) cc_final: 0.7129 (ptp) REVERT: L 300 MET cc_start: 0.6450 (mtt) cc_final: 0.5899 (mtt) REVERT: L 363 MET cc_start: 0.6879 (mpp) cc_final: 0.5930 (mtt) REVERT: L 388 MET cc_start: 0.7689 (tpp) cc_final: 0.7454 (tpp) REVERT: M 254 GLU cc_start: 0.8526 (tt0) cc_final: 0.7986 (tt0) REVERT: M 337 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7611 (m) REVERT: M 417 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7624 (mp0) REVERT: N 101 TRP cc_start: 0.5239 (m100) cc_final: 0.4693 (m100) REVERT: N 195 ASN cc_start: 0.8629 (m-40) cc_final: 0.8354 (m-40) REVERT: N 293 MET cc_start: 0.5148 (tpp) cc_final: 0.4720 (tpt) REVERT: N 299 MET cc_start: 0.7789 (ptp) cc_final: 0.7499 (ptp) REVERT: N 363 MET cc_start: 0.6646 (mpp) cc_final: 0.6037 (mtt) REVERT: O 153 LEU cc_start: 0.9079 (tp) cc_final: 0.8827 (tp) REVERT: O 337 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7347 (m) REVERT: O 429 GLU cc_start: 0.7107 (pp20) cc_final: 0.6887 (pp20) REVERT: P 101 TRP cc_start: 0.5192 (m100) cc_final: 0.4221 (m-10) REVERT: P 300 MET cc_start: 0.6462 (mtt) cc_final: 0.5907 (mtt) REVERT: P 363 MET cc_start: 0.6801 (mpp) cc_final: 0.5826 (mtt) REVERT: P 388 MET cc_start: 0.7689 (tpp) cc_final: 0.7455 (tpp) outliers start: 168 outliers final: 113 residues processed: 994 average time/residue: 0.4670 time to fit residues: 815.0748 Evaluate side-chains 941 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 820 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 270 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 270 PHE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 413 MET Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 386 THR Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 337 THR Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 137 HIS Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 270 PHE Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain J residue 399 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 206 ASN Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 413 MET Chi-restraints excluded: chain L residue 100 ASN Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 270 PHE Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 386 THR Chi-restraints excluded: chain L residue 399 THR Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 194 THR Chi-restraints excluded: chain M residue 337 THR Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 137 HIS Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 270 PHE Chi-restraints excluded: chain N residue 280 GLN Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 374 ILE Chi-restraints excluded: chain N residue 386 THR Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain P residue 100 ASN Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 386 THR Chi-restraints excluded: chain P residue 399 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 223 optimal weight: 0.9980 chunk 598 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 390 optimal weight: 0.0040 chunk 164 optimal weight: 9.9990 chunk 665 optimal weight: 3.9990 chunk 552 optimal weight: 0.4980 chunk 308 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 349 optimal weight: 0.6980 overall best weight: 0.8394 ------------------------------------------------------------------------------- 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 11 GLN B 226 ASN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS D 8 GLN D 226 ASN D 256 ASN ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN F 226 ASN ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 ASN H 256 ASN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN J 226 ASN ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 HIS ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 256 ASN ** L 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN N 226 ASN ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 256 ASN ** P 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 55528 Z= 0.188 Angle : 0.664 11.698 75552 Z= 0.314 Chirality : 0.044 0.210 8312 Planarity : 0.004 0.041 9816 Dihedral : 20.718 165.451 8168 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.24 % Favored : 90.66 % Rotamer: Outliers : 2.97 % Allowed : 20.49 % Favored : 76.54 % 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: -1.27 (0.10), residues: 6896 helix: 0.87 (0.10), residues: 2952 sheet: -1.21 (0.17), residues: 952 loop : -2.55 (0.11), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 346 HIS 0.003 0.001 HIS L 396 PHE 0.018 0.001 PHE C 202 TYR 0.016 0.001 TYR C 312 ARG 0.003 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 852 time to evaluate : 4.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8619 (mmm) cc_final: 0.8352 (mmt) REVERT: A 254 GLU cc_start: 0.8533 (tt0) cc_final: 0.7974 (tt0) REVERT: A 337 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7587 (m) REVERT: B 101 TRP cc_start: 0.5423 (m100) cc_final: 0.4660 (m100) REVERT: B 195 ASN cc_start: 0.8623 (m-40) cc_final: 0.8338 (m-40) REVERT: B 293 MET cc_start: 0.5433 (tpp) cc_final: 0.4855 (tpt) REVERT: B 299 MET cc_start: 0.7765 (ptp) cc_final: 0.7518 (ptp) REVERT: B 310 TYR cc_start: 0.6430 (OUTLIER) cc_final: 0.6087 (t80) REVERT: B 363 MET cc_start: 0.6743 (mpp) cc_final: 0.6024 (mtt) REVERT: C 97 GLU cc_start: 0.6900 (tt0) cc_final: 0.6623 (tt0) REVERT: C 153 LEU cc_start: 0.9057 (tp) cc_final: 0.8697 (tp) REVERT: C 329 ASN cc_start: 0.8881 (t0) cc_final: 0.8630 (p0) REVERT: C 337 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7325 (m) REVERT: C 355 ILE cc_start: 0.6876 (mm) cc_final: 0.6460 (tp) REVERT: D 101 TRP cc_start: 0.5312 (m100) cc_final: 0.4238 (m-10) REVERT: D 299 MET cc_start: 0.7540 (ptp) cc_final: 0.7056 (ptp) REVERT: E 154 MET cc_start: 0.8625 (mmm) cc_final: 0.8334 (mmt) REVERT: E 167 LEU cc_start: 0.8555 (tp) cc_final: 0.8226 (tp) REVERT: E 254 GLU cc_start: 0.8531 (tt0) cc_final: 0.7968 (tt0) REVERT: E 337 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7587 (m) REVERT: F 101 TRP cc_start: 0.5423 (m100) cc_final: 0.4661 (m100) REVERT: F 195 ASN cc_start: 0.8624 (m-40) cc_final: 0.8339 (m-40) REVERT: F 293 MET cc_start: 0.4990 (tpp) cc_final: 0.4568 (tpt) REVERT: F 299 MET cc_start: 0.7773 (ptp) cc_final: 0.7519 (ptp) REVERT: F 363 MET cc_start: 0.6702 (mpp) cc_final: 0.6011 (mtt) REVERT: G 153 LEU cc_start: 0.9041 (tp) cc_final: 0.8676 (tp) REVERT: G 329 ASN cc_start: 0.8883 (t0) cc_final: 0.8631 (p0) REVERT: G 337 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7325 (m) REVERT: G 355 ILE cc_start: 0.6873 (mm) cc_final: 0.6456 (tp) REVERT: H 101 TRP cc_start: 0.5273 (m100) cc_final: 0.4229 (m-10) REVERT: H 299 MET cc_start: 0.7487 (ptp) cc_final: 0.7056 (ptp) REVERT: H 426 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7357 (tm-30) REVERT: I 154 MET cc_start: 0.8622 (mmm) cc_final: 0.8335 (mmt) REVERT: I 254 GLU cc_start: 0.8542 (tt0) cc_final: 0.7982 (tt0) REVERT: I 337 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7588 (m) REVERT: I 417 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7660 (mp0) REVERT: J 101 TRP cc_start: 0.5421 (m100) cc_final: 0.4660 (m100) REVERT: J 195 ASN cc_start: 0.8623 (m-40) cc_final: 0.8339 (m-40) REVERT: J 293 MET cc_start: 0.4987 (tpp) cc_final: 0.4462 (tpt) REVERT: J 299 MET cc_start: 0.7763 (ptp) cc_final: 0.7506 (ptp) REVERT: J 363 MET cc_start: 0.6703 (mpp) cc_final: 0.6018 (mtt) REVERT: K 153 LEU cc_start: 0.9071 (tp) cc_final: 0.8822 (tp) REVERT: K 329 ASN cc_start: 0.8882 (t0) cc_final: 0.8630 (p0) REVERT: K 337 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7324 (m) REVERT: K 355 ILE cc_start: 0.6860 (mm) cc_final: 0.6446 (tp) REVERT: L 101 TRP cc_start: 0.5272 (m100) cc_final: 0.4230 (m-10) REVERT: L 299 MET cc_start: 0.7486 (ptp) cc_final: 0.7052 (ptp) REVERT: L 426 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7354 (tm-30) REVERT: M 254 GLU cc_start: 0.8575 (tt0) cc_final: 0.7999 (tt0) REVERT: M 337 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7587 (m) REVERT: M 417 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7659 (mp0) REVERT: N 101 TRP cc_start: 0.5418 (m100) cc_final: 0.4658 (m100) REVERT: N 195 ASN cc_start: 0.8613 (m-40) cc_final: 0.8335 (m-40) REVERT: N 293 MET cc_start: 0.5130 (tpp) cc_final: 0.4262 (tpt) REVERT: N 299 MET cc_start: 0.7758 (ptp) cc_final: 0.7502 (ptp) REVERT: N 363 MET cc_start: 0.6741 (mpp) cc_final: 0.6029 (mtt) REVERT: O 153 LEU cc_start: 0.9070 (tp) cc_final: 0.8824 (tp) REVERT: O 329 ASN cc_start: 0.8881 (t0) cc_final: 0.8631 (p0) REVERT: O 337 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7325 (m) REVERT: O 355 ILE cc_start: 0.6859 (mm) cc_final: 0.6446 (tp) REVERT: P 101 TRP cc_start: 0.5272 (m100) cc_final: 0.4228 (m-10) REVERT: P 299 MET cc_start: 0.7540 (ptp) cc_final: 0.7056 (ptp) REVERT: P 426 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7333 (tm-30) outliers start: 169 outliers final: 129 residues processed: 976 average time/residue: 0.4738 time to fit residues: 811.7765 Evaluate side-chains 935 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 797 time to evaluate : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 270 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 270 PHE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 386 THR Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 337 THR Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain J residue 124 CYS Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 137 HIS Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 270 PHE Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain J residue 399 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 206 ASN Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain L residue 100 ASN Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 196 THR Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 270 PHE Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 284 LEU Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 386 THR Chi-restraints excluded: chain L residue 399 THR Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 194 THR Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 337 THR Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain N residue 124 CYS Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 137 HIS Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 270 PHE Chi-restraints excluded: chain N residue 280 GLN Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 374 ILE Chi-restraints excluded: chain N residue 386 THR Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 194 THR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain P residue 100 ASN Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 152 ILE Chi-restraints excluded: chain P residue 196 THR Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 284 LEU Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 386 THR Chi-restraints excluded: chain P residue 399 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 641 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 379 optimal weight: 0.0040 chunk 486 optimal weight: 0.2980 chunk 376 optimal weight: 8.9990 chunk 560 optimal weight: 4.9990 chunk 371 optimal weight: 0.6980 chunk 663 optimal weight: 0.6980 chunk 414 optimal weight: 0.0570 chunk 404 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 overall best weight: 0.3510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 HIS G 256 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 256 GLN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS O 256 GLN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 55528 Z= 0.160 Angle : 0.654 11.780 75552 Z= 0.307 Chirality : 0.043 0.152 8312 Planarity : 0.004 0.042 9816 Dihedral : 20.396 162.249 8168 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.21 % Favored : 91.69 % Rotamer: Outliers : 2.63 % Allowed : 21.33 % Favored : 76.04 % 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: -1.17 (0.10), residues: 6896 helix: 0.92 (0.10), residues: 2936 sheet: -1.09 (0.17), residues: 960 loop : -2.48 (0.11), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 346 HIS 0.002 0.001 HIS A 61 PHE 0.023 0.001 PHE N 294 TYR 0.017 0.001 TYR J 310 ARG 0.003 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 865 time to evaluate : 4.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8587 (mmm) cc_final: 0.8307 (mmt) REVERT: A 254 GLU cc_start: 0.8503 (tt0) cc_final: 0.7950 (tt0) REVERT: A 292 THR cc_start: 0.8185 (t) cc_final: 0.7980 (t) REVERT: A 337 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7573 (m) REVERT: A 355 ILE cc_start: 0.7120 (mm) cc_final: 0.6802 (tp) REVERT: A 398 MET cc_start: 0.7552 (mtt) cc_final: 0.7253 (mtt) REVERT: A 417 GLU cc_start: 0.7720 (mp0) cc_final: 0.7140 (mp0) REVERT: B 101 TRP cc_start: 0.5478 (OUTLIER) cc_final: 0.4760 (m100) REVERT: B 195 ASN cc_start: 0.8580 (m-40) cc_final: 0.8306 (m-40) REVERT: B 299 MET cc_start: 0.7629 (ptp) cc_final: 0.7374 (ptp) REVERT: B 310 TYR cc_start: 0.6530 (OUTLIER) cc_final: 0.6196 (t80) REVERT: B 363 MET cc_start: 0.6714 (mpp) cc_final: 0.6028 (mtt) REVERT: C 153 LEU cc_start: 0.8955 (tp) cc_final: 0.8635 (tp) REVERT: C 337 THR cc_start: 0.7794 (OUTLIER) cc_final: 0.7249 (m) REVERT: C 355 ILE cc_start: 0.6767 (mm) cc_final: 0.6363 (tp) REVERT: D 101 TRP cc_start: 0.5206 (m100) cc_final: 0.4086 (m-10) REVERT: D 299 MET cc_start: 0.7487 (ptp) cc_final: 0.7085 (ptp) REVERT: D 300 MET cc_start: 0.6382 (mtt) cc_final: 0.5883 (mtt) REVERT: D 426 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7458 (tm-30) REVERT: E 154 MET cc_start: 0.8580 (mmm) cc_final: 0.8295 (mmt) REVERT: E 254 GLU cc_start: 0.8503 (tt0) cc_final: 0.7943 (tt0) REVERT: E 292 THR cc_start: 0.8373 (t) cc_final: 0.8161 (t) REVERT: E 355 ILE cc_start: 0.7115 (mm) cc_final: 0.6796 (tp) REVERT: E 398 MET cc_start: 0.7552 (mtt) cc_final: 0.7263 (mtt) REVERT: E 417 GLU cc_start: 0.7715 (mp0) cc_final: 0.7134 (mp0) REVERT: F 101 TRP cc_start: 0.5438 (OUTLIER) cc_final: 0.4786 (m100) REVERT: F 195 ASN cc_start: 0.8582 (m-40) cc_final: 0.8307 (m-40) REVERT: F 299 MET cc_start: 0.7625 (ptp) cc_final: 0.7377 (ptp) REVERT: F 310 TYR cc_start: 0.6401 (OUTLIER) cc_final: 0.6182 (t80) REVERT: F 363 MET cc_start: 0.6696 (mpp) cc_final: 0.6078 (mtt) REVERT: G 153 LEU cc_start: 0.8970 (tp) cc_final: 0.8649 (tp) REVERT: G 337 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7249 (m) REVERT: G 355 ILE cc_start: 0.6767 (mm) cc_final: 0.6363 (tp) REVERT: H 101 TRP cc_start: 0.5254 (m100) cc_final: 0.4130 (m-10) REVERT: H 139 LEU cc_start: 0.8872 (mt) cc_final: 0.8618 (mt) REVERT: H 300 MET cc_start: 0.6372 (mtt) cc_final: 0.5861 (mtt) REVERT: H 426 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7461 (tm-30) REVERT: I 154 MET cc_start: 0.8577 (mmm) cc_final: 0.8265 (mmt) REVERT: I 254 GLU cc_start: 0.8543 (tt0) cc_final: 0.7994 (tt0) REVERT: I 292 THR cc_start: 0.8373 (t) cc_final: 0.8162 (t) REVERT: I 355 ILE cc_start: 0.7116 (mm) cc_final: 0.6795 (tp) REVERT: I 398 MET cc_start: 0.7552 (mtt) cc_final: 0.7254 (mtt) REVERT: I 417 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7617 (mp0) REVERT: J 101 TRP cc_start: 0.5435 (OUTLIER) cc_final: 0.4774 (m100) REVERT: J 195 ASN cc_start: 0.8582 (m-40) cc_final: 0.8310 (m-40) REVERT: J 299 MET cc_start: 0.7581 (ptp) cc_final: 0.7337 (ptp) REVERT: J 363 MET cc_start: 0.6713 (mpp) cc_final: 0.6088 (mtt) REVERT: K 153 LEU cc_start: 0.8975 (tp) cc_final: 0.8690 (tp) REVERT: K 337 THR cc_start: 0.7794 (OUTLIER) cc_final: 0.7249 (m) REVERT: K 355 ILE cc_start: 0.6775 (mm) cc_final: 0.6392 (tp) REVERT: L 101 TRP cc_start: 0.5250 (m100) cc_final: 0.4128 (m-10) REVERT: L 300 MET cc_start: 0.6377 (mtt) cc_final: 0.5868 (mtt) REVERT: L 426 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7419 (tm-30) REVERT: M 254 GLU cc_start: 0.8546 (tt0) cc_final: 0.7920 (tt0) REVERT: M 292 THR cc_start: 0.8373 (t) cc_final: 0.8161 (t) REVERT: M 355 ILE cc_start: 0.7113 (mm) cc_final: 0.6794 (tp) REVERT: M 398 MET cc_start: 0.7598 (mtt) cc_final: 0.7300 (mtt) REVERT: M 417 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7618 (mp0) REVERT: N 101 TRP cc_start: 0.5433 (OUTLIER) cc_final: 0.4783 (m100) REVERT: N 195 ASN cc_start: 0.8575 (m-40) cc_final: 0.8302 (m-40) REVERT: N 299 MET cc_start: 0.7574 (ptp) cc_final: 0.7330 (ptp) REVERT: N 363 MET cc_start: 0.6741 (mpp) cc_final: 0.6080 (mtt) REVERT: O 153 LEU cc_start: 0.8974 (tp) cc_final: 0.8690 (tp) REVERT: O 337 THR cc_start: 0.7794 (OUTLIER) cc_final: 0.7250 (m) REVERT: O 355 ILE cc_start: 0.6775 (mm) cc_final: 0.6393 (tp) REVERT: P 101 TRP cc_start: 0.5251 (m100) cc_final: 0.4128 (m-10) REVERT: P 299 MET cc_start: 0.7486 (ptp) cc_final: 0.7085 (ptp) REVERT: P 300 MET cc_start: 0.6377 (mtt) cc_final: 0.5880 (mtt) REVERT: P 426 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7459 (tm-30) outliers start: 150 outliers final: 111 residues processed: 980 average time/residue: 0.4591 time to fit residues: 793.3839 Evaluate side-chains 926 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 804 time to evaluate : 4.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 270 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 270 PHE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 386 THR Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 101 TRP Chi-restraints excluded: chain J residue 124 CYS Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 270 PHE Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 206 ASN Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain L residue 100 ASN Chi-restraints excluded: chain L residue 124 CYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 270 PHE Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 284 LEU Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 386 THR Chi-restraints excluded: chain L residue 399 THR Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 101 TRP Chi-restraints excluded: chain N residue 124 CYS Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 270 PHE Chi-restraints excluded: chain N residue 280 GLN Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 374 ILE Chi-restraints excluded: chain N residue 386 THR Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain P residue 100 ASN Chi-restraints excluded: chain P residue 124 CYS Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 284 LEU Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 386 THR Chi-restraints excluded: chain P residue 399 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 410 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 396 optimal weight: 0.0570 chunk 199 optimal weight: 0.4980 chunk 130 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 421 optimal weight: 0.7980 chunk 451 optimal weight: 1.9990 chunk 327 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 521 optimal weight: 1.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 256 ASN B 334 GLN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** J 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 131 GLN ** L 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 ASN ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 131 GLN ** P 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 55528 Z= 0.195 Angle : 0.666 11.772 75552 Z= 0.315 Chirality : 0.044 0.213 8312 Planarity : 0.004 0.041 9816 Dihedral : 20.349 162.112 8168 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.95 % Favored : 90.95 % Rotamer: Outliers : 3.16 % Allowed : 20.93 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.10), residues: 6896 helix: 0.88 (0.10), residues: 2928 sheet: -1.00 (0.18), residues: 936 loop : -2.45 (0.11), residues: 3032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 346 HIS 0.004 0.001 HIS H 396 PHE 0.016 0.001 PHE N 294 TYR 0.016 0.001 TYR C 312 ARG 0.003 0.000 ARG M 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 828 time to evaluate : 4.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8564 (mmm) cc_final: 0.8323 (mmt) REVERT: A 254 GLU cc_start: 0.8572 (tt0) cc_final: 0.8335 (tt0) REVERT: A 292 THR cc_start: 0.8256 (t) cc_final: 0.8050 (t) REVERT: A 337 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7565 (m) REVERT: A 346 TRP cc_start: 0.8490 (OUTLIER) cc_final: 0.7564 (p-90) REVERT: A 355 ILE cc_start: 0.7060 (mm) cc_final: 0.6713 (tp) REVERT: A 398 MET cc_start: 0.7609 (mtt) cc_final: 0.7302 (mtt) REVERT: A 417 GLU cc_start: 0.7764 (mp0) cc_final: 0.7128 (mp0) REVERT: B 99 ASN cc_start: 0.7069 (OUTLIER) cc_final: 0.6788 (p0) REVERT: B 101 TRP cc_start: 0.5529 (OUTLIER) cc_final: 0.4926 (m100) REVERT: B 137 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.7103 (p-80) REVERT: B 195 ASN cc_start: 0.8681 (m-40) cc_final: 0.8388 (m-40) REVERT: B 293 MET cc_start: 0.4910 (tpp) cc_final: 0.4684 (tpt) REVERT: B 299 MET cc_start: 0.7679 (ptp) cc_final: 0.7403 (ptp) REVERT: B 310 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.6263 (t80) REVERT: B 377 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7192 (tt) REVERT: C 153 LEU cc_start: 0.9057 (tp) cc_final: 0.8780 (tp) REVERT: C 337 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7330 (m) REVERT: C 355 ILE cc_start: 0.6809 (mm) cc_final: 0.6392 (tp) REVERT: D 101 TRP cc_start: 0.5478 (m100) cc_final: 0.4294 (m-10) REVERT: D 300 MET cc_start: 0.6423 (mtt) cc_final: 0.5865 (mtt) REVERT: E 154 MET cc_start: 0.8545 (mmm) cc_final: 0.8233 (mmt) REVERT: E 167 LEU cc_start: 0.8463 (tp) cc_final: 0.8148 (tp) REVERT: E 254 GLU cc_start: 0.8565 (tt0) cc_final: 0.7979 (tt0) REVERT: E 292 THR cc_start: 0.8389 (t) cc_final: 0.8180 (t) REVERT: E 346 TRP cc_start: 0.8493 (OUTLIER) cc_final: 0.7567 (p-90) REVERT: E 355 ILE cc_start: 0.7161 (mm) cc_final: 0.6824 (tp) REVERT: E 398 MET cc_start: 0.7609 (mtt) cc_final: 0.7303 (mtt) REVERT: E 417 GLU cc_start: 0.7761 (mp0) cc_final: 0.7123 (mp0) REVERT: F 99 ASN cc_start: 0.7066 (OUTLIER) cc_final: 0.6782 (p0) REVERT: F 101 TRP cc_start: 0.5530 (OUTLIER) cc_final: 0.4928 (m100) REVERT: F 137 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7107 (p-80) REVERT: F 195 ASN cc_start: 0.8684 (m-40) cc_final: 0.8389 (m-40) REVERT: F 299 MET cc_start: 0.7715 (ptp) cc_final: 0.7429 (ptp) REVERT: G 153 LEU cc_start: 0.9056 (tp) cc_final: 0.8778 (tp) REVERT: G 337 THR cc_start: 0.7830 (OUTLIER) cc_final: 0.7329 (m) REVERT: G 355 ILE cc_start: 0.6808 (mm) cc_final: 0.6393 (tp) REVERT: H 101 TRP cc_start: 0.5502 (m100) cc_final: 0.4302 (m-10) REVERT: H 299 MET cc_start: 0.7453 (ptp) cc_final: 0.7104 (ptp) REVERT: H 300 MET cc_start: 0.6432 (mtt) cc_final: 0.5899 (mtt) REVERT: I 154 MET cc_start: 0.8587 (mmm) cc_final: 0.8320 (mmt) REVERT: I 254 GLU cc_start: 0.8581 (tt0) cc_final: 0.7955 (tt0) REVERT: I 292 THR cc_start: 0.8388 (t) cc_final: 0.8179 (t) REVERT: I 346 TRP cc_start: 0.8493 (OUTLIER) cc_final: 0.7568 (p-90) REVERT: I 355 ILE cc_start: 0.7159 (mm) cc_final: 0.6824 (tp) REVERT: I 398 MET cc_start: 0.7611 (mtt) cc_final: 0.7306 (mtt) REVERT: J 99 ASN cc_start: 0.7066 (OUTLIER) cc_final: 0.6781 (p0) REVERT: J 101 TRP cc_start: 0.5499 (OUTLIER) cc_final: 0.4935 (m100) REVERT: J 137 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7127 (p-80) REVERT: J 195 ASN cc_start: 0.8618 (m-40) cc_final: 0.8331 (m-40) REVERT: J 293 MET cc_start: 0.4844 (tpp) cc_final: 0.4603 (tpt) REVERT: J 299 MET cc_start: 0.7693 (ptp) cc_final: 0.7408 (ptp) REVERT: J 310 TYR cc_start: 0.6922 (t80) cc_final: 0.6704 (t80) REVERT: K 153 LEU cc_start: 0.9009 (tp) cc_final: 0.8713 (tp) REVERT: K 337 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7330 (m) REVERT: K 355 ILE cc_start: 0.6805 (mm) cc_final: 0.6397 (tp) REVERT: L 101 TRP cc_start: 0.5500 (m100) cc_final: 0.4300 (m-10) REVERT: L 299 MET cc_start: 0.7450 (ptp) cc_final: 0.7098 (ptp) REVERT: L 300 MET cc_start: 0.6440 (mtt) cc_final: 0.5908 (mtt) REVERT: M 167 LEU cc_start: 0.8419 (tp) cc_final: 0.8099 (tp) REVERT: M 254 GLU cc_start: 0.8587 (tt0) cc_final: 0.7988 (tt0) REVERT: M 292 THR cc_start: 0.8388 (t) cc_final: 0.8178 (t) REVERT: M 346 TRP cc_start: 0.8493 (OUTLIER) cc_final: 0.7565 (p-90) REVERT: M 355 ILE cc_start: 0.7158 (mm) cc_final: 0.6824 (tp) REVERT: M 398 MET cc_start: 0.7607 (mtt) cc_final: 0.7304 (mtt) REVERT: M 417 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7625 (mp0) REVERT: N 99 ASN cc_start: 0.7072 (OUTLIER) cc_final: 0.6803 (p0) REVERT: N 101 TRP cc_start: 0.5526 (OUTLIER) cc_final: 0.4928 (m100) REVERT: N 137 HIS cc_start: 0.7634 (OUTLIER) cc_final: 0.7073 (p-80) REVERT: N 195 ASN cc_start: 0.8679 (m-40) cc_final: 0.8386 (m-40) REVERT: N 293 MET cc_start: 0.4256 (tpp) cc_final: 0.3828 (tpt) REVERT: N 299 MET cc_start: 0.7684 (ptp) cc_final: 0.7401 (ptp) REVERT: N 310 TYR cc_start: 0.6978 (t80) cc_final: 0.6736 (t80) REVERT: O 153 LEU cc_start: 0.9009 (tp) cc_final: 0.8713 (tp) REVERT: O 337 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7328 (m) REVERT: O 355 ILE cc_start: 0.6807 (mm) cc_final: 0.6397 (tp) REVERT: P 101 TRP cc_start: 0.5498 (m100) cc_final: 0.4299 (m-10) REVERT: P 300 MET cc_start: 0.6419 (mtt) cc_final: 0.5860 (mtt) outliers start: 180 outliers final: 133 residues processed: 967 average time/residue: 0.4907 time to fit residues: 841.2846 Evaluate side-chains 961 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 805 time to evaluate : 4.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 185 TYR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 270 PHE Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 346 TRP Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 270 PHE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 280 GLN Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 386 THR Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 346 TRP Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 101 TRP Chi-restraints excluded: chain J residue 124 CYS Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 137 HIS Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 270 PHE Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 206 ASN Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain L residue 100 ASN Chi-restraints excluded: chain L residue 124 CYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 270 PHE Chi-restraints excluded: chain L residue 280 GLN Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 284 LEU Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 386 THR Chi-restraints excluded: chain L residue 399 THR Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 346 TRP Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 101 TRP Chi-restraints excluded: chain N residue 124 CYS Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 137 HIS Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 270 PHE Chi-restraints excluded: chain N residue 280 GLN Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 374 ILE Chi-restraints excluded: chain N residue 386 THR Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain O residue 238 ILE Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain P residue 100 ASN Chi-restraints excluded: chain P residue 124 CYS Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 280 GLN Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 284 LEU Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 386 THR Chi-restraints excluded: chain P residue 399 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 603 optimal weight: 3.9990 chunk 635 optimal weight: 3.9990 chunk 579 optimal weight: 0.7980 chunk 617 optimal weight: 0.7980 chunk 371 optimal weight: 0.7980 chunk 269 optimal weight: 4.9990 chunk 485 optimal weight: 0.1980 chunk 189 optimal weight: 2.9990 chunk 558 optimal weight: 0.6980 chunk 584 optimal weight: 2.9990 chunk 615 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 11 GLN B 100 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN F 100 ASN ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 ASN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN J 100 ASN ** J 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 ASN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 ASN ** N 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 55528 Z= 0.176 Angle : 0.675 12.933 75552 Z= 0.315 Chirality : 0.044 0.176 8312 Planarity : 0.004 0.042 9816 Dihedral : 20.130 160.825 8168 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.48 % Favored : 91.42 % Rotamer: Outliers : 3.05 % Allowed : 21.88 % Favored : 75.07 % 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: -1.16 (0.10), residues: 6896 helix: 0.86 (0.10), residues: 2920 sheet: -0.94 (0.18), residues: 968 loop : -2.43 (0.11), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 346 HIS 0.003 0.001 HIS D 396 PHE 0.010 0.001 PHE N 367 TYR 0.015 0.001 TYR C 312 ARG 0.003 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 834 time to evaluate : 4.576 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: A 154 MET cc_start: 0.8360 (mmm) cc_final: 0.8131 (mmt) REVERT: A 254 GLU cc_start: 0.8579 (tt0) cc_final: 0.7985 (tt0) REVERT: A 337 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7613 (m) REVERT: A 355 ILE cc_start: 0.7043 (mm) cc_final: 0.6681 (tp) REVERT: A 398 MET cc_start: 0.7564 (mtt) cc_final: 0.7280 (mtt) REVERT: A 417 GLU cc_start: 0.7801 (mp0) cc_final: 0.7161 (mp0) REVERT: B 101 TRP cc_start: 0.5764 (m100) cc_final: 0.5094 (m100) REVERT: B 137 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7189 (p-80) REVERT: B 147 MET cc_start: 0.6670 (tpp) cc_final: 0.6246 (tpp) REVERT: B 195 ASN cc_start: 0.8708 (m-40) cc_final: 0.8408 (m-40) REVERT: B 299 MET cc_start: 0.7608 (ptp) cc_final: 0.7275 (ptp) REVERT: B 323 MET cc_start: 0.8672 (mpp) cc_final: 0.8101 (mpp) REVERT: B 377 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7130 (tt) REVERT: B 384 GLN cc_start: 0.6710 (mm-40) cc_final: 0.6117 (mm-40) REVERT: C 153 LEU cc_start: 0.9017 (tp) cc_final: 0.8758 (tp) REVERT: C 337 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7303 (m) REVERT: C 355 ILE cc_start: 0.6789 (mm) cc_final: 0.6381 (tp) REVERT: D 101 TRP cc_start: 0.5491 (OUTLIER) cc_final: 0.4270 (m-10) REVERT: D 299 MET cc_start: 0.7385 (ptp) cc_final: 0.7042 (ptp) REVERT: D 300 MET cc_start: 0.6264 (mtt) cc_final: 0.5754 (mtt) REVERT: E 167 LEU cc_start: 0.8417 (tp) cc_final: 0.8096 (tp) REVERT: E 254 GLU cc_start: 0.8571 (tt0) cc_final: 0.7950 (tt0) REVERT: E 292 THR cc_start: 0.8351 (t) cc_final: 0.8140 (t) REVERT: E 355 ILE cc_start: 0.7038 (mm) cc_final: 0.6671 (tp) REVERT: E 398 MET cc_start: 0.7567 (mtt) cc_final: 0.7286 (mtt) REVERT: E 417 GLU cc_start: 0.7799 (mp0) cc_final: 0.7159 (mp0) REVERT: F 101 TRP cc_start: 0.5745 (m100) cc_final: 0.5071 (m100) REVERT: F 137 HIS cc_start: 0.7717 (OUTLIER) cc_final: 0.7190 (p-80) REVERT: F 147 MET cc_start: 0.6667 (tpp) cc_final: 0.6245 (tpp) REVERT: F 195 ASN cc_start: 0.8709 (m-40) cc_final: 0.8409 (m-40) REVERT: F 299 MET cc_start: 0.7638 (ptp) cc_final: 0.7299 (ptp) REVERT: F 310 TYR cc_start: 0.6933 (t80) cc_final: 0.6578 (t80) REVERT: F 323 MET cc_start: 0.8671 (mpp) cc_final: 0.8104 (mpp) REVERT: F 384 GLN cc_start: 0.6712 (mm-40) cc_final: 0.6118 (mm-40) REVERT: G 153 LEU cc_start: 0.8976 (tp) cc_final: 0.8652 (tp) REVERT: G 337 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7303 (m) REVERT: G 355 ILE cc_start: 0.6790 (mm) cc_final: 0.6379 (tp) REVERT: H 101 TRP cc_start: 0.5579 (OUTLIER) cc_final: 0.4417 (m-10) REVERT: H 299 MET cc_start: 0.7377 (ptp) cc_final: 0.7057 (ptp) REVERT: H 300 MET cc_start: 0.6282 (mtt) cc_final: 0.5773 (mtt) REVERT: H 426 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7460 (tm-30) REVERT: I 154 MET cc_start: 0.8418 (mmm) cc_final: 0.8154 (mmt) REVERT: I 254 GLU cc_start: 0.8579 (tt0) cc_final: 0.8005 (tt0) REVERT: I 292 THR cc_start: 0.8342 (t) cc_final: 0.8129 (t) REVERT: I 355 ILE cc_start: 0.7040 (mm) cc_final: 0.6676 (tp) REVERT: I 398 MET cc_start: 0.7566 (mtt) cc_final: 0.7287 (mtt) REVERT: I 417 GLU cc_start: 0.7730 (mp0) cc_final: 0.7146 (mp0) REVERT: J 101 TRP cc_start: 0.5723 (m100) cc_final: 0.5053 (m100) REVERT: J 137 HIS cc_start: 0.7636 (OUTLIER) cc_final: 0.7125 (p-80) REVERT: J 147 MET cc_start: 0.6436 (tpp) cc_final: 0.6019 (tpp) REVERT: J 195 ASN cc_start: 0.8681 (m-40) cc_final: 0.8373 (m-40) REVERT: J 299 MET cc_start: 0.7596 (ptp) cc_final: 0.7276 (ptp) REVERT: J 310 TYR cc_start: 0.6820 (t80) cc_final: 0.6600 (t80) REVERT: J 323 MET cc_start: 0.8690 (mpp) cc_final: 0.7835 (mpp) REVERT: J 384 GLN cc_start: 0.6690 (mm-40) cc_final: 0.6092 (mm-40) REVERT: K 153 LEU cc_start: 0.8995 (tp) cc_final: 0.8691 (tp) REVERT: K 337 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7303 (m) REVERT: K 355 ILE cc_start: 0.6784 (mm) cc_final: 0.6377 (tp) REVERT: L 101 TRP cc_start: 0.5578 (OUTLIER) cc_final: 0.4415 (m-10) REVERT: L 299 MET cc_start: 0.7374 (ptp) cc_final: 0.7052 (ptp) REVERT: L 300 MET cc_start: 0.6282 (mtt) cc_final: 0.5775 (mtt) REVERT: L 426 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7414 (tm-30) REVERT: M 167 LEU cc_start: 0.8368 (tp) cc_final: 0.8054 (tp) REVERT: M 254 GLU cc_start: 0.8589 (tt0) cc_final: 0.8011 (tt0) REVERT: M 292 THR cc_start: 0.8341 (t) cc_final: 0.8128 (t) REVERT: M 355 ILE cc_start: 0.7038 (mm) cc_final: 0.6669 (tp) REVERT: M 398 MET cc_start: 0.7562 (mtt) cc_final: 0.7283 (mtt) REVERT: M 417 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7568 (mp0) REVERT: N 101 TRP cc_start: 0.5746 (m100) cc_final: 0.5070 (m100) REVERT: N 137 HIS cc_start: 0.7704 (OUTLIER) cc_final: 0.7179 (p-80) REVERT: N 147 MET cc_start: 0.6651 (tpp) cc_final: 0.6241 (tpp) REVERT: N 195 ASN cc_start: 0.8699 (m-40) cc_final: 0.8401 (m-40) REVERT: N 299 MET cc_start: 0.7635 (ptp) cc_final: 0.7305 (ptp) REVERT: N 310 TYR cc_start: 0.6986 (t80) cc_final: 0.6718 (t80) REVERT: N 323 MET cc_start: 0.8690 (mpp) cc_final: 0.8298 (mpp) REVERT: N 384 GLN cc_start: 0.6691 (mm-40) cc_final: 0.6093 (mm-40) REVERT: O 153 LEU cc_start: 0.8993 (tp) cc_final: 0.8692 (tp) REVERT: O 337 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7304 (m) REVERT: O 355 ILE cc_start: 0.6782 (mm) cc_final: 0.6376 (tp) REVERT: P 101 TRP cc_start: 0.5577 (OUTLIER) cc_final: 0.4415 (m-10) REVERT: P 299 MET cc_start: 0.7381 (ptp) cc_final: 0.7041 (ptp) REVERT: P 300 MET cc_start: 0.6263 (mtt) cc_final: 0.5751 (mtt) REVERT: P 426 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7463 (tm-30) outliers start: 174 outliers final: 145 residues processed: 972 average time/residue: 0.4543 time to fit residues: 775.1147 Evaluate side-chains 979 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 820 time to evaluate : 4.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 185 TYR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 270 PHE Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 270 PHE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 280 GLN Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 386 THR Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 124 CYS Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 137 HIS Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 270 PHE Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 206 ASN Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain L residue 100 ASN Chi-restraints excluded: chain L residue 101 TRP Chi-restraints excluded: chain L residue 124 CYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 270 PHE Chi-restraints excluded: chain L residue 280 GLN Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 284 LEU Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 386 THR Chi-restraints excluded: chain L residue 399 THR Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 324 VAL Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 124 CYS Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 137 HIS Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 270 PHE Chi-restraints excluded: chain N residue 280 GLN Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 374 ILE Chi-restraints excluded: chain N residue 386 THR Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain O residue 238 ILE Chi-restraints excluded: chain O residue 324 VAL Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain P residue 100 ASN Chi-restraints excluded: chain P residue 101 TRP Chi-restraints excluded: chain P residue 124 CYS Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 152 ILE Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 280 GLN Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 284 LEU Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 386 THR Chi-restraints excluded: chain P residue 399 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 405 optimal weight: 0.4980 chunk 653 optimal weight: 7.9990 chunk 398 optimal weight: 0.0970 chunk 309 optimal weight: 7.9990 chunk 454 optimal weight: 0.0040 chunk 685 optimal weight: 0.9980 chunk 630 optimal weight: 5.9990 chunk 545 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 421 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 100 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN F 100 ASN ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN J 99 ASN J 100 ASN J 256 ASN ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN ** L 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN N 100 ASN ** N 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 55528 Z= 0.171 Angle : 0.683 12.073 75552 Z= 0.319 Chirality : 0.044 0.188 8312 Planarity : 0.004 0.042 9816 Dihedral : 19.974 160.456 8168 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.80 % Favored : 91.10 % Rotamer: Outliers : 3.00 % Allowed : 22.00 % 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: -1.11 (0.10), residues: 6896 helix: 0.94 (0.10), residues: 2880 sheet: -0.86 (0.18), residues: 968 loop : -2.44 (0.10), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 346 HIS 0.003 0.001 HIS E 406 PHE 0.021 0.001 PHE F 294 TYR 0.016 0.001 TYR E 103 ARG 0.003 0.000 ARG A 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13792 Ramachandran restraints generated. 6896 Oldfield, 0 Emsley, 6896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 858 time to evaluate : 4.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.8577 (tt0) cc_final: 0.8007 (tt0) REVERT: A 337 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7589 (m) REVERT: A 355 ILE cc_start: 0.7034 (mm) cc_final: 0.6672 (tp) REVERT: A 398 MET cc_start: 0.7533 (mtt) cc_final: 0.7231 (mtt) REVERT: A 417 GLU cc_start: 0.7793 (mp0) cc_final: 0.7172 (mp0) REVERT: B 101 TRP cc_start: 0.5582 (OUTLIER) cc_final: 0.4806 (m100) REVERT: B 137 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.7181 (p-80) REVERT: B 147 MET cc_start: 0.6544 (tpp) cc_final: 0.6152 (tpp) REVERT: B 195 ASN cc_start: 0.8703 (m-40) cc_final: 0.8405 (m-40) REVERT: B 299 MET cc_start: 0.7664 (ptp) cc_final: 0.7322 (ptp) REVERT: B 310 TYR cc_start: 0.7044 (t80) cc_final: 0.6563 (t80) REVERT: B 323 MET cc_start: 0.8658 (mpp) cc_final: 0.8003 (mpp) REVERT: B 377 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7022 (tt) REVERT: B 384 GLN cc_start: 0.6723 (mm-40) cc_final: 0.6145 (mm-40) REVERT: C 153 LEU cc_start: 0.9021 (tp) cc_final: 0.8774 (tp) REVERT: C 337 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7374 (m) REVERT: C 355 ILE cc_start: 0.6723 (mm) cc_final: 0.6322 (tp) REVERT: D 101 TRP cc_start: 0.5453 (OUTLIER) cc_final: 0.4242 (m-10) REVERT: D 299 MET cc_start: 0.7377 (ptp) cc_final: 0.7025 (ptp) REVERT: D 300 MET cc_start: 0.6177 (mtt) cc_final: 0.5672 (mtt) REVERT: E 167 LEU cc_start: 0.8458 (tp) cc_final: 0.8110 (tp) REVERT: E 254 GLU cc_start: 0.8567 (tt0) cc_final: 0.8092 (tt0) REVERT: E 292 THR cc_start: 0.8344 (t) cc_final: 0.8130 (t) REVERT: E 355 ILE cc_start: 0.7021 (mm) cc_final: 0.6666 (tp) REVERT: E 398 MET cc_start: 0.7483 (mtt) cc_final: 0.7189 (mtt) REVERT: E 417 GLU cc_start: 0.7792 (mp0) cc_final: 0.7171 (mp0) REVERT: F 101 TRP cc_start: 0.5585 (OUTLIER) cc_final: 0.4810 (m100) REVERT: F 137 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.7181 (p-80) REVERT: F 147 MET cc_start: 0.6542 (tpp) cc_final: 0.6150 (tpp) REVERT: F 195 ASN cc_start: 0.8703 (m-40) cc_final: 0.8394 (m-40) REVERT: F 293 MET cc_start: 0.5069 (tpp) cc_final: 0.4668 (tpt) REVERT: F 299 MET cc_start: 0.7590 (ptp) cc_final: 0.7362 (ptp) REVERT: F 310 TYR cc_start: 0.7125 (t80) cc_final: 0.6586 (t80) REVERT: F 323 MET cc_start: 0.8659 (mpp) cc_final: 0.8270 (mpp) REVERT: F 384 GLN cc_start: 0.6690 (mm-40) cc_final: 0.6116 (mm-40) REVERT: G 153 LEU cc_start: 0.8958 (tp) cc_final: 0.8642 (tp) REVERT: G 337 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7377 (m) REVERT: G 355 ILE cc_start: 0.6722 (mm) cc_final: 0.6321 (tp) REVERT: H 101 TRP cc_start: 0.5646 (OUTLIER) cc_final: 0.4270 (m-10) REVERT: H 299 MET cc_start: 0.7327 (ptp) cc_final: 0.6992 (ptp) REVERT: H 300 MET cc_start: 0.6201 (mtt) cc_final: 0.5694 (mtt) REVERT: H 426 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7459 (tm-30) REVERT: I 154 MET cc_start: 0.8426 (mmm) cc_final: 0.8164 (mmt) REVERT: I 254 GLU cc_start: 0.8578 (tt0) cc_final: 0.8093 (tt0) REVERT: I 292 THR cc_start: 0.8343 (t) cc_final: 0.8130 (t) REVERT: I 355 ILE cc_start: 0.7031 (mm) cc_final: 0.6670 (tp) REVERT: I 398 MET cc_start: 0.7480 (mtt) cc_final: 0.7188 (mtt) REVERT: I 417 GLU cc_start: 0.7700 (mp0) cc_final: 0.7090 (mp0) REVERT: J 101 TRP cc_start: 0.5588 (OUTLIER) cc_final: 0.4809 (m100) REVERT: J 137 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.7132 (p-80) REVERT: J 195 ASN cc_start: 0.8691 (m-40) cc_final: 0.8399 (m-40) REVERT: J 299 MET cc_start: 0.7610 (ptp) cc_final: 0.7384 (ptp) REVERT: J 310 TYR cc_start: 0.6901 (t80) cc_final: 0.6607 (t80) REVERT: J 323 MET cc_start: 0.8673 (mpp) cc_final: 0.8305 (mpp) REVERT: J 384 GLN cc_start: 0.6705 (mm-40) cc_final: 0.6120 (mm-40) REVERT: K 153 LEU cc_start: 0.8991 (tp) cc_final: 0.8688 (tp) REVERT: K 337 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7375 (m) REVERT: K 355 ILE cc_start: 0.6719 (mm) cc_final: 0.6321 (tp) REVERT: L 101 TRP cc_start: 0.5649 (OUTLIER) cc_final: 0.4269 (m-10) REVERT: L 299 MET cc_start: 0.7327 (ptp) cc_final: 0.6991 (ptp) REVERT: L 300 MET cc_start: 0.6202 (mtt) cc_final: 0.5699 (mtt) REVERT: M 167 LEU cc_start: 0.8358 (tp) cc_final: 0.8027 (tp) REVERT: M 254 GLU cc_start: 0.8589 (tt0) cc_final: 0.8011 (tt0) REVERT: M 292 THR cc_start: 0.8344 (t) cc_final: 0.8131 (t) REVERT: M 355 ILE cc_start: 0.7021 (mm) cc_final: 0.6666 (tp) REVERT: M 398 MET cc_start: 0.7475 (mtt) cc_final: 0.7183 (mtt) REVERT: M 417 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7572 (mp0) REVERT: N 101 TRP cc_start: 0.5599 (OUTLIER) cc_final: 0.4821 (m100) REVERT: N 137 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.7159 (p-80) REVERT: N 147 MET cc_start: 0.6566 (tpp) cc_final: 0.6175 (tpp) REVERT: N 195 ASN cc_start: 0.8699 (m-40) cc_final: 0.8403 (m-40) REVERT: N 299 MET cc_start: 0.7605 (ptp) cc_final: 0.7262 (ptp) REVERT: N 310 TYR cc_start: 0.7005 (t80) cc_final: 0.6652 (t80) REVERT: N 323 MET cc_start: 0.8674 (mpp) cc_final: 0.8306 (mpp) REVERT: N 384 GLN cc_start: 0.6702 (mm-40) cc_final: 0.6119 (mm-40) REVERT: O 153 LEU cc_start: 0.8989 (tp) cc_final: 0.8689 (tp) REVERT: O 337 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7367 (m) REVERT: O 355 ILE cc_start: 0.6720 (mm) cc_final: 0.6323 (tp) REVERT: P 101 TRP cc_start: 0.5645 (OUTLIER) cc_final: 0.4269 (m-10) REVERT: P 299 MET cc_start: 0.7376 (ptp) cc_final: 0.7026 (ptp) REVERT: P 300 MET cc_start: 0.6173 (mtt) cc_final: 0.5667 (mtt) REVERT: P 426 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7459 (tm-30) outliers start: 171 outliers final: 141 residues processed: 989 average time/residue: 0.4623 time to fit residues: 801.5233 Evaluate side-chains 997 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 838 time to evaluate : 4.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 185 TYR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 270 PHE Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 270 PHE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 280 GLN Chi-restraints excluded: chain H residue 281 TYR Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 386 THR Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 101 TRP Chi-restraints excluded: chain J residue 124 CYS Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 137 HIS Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 270 PHE Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 206 ASN Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain L residue 100 ASN Chi-restraints excluded: chain L residue 101 TRP Chi-restraints excluded: chain L residue 124 CYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 270 PHE Chi-restraints excluded: chain L residue 280 GLN Chi-restraints excluded: chain L residue 281 TYR Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 386 THR Chi-restraints excluded: chain L residue 399 THR Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 324 VAL Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 101 TRP Chi-restraints excluded: chain N residue 124 CYS Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 137 HIS Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 270 PHE Chi-restraints excluded: chain N residue 280 GLN Chi-restraints excluded: chain N residue 281 TYR Chi-restraints excluded: chain N residue 374 ILE Chi-restraints excluded: chain N residue 386 THR Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain O residue 238 ILE Chi-restraints excluded: chain O residue 324 VAL Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain P residue 100 ASN Chi-restraints excluded: chain P residue 101 TRP Chi-restraints excluded: chain P residue 124 CYS Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 280 GLN Chi-restraints excluded: chain P residue 281 TYR Chi-restraints excluded: chain P residue 284 LEU Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 386 THR Chi-restraints excluded: chain P residue 399 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 433 optimal weight: 0.0050 chunk 581 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 chunk 503 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 546 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 561 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 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 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 139 HIS ** 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 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.139952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.121200 restraints weight = 141485.603| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 4.01 r_work: 0.3776 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 55528 Z= 0.242 Angle : 0.996 59.200 75552 Z= 0.554 Chirality : 0.055 1.092 8312 Planarity : 0.005 0.138 9816 Dihedral : 19.980 160.446 8168 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.77 % Favored : 91.07 % Rotamer: Outliers : 2.93 % Allowed : 21.93 % Favored : 75.14 % Cbeta Deviations : 0.12 % 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: -1.11 (0.10), residues: 6896 helix: 0.93 (0.10), residues: 2880 sheet: -0.84 (0.18), residues: 968 loop : -2.44 (0.10), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 346 HIS 0.006 0.001 HIS M 139 PHE 0.013 0.001 PHE F 294 TYR 0.014 0.001 TYR O 312 ARG 0.002 0.000 ARG A 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13465.95 seconds wall clock time: 237 minutes 5.79 seconds (14225.79 seconds total)