Starting phenix.real_space_refine (version: dev) on Wed Feb 22 03:01:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2023/7lxb_23569_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2023/7lxb_23569.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2023/7lxb_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_2023/7lxb_23569_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2023/7lxb_23569_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2023/7lxb_23569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2023/7lxb_23569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2023/7lxb_23569_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxb_23569/02_2023/7lxb_23569_neut_updated.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.034 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 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 22.01, per 1000 atoms: 0.41 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: 16.40 Conformation dependent library (CDL) restraints added in 6.2 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: 3.99 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: 14.34 Time building geometry restraints manager: 17.90 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 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. 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: 4.490 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: 0.030 Extract box with map and model: 20.010 Check model and map are aligned: 0.600 Process input model: 98.040 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Set scattering table: 0.360 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 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 % 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 *********************** 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 : 4.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 8 residues processed: 1128 average time/residue: 0.4735 time to fit residues: 928.9588 Evaluate side-chains 831 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 823 time to evaluate : 4.661 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3767 time to fit residues: 12.0100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** G 8 HIS ** 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** ** K 8 HIS ** 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** ** O 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN P 100 ASN ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 55528 Z= 0.188 Angle : 0.703 11.745 75552 Z= 0.338 Chirality : 0.046 0.168 8312 Planarity : 0.005 0.059 9816 Dihedral : 21.808 168.699 8168 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.15 % Favored : 90.75 % Rotamer Outliers : 0.93 % 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: -1.77 (0.10), residues: 6896 helix: 0.74 (0.10), residues: 2824 sheet: -1.68 (0.16), residues: 1000 loop : -2.95 (0.10), residues: 3072 *********************** 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 1034 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 981 time to evaluate : 4.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 28 residues processed: 992 average time/residue: 0.4842 time to fit residues: 841.6603 Evaluate side-chains 891 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 863 time to evaluate : 4.643 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3988 time to fit residues: 27.3230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 347 optimal weight: 0.4980 chunk 193 optimal weight: 0.0870 chunk 519 optimal weight: 1.9990 chunk 425 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 625 optimal weight: 0.9990 chunk 676 optimal weight: 1.9990 chunk 557 optimal weight: 0.9990 chunk 620 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 502 optimal weight: 2.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 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 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** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 256 ASN ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 256 ASN ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1785 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= 0.188 Angle : 0.670 12.209 75552 Z= 0.318 Chirality : 0.045 0.193 8312 Planarity : 0.004 0.043 9816 Dihedral : 21.455 171.668 8168 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.22 % Favored : 90.68 % Rotamer Outliers : 1.77 % 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: -1.57 (0.10), residues: 6896 helix: 0.77 (0.10), residues: 2848 sheet: -1.47 (0.16), residues: 968 loop : -2.75 (0.10), residues: 3080 *********************** 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 1027 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 926 time to evaluate : 4.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 52 residues processed: 999 average time/residue: 0.4822 time to fit residues: 843.9946 Evaluate side-chains 880 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 828 time to evaluate : 4.592 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.4052 time to fit residues: 46.0100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 618 optimal weight: 0.9990 chunk 470 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 chunk 69 optimal weight: 0.3980 chunk 298 optimal weight: 2.9990 chunk 420 optimal weight: 10.0000 chunk 628 optimal weight: 0.0060 chunk 665 optimal weight: 3.9990 chunk 328 optimal weight: 1.9990 chunk 595 optimal weight: 4.9990 chunk 179 optimal weight: 0.3980 overall best weight: 0.7600 ------------------------------------------------------------------------------- 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 ** 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 226 ASN 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 ** F 226 ASN ** 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 ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** 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 226 ASN 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 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 226 ASN P 334 GLN ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2116 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= 0.184 Angle : 0.667 12.025 75552 Z= 0.317 Chirality : 0.044 0.263 8312 Planarity : 0.004 0.042 9816 Dihedral : 21.193 172.132 8168 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.01 % Favored : 90.89 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.10), residues: 6896 helix: 0.83 (0.10), residues: 2864 sheet: -1.42 (0.17), residues: 976 loop : -2.63 (0.10), residues: 3056 *********************** 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 989 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 909 time to evaluate : 4.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 51 residues processed: 969 average time/residue: 0.4825 time to fit residues: 819.2500 Evaluate side-chains 890 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 839 time to evaluate : 4.747 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.3972 time to fit residues: 44.3972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 553 optimal weight: 0.8980 chunk 377 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 495 optimal weight: 5.9990 chunk 274 optimal weight: 2.9990 chunk 567 optimal weight: 0.9990 chunk 459 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 339 optimal weight: 0.5980 chunk 596 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN G 28 HIS ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 226 ASN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 423 GLN ** 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** J 423 GLN K 28 HIS ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN ** L 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 423 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** N 423 GLN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** P 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2252 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= 0.188 Angle : 0.665 11.843 75552 Z= 0.316 Chirality : 0.044 0.247 8312 Planarity : 0.004 0.047 9816 Dihedral : 20.917 169.077 8168 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.48 % Favored : 90.41 % Rotamer Outliers : 1.18 % 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: 0.92 (0.10), residues: 2864 sheet: -1.18 (0.17), residues: 968 loop : -2.54 (0.10), residues: 3064 *********************** 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 961 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 894 time to evaluate : 4.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 21 residues processed: 943 average time/residue: 0.4823 time to fit residues: 797.1677 Evaluate side-chains 836 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 815 time to evaluate : 4.708 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4477 time to fit residues: 23.5501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 223 optimal weight: 0.7980 chunk 598 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 390 optimal weight: 0.0470 chunk 164 optimal weight: 4.9990 chunk 665 optimal weight: 0.6980 chunk 552 optimal weight: 5.9990 chunk 308 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 349 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 131 GLN B 226 ASN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN D 8 GLN ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN F 226 ASN ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** H 423 GLN ** 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 ** L 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 337 ASN ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN N 131 GLN N 226 ASN ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS O 256 GLN P 6 HIS ** 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** ** P 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2551 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= 0.169 Angle : 0.647 11.682 75552 Z= 0.306 Chirality : 0.044 0.246 8312 Planarity : 0.004 0.042 9816 Dihedral : 20.590 165.638 8168 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.35 % Favored : 91.55 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.10), residues: 6896 helix: 0.95 (0.10), residues: 2856 sheet: -1.12 (0.17), residues: 976 loop : -2.51 (0.10), residues: 3064 *********************** 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 951 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 862 time to evaluate : 4.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 49 residues processed: 931 average time/residue: 0.4881 time to fit residues: 806.1576 Evaluate side-chains 870 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 821 time to evaluate : 4.666 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.4284 time to fit residues: 46.0978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 641 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 379 optimal weight: 0.0060 chunk 486 optimal weight: 0.4980 chunk 376 optimal weight: 7.9990 chunk 560 optimal weight: 4.9990 chunk 371 optimal weight: 2.9990 chunk 663 optimal weight: 0.8980 chunk 414 optimal weight: 0.5980 chunk 404 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** 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 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 423 GLN ** 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 131 GLN ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 HIS ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2683 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= 0.168 Angle : 0.657 11.709 75552 Z= 0.311 Chirality : 0.044 0.238 8312 Planarity : 0.004 0.042 9816 Dihedral : 20.404 162.362 8168 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.61 % Favored : 91.28 % Rotamer Outliers : 0.68 % 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: 0.94 (0.10), residues: 2864 sheet: -0.94 (0.18), residues: 952 loop : -2.45 (0.10), residues: 3080 *********************** 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 914 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 875 time to evaluate : 4.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 15 residues processed: 897 average time/residue: 0.4789 time to fit residues: 760.2677 Evaluate side-chains 835 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 820 time to evaluate : 4.686 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4503 time to fit residues: 18.5374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 410 optimal weight: 0.9990 chunk 264 optimal weight: 5.9990 chunk 396 optimal weight: 0.0020 chunk 199 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 421 optimal weight: 0.7980 chunk 451 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 521 optimal weight: 7.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 416 ASN ** 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** D 423 GLN E 206 ASN ** F 8 GLN ** 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 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 GLN I 206 ASN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 ASN ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 423 GLN M 206 ASN ** N 8 GLN ** 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** P 423 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2881 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= 0.178 Angle : 0.661 11.725 75552 Z= 0.312 Chirality : 0.044 0.257 8312 Planarity : 0.004 0.042 9816 Dihedral : 20.348 161.677 8168 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.24 % Favored : 91.66 % Rotamer Outliers : 1.09 % 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: -1.13 (0.10), residues: 6896 helix: 0.97 (0.10), residues: 2840 sheet: -0.95 (0.17), residues: 984 loop : -2.43 (0.10), residues: 3072 *********************** 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 912 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 850 time to evaluate : 4.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 24 residues processed: 896 average time/residue: 0.5263 time to fit residues: 837.8625 Evaluate side-chains 843 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 819 time to evaluate : 4.680 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4498 time to fit residues: 26.0802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 603 optimal weight: 2.9990 chunk 635 optimal weight: 0.7980 chunk 579 optimal weight: 0.0870 chunk 617 optimal weight: 2.9990 chunk 371 optimal weight: 0.0010 chunk 269 optimal weight: 0.9980 chunk 485 optimal weight: 0.7980 chunk 189 optimal weight: 0.0470 chunk 558 optimal weight: 0.8980 chunk 584 optimal weight: 0.6980 chunk 615 optimal weight: 0.9990 overall best weight: 0.3262 ------------------------------------------------------------------------------- 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 416 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** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** 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 14 ASN ** 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** ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** 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 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 55528 Z= 0.165 Angle : 0.680 12.855 75552 Z= 0.317 Chirality : 0.044 0.266 8312 Planarity : 0.004 0.043 9816 Dihedral : 20.138 161.176 8168 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.99 % Favored : 91.91 % Rotamer Outliers : 0.25 % 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: -1.05 (0.10), residues: 6896 helix: 1.04 (0.10), residues: 2816 sheet: -0.82 (0.18), residues: 952 loop : -2.39 (0.10), residues: 3128 *********************** 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 891 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 877 time to evaluate : 4.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 882 average time/residue: 0.4847 time to fit residues: 749.8897 Evaluate side-chains 813 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 807 time to evaluate : 4.678 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4992 time to fit residues: 11.3329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 405 optimal weight: 0.9980 chunk 653 optimal weight: 6.9990 chunk 398 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 454 optimal weight: 5.9990 chunk 685 optimal weight: 0.7980 chunk 630 optimal weight: 5.9990 chunk 545 optimal weight: 0.0040 chunk 56 optimal weight: 5.9990 chunk 421 optimal weight: 2.9990 chunk 334 optimal weight: 4.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 HIS ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** 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 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 14 ASN ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 131 GLN ** P 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 55528 Z= 0.247 Angle : 0.723 11.770 75552 Z= 0.341 Chirality : 0.046 0.254 8312 Planarity : 0.004 0.042 9816 Dihedral : 20.246 162.743 8168 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.24 % Favored : 90.66 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.10), residues: 6896 helix: 0.80 (0.10), residues: 2880 sheet: -0.81 (0.18), residues: 960 loop : -2.40 (0.10), residues: 3056 ********************** 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 840 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 821 time to evaluate : 4.705 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 830 average time/residue: 0.4801 time to fit residues: 702.9035 Evaluate side-chains 810 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 796 time to evaluate : 4.661 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4331 time to fit residues: 17.3374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 433 optimal weight: 2.9990 chunk 581 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 chunk 503 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 546 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 561 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** 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** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 ASN ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 ASN ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.138909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.120112 restraints weight = 141168.517| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.98 r_work: 0.3759 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 55528 Z= 0.214 Angle : 0.711 11.910 75552 Z= 0.334 Chirality : 0.045 0.230 8312 Planarity : 0.004 0.041 9816 Dihedral : 20.081 160.035 8168 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.86 % Favored : 91.04 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.10), residues: 6896 helix: 0.76 (0.10), residues: 2880 sheet: -0.79 (0.18), residues: 960 loop : -2.39 (0.10), residues: 3056 =============================================================================== Job complete usr+sys time: 13282.32 seconds wall clock time: 234 minutes 11.14 seconds (14051.14 seconds total)