Starting phenix.real_space_refine (version: dev) on Sun May 15 16:24:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/05_2022/7d60_30586_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/05_2022/7d60_30586.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/05_2022/7d60_30586_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/05_2022/7d60_30586_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/05_2022/7d60_30586_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/05_2022/7d60_30586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/05_2022/7d60_30586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/05_2022/7d60_30586_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/05_2022/7d60_30586_updated.pdb" } resolution = 2.61 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 26664 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "C" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "E" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "F" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "G" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "H" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "I" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "J" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "K" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Time building chain proxies: 14.75, per 1000 atoms: 0.55 Number of scatterers: 26664 At special positions: 0 Unit cell: (155.1, 156.2, 105.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 220 16.00 P 55 15.00 O 4862 8.00 N 4224 7.00 C 17303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 127 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 149 " distance=2.04 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 127 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 127 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 158 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 127 " distance=2.04 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 158 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 127 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 158 " distance=2.03 Simple disulfide: pdb=" SG CYS F 142 " - pdb=" SG CYS F 149 " distance=2.04 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 127 " distance=2.04 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 158 " distance=2.03 Simple disulfide: pdb=" SG CYS G 142 " - pdb=" SG CYS G 149 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 127 " distance=2.04 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 158 " distance=2.03 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 149 " distance=2.04 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 127 " distance=2.04 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 158 " distance=2.03 Simple disulfide: pdb=" SG CYS I 142 " - pdb=" SG CYS I 149 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 127 " distance=2.04 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 158 " distance=2.03 Simple disulfide: pdb=" SG CYS J 142 " - pdb=" SG CYS J 149 " distance=2.04 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 127 " distance=2.04 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 158 " distance=2.03 Simple disulfide: pdb=" SG CYS K 142 " - pdb=" SG CYS K 149 " distance=2.04 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: 9.91 Conformation dependent library (CDL) restraints added in 3.8 seconds 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6006 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 176 helices and 0 sheets defined 68.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 10 through 13 No H-bonds generated for 'chain 'A' and resid 10 through 13' Processing helix chain 'A' and resid 15 through 37 removed outlier: 3.956A pdb=" N TYR A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Proline residue: A 58 - end of helix removed outlier: 3.562A pdb=" N PHE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) 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 95 through 106 Processing helix chain 'A' and resid 109 through 120 removed outlier: 3.648A pdb=" N VAL A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 138 through 141 No H-bonds generated for 'chain 'A' and resid 138 through 141' Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 246 removed outlier: 3.559A pdb=" N LYS A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 266 removed outlier: 3.763A pdb=" N SER A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 10 through 13 No H-bonds generated for 'chain 'B' and resid 10 through 13' Processing helix chain 'B' and resid 15 through 37 removed outlier: 3.957A pdb=" N TYR B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 68 removed outlier: 3.617A pdb=" N PHE B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 55 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Proline residue: B 58 - end of helix removed outlier: 3.561A pdb=" N PHE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 95 through 106 Processing helix chain 'B' and resid 109 through 120 removed outlier: 3.648A pdb=" N VAL B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 138 through 141 No H-bonds generated for 'chain 'B' and resid 138 through 141' Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 246 removed outlier: 3.559A pdb=" N LYS B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.764A pdb=" N SER B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 10 through 13 No H-bonds generated for 'chain 'C' and resid 10 through 13' Processing helix chain 'C' and resid 15 through 37 removed outlier: 3.956A pdb=" N TYR C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Proline residue: C 58 - end of helix removed outlier: 3.561A pdb=" N PHE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) 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 95 through 106 Processing helix chain 'C' and resid 109 through 120 removed outlier: 3.647A pdb=" N VAL C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 138 through 141 No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 168 through 203 removed outlier: 3.777A pdb=" N LEU C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 246 removed outlier: 3.560A pdb=" N LYS C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 224 " --> pdb=" O GLN C 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C 225 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 266 removed outlier: 3.764A pdb=" N SER C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 287 Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'D' and resid 10 through 13 No H-bonds generated for 'chain 'D' and resid 10 through 13' Processing helix chain 'D' and resid 15 through 37 removed outlier: 3.956A pdb=" N TYR D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Proline residue: D 58 - end of helix removed outlier: 3.561A pdb=" N PHE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 95 through 106 Processing helix chain 'D' and resid 109 through 120 removed outlier: 3.647A pdb=" N VAL D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 130 Processing helix chain 'D' and resid 138 through 141 No H-bonds generated for 'chain 'D' and resid 138 through 141' Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 246 removed outlier: 3.560A pdb=" N LYS D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 266 removed outlier: 3.765A pdb=" N SER D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 10 through 13 No H-bonds generated for 'chain 'E' and resid 10 through 13' Processing helix chain 'E' and resid 15 through 37 removed outlier: 3.957A pdb=" N TYR E 20 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Proline residue: E 58 - end of helix removed outlier: 3.562A pdb=" N PHE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) 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 95 through 106 Processing helix chain 'E' and resid 109 through 120 removed outlier: 3.648A pdb=" N VAL E 117 " --> pdb=" O MET E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 130 Processing helix chain 'E' and resid 138 through 141 No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU E 173 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 175 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN E 176 " --> pdb=" O LYS E 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN E 180 " --> pdb=" O GLN E 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 187 " --> pdb=" O GLY E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 246 removed outlier: 3.560A pdb=" N LYS E 221 " --> pdb=" O THR E 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E 225 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS E 236 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E 245 " --> pdb=" O ASN E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 266 removed outlier: 3.763A pdb=" N SER E 266 " --> pdb=" O TRP E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'F' and resid 3 through 8 Processing helix chain 'F' and resid 10 through 13 No H-bonds generated for 'chain 'F' and resid 10 through 13' Processing helix chain 'F' and resid 15 through 37 removed outlier: 3.956A pdb=" N TYR F 20 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA F 24 " --> pdb=" O TYR F 20 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 36 " --> pdb=" O ARG F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 55 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Proline residue: F 58 - end of helix removed outlier: 3.561A pdb=" N PHE F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU F 76 " --> pdb=" O ARG F 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 95 through 106 Processing helix chain 'F' and resid 109 through 120 removed outlier: 3.647A pdb=" N VAL F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 130 Processing helix chain 'F' and resid 138 through 141 No H-bonds generated for 'chain 'F' and resid 138 through 141' Processing helix chain 'F' and resid 147 through 149 No H-bonds generated for 'chain 'F' and resid 147 through 149' Processing helix chain 'F' and resid 153 through 155 No H-bonds generated for 'chain 'F' and resid 153 through 155' Processing helix chain 'F' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER F 174 " --> pdb=" O GLU F 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 175 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN F 176 " --> pdb=" O LYS F 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN F 180 " --> pdb=" O GLN F 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU F 182 " --> pdb=" O GLN F 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 187 " --> pdb=" O GLY F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 246 removed outlier: 3.560A pdb=" N LYS F 221 " --> pdb=" O THR F 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU F 224 " --> pdb=" O GLN F 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN F 225 " --> pdb=" O LYS F 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE F 245 " --> pdb=" O ASN F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 266 removed outlier: 3.763A pdb=" N SER F 266 " --> pdb=" O TRP F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 287 Processing helix chain 'G' and resid 3 through 8 Processing helix chain 'G' and resid 10 through 13 No H-bonds generated for 'chain 'G' and resid 10 through 13' Processing helix chain 'G' and resid 15 through 37 removed outlier: 3.957A pdb=" N TYR G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA G 24 " --> pdb=" O TYR G 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G 55 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) Proline residue: G 58 - end of helix removed outlier: 3.561A pdb=" N PHE G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU G 76 " --> pdb=" O ARG G 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) 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 95 through 106 Processing helix chain 'G' and resid 109 through 120 removed outlier: 3.647A pdb=" N VAL G 117 " --> pdb=" O MET G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 130 Processing helix chain 'G' and resid 138 through 141 No H-bonds generated for 'chain 'G' and resid 138 through 141' Processing helix chain 'G' and resid 147 through 149 No H-bonds generated for 'chain 'G' and resid 147 through 149' Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER G 174 " --> pdb=" O GLU G 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN G 176 " --> pdb=" O LYS G 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN G 178 " --> pdb=" O SER G 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN G 180 " --> pdb=" O GLN G 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 182 " --> pdb=" O GLN G 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 187 " --> pdb=" O GLY G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 246 removed outlier: 3.559A pdb=" N LYS G 221 " --> pdb=" O THR G 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU G 224 " --> pdb=" O GLN G 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN G 225 " --> pdb=" O LYS G 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE G 245 " --> pdb=" O ASN G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 266 removed outlier: 3.764A pdb=" N SER G 266 " --> pdb=" O TRP G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 287 Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 10 through 13 No H-bonds generated for 'chain 'H' and resid 10 through 13' Processing helix chain 'H' and resid 15 through 37 removed outlier: 3.956A pdb=" N TYR H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU H 33 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE H 54 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 55 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Proline residue: H 58 - end of helix removed outlier: 3.561A pdb=" N PHE H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 95 through 106 Processing helix chain 'H' and resid 109 through 120 removed outlier: 3.648A pdb=" N VAL H 117 " --> pdb=" O MET H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 130 Processing helix chain 'H' and resid 138 through 141 No H-bonds generated for 'chain 'H' and resid 138 through 141' Processing helix chain 'H' and resid 147 through 149 No H-bonds generated for 'chain 'H' and resid 147 through 149' Processing helix chain 'H' and resid 153 through 155 No H-bonds generated for 'chain 'H' and resid 153 through 155' Processing helix chain 'H' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU H 173 " --> pdb=" O GLU H 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER H 174 " --> pdb=" O GLU H 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU H 175 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN H 176 " --> pdb=" O LYS H 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN H 180 " --> pdb=" O GLN H 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 182 " --> pdb=" O GLN H 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE H 187 " --> pdb=" O GLY H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 246 removed outlier: 3.560A pdb=" N LYS H 221 " --> pdb=" O THR H 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS H 223 " --> pdb=" O ALA H 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU H 224 " --> pdb=" O GLN H 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN H 225 " --> pdb=" O LYS H 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN H 235 " --> pdb=" O LEU H 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE H 245 " --> pdb=" O ASN H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 266 removed outlier: 3.764A pdb=" N SER H 266 " --> pdb=" O TRP H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 287 Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 10 through 13 No H-bonds generated for 'chain 'I' and resid 10 through 13' Processing helix chain 'I' and resid 15 through 37 removed outlier: 3.956A pdb=" N TYR I 20 " --> pdb=" O THR I 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE I 54 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU I 55 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE I 56 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Proline residue: I 58 - end of helix removed outlier: 3.561A pdb=" N PHE I 67 " --> pdb=" O LEU I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 77 removed outlier: 3.612A pdb=" N LEU I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE I 77 " --> pdb=" O SER I 73 " (cutoff:3.500A) 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 95 through 106 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.647A pdb=" N VAL I 117 " --> pdb=" O MET I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 130 Processing helix chain 'I' and resid 138 through 141 No H-bonds generated for 'chain 'I' and resid 138 through 141' Processing helix chain 'I' and resid 147 through 149 No H-bonds generated for 'chain 'I' and resid 147 through 149' Processing helix chain 'I' and resid 153 through 155 No H-bonds generated for 'chain 'I' and resid 153 through 155' Processing helix chain 'I' and resid 168 through 203 removed outlier: 3.777A pdb=" N LEU I 173 " --> pdb=" O GLU I 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER I 174 " --> pdb=" O GLU I 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU I 175 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN I 176 " --> pdb=" O LYS I 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN I 178 " --> pdb=" O SER I 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN I 180 " --> pdb=" O GLN I 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU I 182 " --> pdb=" O GLN I 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE I 187 " --> pdb=" O GLY I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 246 removed outlier: 3.559A pdb=" N LYS I 221 " --> pdb=" O THR I 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS I 223 " --> pdb=" O ALA I 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU I 224 " --> pdb=" O GLN I 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN I 225 " --> pdb=" O LYS I 221 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN I 235 " --> pdb=" O LEU I 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS I 236 " --> pdb=" O ASP I 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE I 245 " --> pdb=" O ASN I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 266 removed outlier: 3.765A pdb=" N SER I 266 " --> pdb=" O TRP I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 287 Processing helix chain 'J' and resid 3 through 8 Processing helix chain 'J' and resid 10 through 13 No H-bonds generated for 'chain 'J' and resid 10 through 13' Processing helix chain 'J' and resid 15 through 37 removed outlier: 3.956A pdb=" N TYR J 20 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA J 24 " --> pdb=" O TYR J 20 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU J 33 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU J 55 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Proline residue: J 58 - end of helix removed outlier: 3.561A pdb=" N PHE J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU J 76 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE J 77 " --> pdb=" O SER J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 86 No H-bonds generated for 'chain 'J' and resid 84 through 86' Processing helix chain 'J' and resid 95 through 106 Processing helix chain 'J' and resid 109 through 120 removed outlier: 3.647A pdb=" N VAL J 117 " --> pdb=" O MET J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 130 Processing helix chain 'J' and resid 138 through 141 No H-bonds generated for 'chain 'J' and resid 138 through 141' Processing helix chain 'J' and resid 147 through 149 No H-bonds generated for 'chain 'J' and resid 147 through 149' Processing helix chain 'J' and resid 153 through 155 No H-bonds generated for 'chain 'J' and resid 153 through 155' Processing helix chain 'J' and resid 168 through 203 removed outlier: 3.777A pdb=" N LEU J 173 " --> pdb=" O GLU J 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER J 174 " --> pdb=" O GLU J 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU J 175 " --> pdb=" O LEU J 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN J 176 " --> pdb=" O LYS J 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN J 178 " --> pdb=" O SER J 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN J 180 " --> pdb=" O GLN J 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU J 182 " --> pdb=" O GLN J 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE J 187 " --> pdb=" O GLY J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 246 removed outlier: 3.559A pdb=" N LYS J 221 " --> pdb=" O THR J 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS J 223 " --> pdb=" O ALA J 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU J 224 " --> pdb=" O GLN J 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN J 225 " --> pdb=" O LYS J 221 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN J 235 " --> pdb=" O LEU J 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS J 236 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE J 245 " --> pdb=" O ASN J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 266 removed outlier: 3.764A pdb=" N SER J 266 " --> pdb=" O TRP J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 287 Processing helix chain 'K' and resid 3 through 8 Processing helix chain 'K' and resid 10 through 13 No H-bonds generated for 'chain 'K' and resid 10 through 13' Processing helix chain 'K' and resid 15 through 37 removed outlier: 3.957A pdb=" N TYR K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA K 24 " --> pdb=" O TYR K 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU K 33 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE K 56 " --> pdb=" O LEU K 52 " (cutoff:3.500A) Proline residue: K 58 - end of helix removed outlier: 3.561A pdb=" N PHE K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU K 76 " --> pdb=" O ARG K 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE K 77 " --> pdb=" O SER K 73 " (cutoff:3.500A) 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 95 through 106 Processing helix chain 'K' and resid 109 through 120 removed outlier: 3.647A pdb=" N VAL K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 130 Processing helix chain 'K' and resid 138 through 141 No H-bonds generated for 'chain 'K' and resid 138 through 141' Processing helix chain 'K' and resid 147 through 149 No H-bonds generated for 'chain 'K' and resid 147 through 149' Processing helix chain 'K' and resid 153 through 155 No H-bonds generated for 'chain 'K' and resid 153 through 155' Processing helix chain 'K' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU K 173 " --> pdb=" O GLU K 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER K 174 " --> pdb=" O GLU K 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU K 175 " --> pdb=" O LEU K 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN K 176 " --> pdb=" O LYS K 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN K 178 " --> pdb=" O SER K 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN K 180 " --> pdb=" O GLN K 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU K 182 " --> pdb=" O GLN K 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE K 187 " --> pdb=" O GLY K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 246 removed outlier: 3.560A pdb=" N LYS K 221 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS K 223 " --> pdb=" O ALA K 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU K 224 " --> pdb=" O GLN K 220 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN K 225 " --> pdb=" O LYS K 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN K 235 " --> pdb=" O LEU K 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS K 236 " --> pdb=" O ASP K 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE K 245 " --> pdb=" O ASN K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 266 removed outlier: 3.764A pdb=" N SER K 266 " --> pdb=" O TRP K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 287 1166 hydrogen bonds defined for protein. 3498 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: 7.57 Time building geometry restraints manager: 10.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3960 1.31 - 1.43: 7954 1.43 - 1.56: 15047 1.56 - 1.69: 55 1.69 - 1.82: 286 Bond restraints: 27302 Sorted by residual: bond pdb=" CB PRO C 111 " pdb=" CG PRO C 111 " ideal model delta sigma weight residual 1.492 1.422 0.070 5.00e-02 4.00e+02 1.94e+00 bond pdb=" CB PRO D 111 " pdb=" CG PRO D 111 " ideal model delta sigma weight residual 1.492 1.422 0.070 5.00e-02 4.00e+02 1.94e+00 bond pdb=" CB PRO K 111 " pdb=" CG PRO K 111 " ideal model delta sigma weight residual 1.492 1.422 0.070 5.00e-02 4.00e+02 1.93e+00 bond pdb=" CB PRO J 111 " pdb=" CG PRO J 111 " ideal model delta sigma weight residual 1.492 1.423 0.069 5.00e-02 4.00e+02 1.93e+00 bond pdb=" CB PRO I 111 " pdb=" CG PRO I 111 " ideal model delta sigma weight residual 1.492 1.423 0.069 5.00e-02 4.00e+02 1.93e+00 ... (remaining 27297 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.13: 686 107.13 - 113.88: 15299 113.88 - 120.63: 12093 120.63 - 127.37: 8379 127.37 - 134.12: 316 Bond angle restraints: 36773 Sorted by residual: angle pdb=" N ILE A 87 " pdb=" CA ILE A 87 " pdb=" C ILE A 87 " ideal model delta sigma weight residual 113.42 107.17 6.25 1.17e+00 7.31e-01 2.85e+01 angle pdb=" N ILE K 87 " pdb=" CA ILE K 87 " pdb=" C ILE K 87 " ideal model delta sigma weight residual 113.42 107.20 6.22 1.17e+00 7.31e-01 2.83e+01 angle pdb=" N ILE D 87 " pdb=" CA ILE D 87 " pdb=" C ILE D 87 " ideal model delta sigma weight residual 113.42 107.20 6.22 1.17e+00 7.31e-01 2.82e+01 angle pdb=" N ILE H 87 " pdb=" CA ILE H 87 " pdb=" C ILE H 87 " ideal model delta sigma weight residual 113.42 107.20 6.22 1.17e+00 7.31e-01 2.82e+01 angle pdb=" N ILE G 87 " pdb=" CA ILE G 87 " pdb=" C ILE G 87 " ideal model delta sigma weight residual 113.42 107.21 6.21 1.17e+00 7.31e-01 2.82e+01 ... (remaining 36768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 13583 16.88 - 33.77: 1894 33.77 - 50.65: 418 50.65 - 67.54: 66 67.54 - 84.42: 44 Dihedral angle restraints: 16005 sinusoidal: 6743 harmonic: 9262 Sorted by residual: dihedral pdb=" CA LYS D 221 " pdb=" C LYS D 221 " pdb=" N GLU D 222 " pdb=" CA GLU D 222 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LYS E 221 " pdb=" C LYS E 221 " pdb=" N GLU E 222 " pdb=" CA GLU E 222 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LYS C 221 " pdb=" C LYS C 221 " pdb=" N GLU C 222 " pdb=" CA GLU C 222 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 16002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2389 0.041 - 0.082: 1262 0.082 - 0.123: 220 0.123 - 0.164: 23 0.164 - 0.205: 22 Chirality restraints: 3916 Sorted by residual: chirality pdb=" CA PRO D 165 " pdb=" N PRO D 165 " pdb=" C PRO D 165 " pdb=" CB PRO D 165 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO K 165 " pdb=" N PRO K 165 " pdb=" C PRO K 165 " pdb=" CB PRO K 165 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PRO E 165 " pdb=" N PRO E 165 " pdb=" C PRO E 165 " pdb=" CB PRO E 165 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3913 not shown) Planarity restraints: 4499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA J 110 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO J 111 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO J 111 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO J 111 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 110 " 0.048 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO C 111 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 111 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 111 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 110 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO G 111 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO G 111 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 111 " -0.040 5.00e-02 4.00e+02 ... (remaining 4496 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 9644 2.90 - 3.40: 22563 3.40 - 3.90: 39595 3.90 - 4.40: 47842 4.40 - 4.90: 82005 Nonbonded interactions: 201649 Sorted by model distance: nonbonded pdb=" O LEU A 231 " pdb=" NZ LYS K 221 " model vdw 2.395 2.520 nonbonded pdb=" NZ LYS B 221 " pdb=" O LEU C 231 " model vdw 2.401 2.520 nonbonded pdb=" NZ LYS A 221 " pdb=" O LEU B 231 " model vdw 2.404 2.520 nonbonded pdb=" NZ LYS E 221 " pdb=" O LEU F 231 " model vdw 2.405 2.520 nonbonded pdb=" NZ LYS I 221 " pdb=" O LEU J 231 " model vdw 2.409 2.520 ... (remaining 201644 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 5 Type Number sf(0) Gaussians P 55 5.49 5 S 220 5.16 5 C 17303 2.51 5 N 4224 2.21 5 O 4862 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: 1.870 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: 0.010 Extract box with map and model: 10.550 Check model and map are aligned: 0.400 Convert atoms to be neutral: 0.210 Process input model: 64.660 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 : 0.006 0.070 27302 Z= 0.385 Angle : 0.885 10.774 36773 Z= 0.453 Chirality : 0.048 0.205 3916 Planarity : 0.007 0.072 4499 Dihedral : 16.437 84.422 9900 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.95 (0.08), residues: 3146 helix: -4.81 (0.03), residues: 2409 sheet: None (None), residues: 0 loop : -2.59 (0.19), residues: 737 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 721 time to evaluate : 3.326 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 721 average time/residue: 1.5839 time to fit residues: 1297.4912 Evaluate side-chains 486 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 3.149 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 93 optimal weight: 0.1980 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 279 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 178 GLN A 225 GLN A 248 ASN B 83 ASN B 168 ASN B 248 ASN B 276 GLN C 225 GLN C 248 ASN C 276 GLN C 287 ASN D 83 ASN D 248 ASN E 102 GLN E 248 ASN E 276 GLN F 168 ASN F 225 GLN F 248 ASN G 102 GLN G 178 GLN G 220 GLN G 248 ASN H 83 ASN H 220 GLN H 276 GLN I 83 ASN I 248 ASN I 273 GLN I 276 GLN J 83 ASN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 ASN K 83 ASN K 178 GLN K 220 GLN K 248 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 27302 Z= 0.155 Angle : 0.567 9.483 36773 Z= 0.296 Chirality : 0.036 0.126 3916 Planarity : 0.005 0.045 4499 Dihedral : 10.566 57.960 3982 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 2.33 % 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: -3.47 (0.13), residues: 3146 helix: -2.24 (0.09), residues: 2387 sheet: None (None), residues: 0 loop : -1.70 (0.22), residues: 759 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 472 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 28 residues processed: 510 average time/residue: 1.3905 time to fit residues: 822.0275 Evaluate side-chains 437 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 409 time to evaluate : 3.035 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 17 residues processed: 11 average time/residue: 0.6553 time to fit residues: 13.6663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 280 optimal weight: 20.0000 chunk 302 optimal weight: 0.9990 chunk 249 optimal weight: 0.8980 chunk 277 optimal weight: 0.0060 chunk 95 optimal weight: 0.0670 chunk 224 optimal weight: 10.0000 overall best weight: 0.5934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 102 GLN D 168 ASN E 102 GLN E 176 GLN F 176 GLN F 273 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 168 ASN G 220 GLN G 276 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 168 ASN H 276 GLN I 273 GLN I 276 GLN J 168 ASN J 176 GLN J 220 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 ASN K 276 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 27302 Z= 0.130 Angle : 0.495 7.984 36773 Z= 0.253 Chirality : 0.035 0.129 3916 Planarity : 0.004 0.035 4499 Dihedral : 9.444 59.067 3982 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 2.79 % 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: -1.35 (0.15), residues: 3146 helix: -0.59 (0.11), residues: 2376 sheet: None (None), residues: 0 loop : -1.40 (0.23), residues: 770 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 426 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 33 residues processed: 474 average time/residue: 1.4403 time to fit residues: 788.6672 Evaluate side-chains 425 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 392 time to evaluate : 3.457 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 24 residues processed: 10 average time/residue: 0.7535 time to fit residues: 14.0478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 2.9990 chunk 210 optimal weight: 0.0470 chunk 145 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 281 optimal weight: 0.4980 chunk 297 optimal weight: 0.2980 chunk 146 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 ASN C 102 GLN C 168 ASN C 178 GLN C 248 ASN C 276 GLN D 176 GLN E 102 GLN E 176 GLN E 273 GLN F 102 GLN F 176 GLN F 273 GLN G 273 GLN H 102 GLN H 273 GLN H 276 GLN I 102 GLN I 168 ASN I 273 GLN J 47 ASN J 176 GLN J 178 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 273 GLN K 276 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 27302 Z= 0.123 Angle : 0.467 7.904 36773 Z= 0.239 Chirality : 0.034 0.140 3916 Planarity : 0.003 0.034 4499 Dihedral : 9.022 59.697 3982 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 3.40 % 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: -0.57 (0.16), residues: 3146 helix: 0.06 (0.11), residues: 2398 sheet: None (None), residues: 0 loop : -1.47 (0.23), residues: 748 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 400 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 52 residues processed: 463 average time/residue: 1.4388 time to fit residues: 770.1932 Evaluate side-chains 427 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 375 time to evaluate : 3.063 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 37 residues processed: 16 average time/residue: 0.3594 time to fit residues: 13.2564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 4 optimal weight: 0.3980 chunk 221 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 254 optimal weight: 3.9990 chunk 205 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 267 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN D 176 GLN D 273 GLN E 102 GLN E 176 GLN F 102 GLN F 176 GLN F 273 GLN F 276 GLN G 273 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 168 ASN H 273 GLN I 102 GLN I 273 GLN J 176 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 273 GLN K 276 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 27302 Z= 0.117 Angle : 0.460 8.310 36773 Z= 0.233 Chirality : 0.034 0.136 3916 Planarity : 0.003 0.031 4499 Dihedral : 8.632 59.442 3982 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 3.08 % 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: -0.05 (0.16), residues: 3146 helix: 0.45 (0.11), residues: 2398 sheet: None (None), residues: 0 loop : -1.36 (0.23), residues: 748 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 406 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 46 residues processed: 469 average time/residue: 1.3668 time to fit residues: 742.1512 Evaluate side-chains 426 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 380 time to evaluate : 2.959 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 36 residues processed: 10 average time/residue: 0.4070 time to fit residues: 10.4602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 7.9990 chunk 268 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 137 optimal weight: 0.3980 chunk 24 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 156 optimal weight: 0.4980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN B 273 GLN C 276 GLN D 273 GLN E 102 GLN E 176 GLN E 273 GLN F 102 GLN F 176 GLN F 273 GLN F 276 GLN G 102 GLN G 273 GLN H 102 GLN H 273 GLN I 102 GLN I 248 ASN I 273 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN K 168 ASN K 273 GLN K 276 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 27302 Z= 0.203 Angle : 0.532 7.985 36773 Z= 0.271 Chirality : 0.038 0.148 3916 Planarity : 0.003 0.057 4499 Dihedral : 8.839 59.999 3982 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 3.76 % 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: -0.17 (0.16), residues: 3146 helix: 0.41 (0.11), residues: 2420 sheet: None (None), residues: 0 loop : -1.61 (0.23), residues: 726 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 406 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 61 residues processed: 475 average time/residue: 1.3826 time to fit residues: 761.9825 Evaluate side-chains 447 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 386 time to evaluate : 3.019 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 43 residues processed: 18 average time/residue: 0.4170 time to fit residues: 15.4330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 169 optimal weight: 0.0070 chunk 217 optimal weight: 0.8980 chunk 168 optimal weight: 9.9990 chunk 250 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 296 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 273 GLN B 273 GLN C 168 ASN D 273 GLN E 102 GLN F 102 GLN F 273 GLN F 276 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 273 GLN H 102 GLN H 273 GLN I 102 GLN I 273 GLN J 168 ASN J 176 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 27302 Z= 0.135 Angle : 0.476 8.735 36773 Z= 0.243 Chirality : 0.035 0.136 3916 Planarity : 0.003 0.051 4499 Dihedral : 8.356 59.803 3982 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 2.86 % 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: 0.43 (0.16), residues: 3146 helix: 0.87 (0.11), residues: 2343 sheet: None (None), residues: 0 loop : -1.30 (0.23), residues: 803 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 399 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 50 residues processed: 459 average time/residue: 1.3665 time to fit residues: 728.5222 Evaluate side-chains 430 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 380 time to evaluate : 3.047 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 41 residues processed: 10 average time/residue: 0.4104 time to fit residues: 10.1620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 0.0670 chunk 118 optimal weight: 1.9990 chunk 177 optimal weight: 0.0570 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 233 optimal weight: 0.0170 overall best weight: 0.2072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 273 GLN B 273 GLN D 168 ASN D 273 GLN F 102 GLN F 273 GLN F 276 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN G 273 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 273 GLN I 102 GLN I 168 ASN I 273 GLN J 176 GLN J 178 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 276 GLN K 273 GLN K 276 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 27302 Z= 0.109 Angle : 0.455 10.701 36773 Z= 0.230 Chirality : 0.034 0.129 3916 Planarity : 0.003 0.048 4499 Dihedral : 7.699 59.800 3982 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 2.61 % 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: 1.04 (0.16), residues: 3146 helix: 1.29 (0.12), residues: 2332 sheet: None (None), residues: 0 loop : -0.95 (0.24), residues: 814 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 407 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 40 residues processed: 464 average time/residue: 1.3118 time to fit residues: 712.3804 Evaluate side-chains 407 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 367 time to evaluate : 2.830 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 35 residues processed: 7 average time/residue: 0.4165 time to fit residues: 8.3596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 3.9990 chunk 284 optimal weight: 0.7980 chunk 259 optimal weight: 3.9990 chunk 276 optimal weight: 0.4980 chunk 166 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 217 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 249 optimal weight: 1.9990 chunk 261 optimal weight: 0.4980 chunk 275 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 273 GLN B 273 GLN D 273 GLN E 273 GLN F 102 GLN F 273 GLN F 276 GLN G 273 GLN H 102 GLN H 273 GLN I 102 GLN I 168 ASN I 273 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 273 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 27302 Z= 0.126 Angle : 0.484 11.821 36773 Z= 0.241 Chirality : 0.035 0.135 3916 Planarity : 0.003 0.048 4499 Dihedral : 7.630 59.735 3982 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 2.18 % 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: 1.22 (0.16), residues: 3146 helix: 1.44 (0.12), residues: 2321 sheet: None (None), residues: 0 loop : -0.94 (0.23), residues: 825 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 366 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 46 residues processed: 414 average time/residue: 1.3352 time to fit residues: 645.3312 Evaluate side-chains 400 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 354 time to evaluate : 2.960 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 39 residues processed: 9 average time/residue: 0.2819 time to fit residues: 8.6303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.8980 chunk 292 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 306 optimal weight: 5.9990 chunk 282 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 25 optimal weight: 0.0060 chunk 188 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 273 GLN B 273 GLN D 273 GLN F 102 GLN F 273 GLN F 276 GLN G 273 GLN H 102 GLN H 273 GLN I 273 GLN I 275 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 273 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 27302 Z= 0.133 Angle : 0.494 12.255 36773 Z= 0.245 Chirality : 0.035 0.136 3916 Planarity : 0.003 0.047 4499 Dihedral : 7.607 59.764 3982 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 1.97 % 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: 1.25 (0.16), residues: 3146 helix: 1.43 (0.12), residues: 2332 sheet: None (None), residues: 0 loop : -0.85 (0.24), residues: 814 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 370 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 42 residues processed: 414 average time/residue: 1.3853 time to fit residues: 671.4193 Evaluate side-chains 402 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 360 time to evaluate : 3.037 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 35 residues processed: 8 average time/residue: 0.4290 time to fit residues: 9.3795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 0.5980 chunk 260 optimal weight: 0.0010 chunk 74 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 36 optimal weight: 0.0050 chunk 67 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 251 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 168 ASN A 273 GLN B 273 GLN D 273 GLN F 102 GLN F 273 GLN F 276 GLN G 273 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 273 GLN I 275 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 273 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.162411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120051 restraints weight = 27860.715| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.88 r_work: 0.3361 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 1.66 restraints_weight: 0.2500 r_work: 0.3326 rms_B_bonded: 1.76 restraints_weight: 0.1250 r_work: 0.3307 rms_B_bonded: 1.92 restraints_weight: 0.0625 r_work: 0.3286 rms_B_bonded: 2.14 restraints_weight: 0.0312 r_work: 0.3263 rms_B_bonded: 2.42 restraints_weight: 0.0156 r_work: 0.3237 rms_B_bonded: 2.78 restraints_weight: 0.0078 r_work: 0.3208 rms_B_bonded: 3.21 restraints_weight: 0.0039 r_work: 0.3175 rms_B_bonded: 3.74 restraints_weight: 0.0020 r_work: 0.3137 rms_B_bonded: 4.39 restraints_weight: 0.0010 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 27302 Z= 0.118 Angle : 0.478 10.688 36773 Z= 0.237 Chirality : 0.034 0.132 3916 Planarity : 0.003 0.046 4499 Dihedral : 7.335 59.774 3982 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.16), residues: 3146 helix: 1.58 (0.12), residues: 2332 sheet: None (None), residues: 0 loop : -0.80 (0.24), residues: 814 =============================================================================== Job complete usr+sys time: 10516.78 seconds wall clock time: 186 minutes 58.22 seconds (11218.22 seconds total)