Starting phenix.real_space_refine (version: dev) on Thu May 12 22:00:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq9_6677/05_2022/5wq9_6677_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq9_6677/05_2022/5wq9_6677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq9_6677/05_2022/5wq9_6677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq9_6677/05_2022/5wq9_6677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq9_6677/05_2022/5wq9_6677_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq9_6677/05_2022/5wq9_6677_neut.pdb" } resolution = 4.22 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 253": "OE1" <-> "OE2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 521": "NH1" <-> "NH2" Residue "A ARG 598": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 521": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B ARG 604": "NH1" <-> "NH2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 521": "NH1" <-> "NH2" Residue "C ARG 598": "NH1" <-> "NH2" Residue "C ARG 604": "NH1" <-> "NH2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D ARG 521": "NH1" <-> "NH2" Residue "D ARG 598": "NH1" <-> "NH2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E ARG 517": "NH1" <-> "NH2" Residue "E ARG 521": "NH1" <-> "NH2" Residue "E ARG 598": "NH1" <-> "NH2" Residue "E ARG 604": "NH1" <-> "NH2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F ARG 517": "NH1" <-> "NH2" Residue "F ARG 521": "NH1" <-> "NH2" Residue "F ARG 598": "NH1" <-> "NH2" Residue "F ARG 604": "NH1" <-> "NH2" Residue "G GLU 253": "OE1" <-> "OE2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "G ARG 521": "NH1" <-> "NH2" Residue "G ARG 598": "NH1" <-> "NH2" Residue "G ARG 604": "NH1" <-> "NH2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "H ARG 517": "NH1" <-> "NH2" Residue "H ARG 521": "NH1" <-> "NH2" Residue "H ARG 598": "NH1" <-> "NH2" Residue "H ARG 604": "NH1" <-> "NH2" Residue "I GLU 253": "OE1" <-> "OE2" Residue "I ARG 517": "NH1" <-> "NH2" Residue "I ARG 521": "NH1" <-> "NH2" Residue "I ARG 598": "NH1" <-> "NH2" Residue "I ARG 604": "NH1" <-> "NH2" Residue "J GLU 253": "OE1" <-> "OE2" Residue "J ARG 517": "NH1" <-> "NH2" Residue "J ARG 521": "NH1" <-> "NH2" Residue "J ARG 598": "NH1" <-> "NH2" Residue "J ARG 604": "NH1" <-> "NH2" Residue "K GLU 253": "OE1" <-> "OE2" Residue "K ARG 517": "NH1" <-> "NH2" Residue "K ARG 521": "NH1" <-> "NH2" Residue "K ARG 598": "NH1" <-> "NH2" Residue "K ARG 604": "NH1" <-> "NH2" Residue "L GLU 253": "OE1" <-> "OE2" Residue "L ARG 517": "NH1" <-> "NH2" Residue "L ARG 521": "NH1" <-> "NH2" Residue "L ARG 598": "NH1" <-> "NH2" Residue "L ARG 604": "NH1" <-> "NH2" Residue "M GLU 253": "OE1" <-> "OE2" Residue "M ARG 517": "NH1" <-> "NH2" Residue "M ARG 521": "NH1" <-> "NH2" Residue "M ARG 598": "NH1" <-> "NH2" Residue "M ARG 604": "NH1" <-> "NH2" Residue "N GLU 253": "OE1" <-> "OE2" Residue "N ARG 517": "NH1" <-> "NH2" Residue "N ARG 521": "NH1" <-> "NH2" Residue "N ARG 598": "NH1" <-> "NH2" Residue "N ARG 604": "NH1" <-> "NH2" Residue "O GLU 253": "OE1" <-> "OE2" Residue "O ARG 517": "NH1" <-> "NH2" Residue "O ARG 521": "NH1" <-> "NH2" Residue "O ARG 598": "NH1" <-> "NH2" Residue "O ARG 604": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 56340 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Chain: "B" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Chain: "C" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Chain: "D" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Chain: "E" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Chain: "F" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Chain: "G" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Chain: "H" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Chain: "I" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Chain: "J" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Chain: "K" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Chain: "L" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Chain: "M" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Chain: "N" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Chain: "O" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 12, 'TRANS': 479, 'PCIS': 1} Chain breaks: 5 Time building chain proxies: 23.57, per 1000 atoms: 0.42 Number of scatterers: 56340 At special positions: 0 Unit cell: (175.56, 174.24, 203.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 195 16.00 O 11100 8.00 N 9840 7.00 C 35205 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.84 Conformation dependent library (CDL) restraints added in 6.4 seconds 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13770 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 62 sheets defined 33.3% alpha, 50.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 161 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL A 623 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU B 308 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 Processing helix chain 'B' and resid 397 through 405 Processing helix chain 'B' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE B 558 " --> pdb=" O LEU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL B 623 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN B 645 " --> pdb=" O ALA B 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 114 Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL C 262 " --> pdb=" O VAL C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU C 308 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 Processing helix chain 'C' and resid 397 through 405 Processing helix chain 'C' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE C 558 " --> pdb=" O LEU C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL C 623 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN C 645 " --> pdb=" O ALA C 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 114 Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU D 308 " --> pdb=" O ASN D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 370 Processing helix chain 'D' and resid 397 through 405 Processing helix chain 'D' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE D 558 " --> pdb=" O LEU D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA D 592 " --> pdb=" O ASP D 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL D 623 " --> pdb=" O ASP D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN D 645 " --> pdb=" O ALA D 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 114 Processing helix chain 'E' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 161 Processing helix chain 'E' and resid 176 through 186 Processing helix chain 'E' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU E 232 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL E 262 " --> pdb=" O VAL E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU E 308 " --> pdb=" O ASN E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 370 Processing helix chain 'E' and resid 397 through 405 Processing helix chain 'E' and resid 553 through 558 removed outlier: 4.070A pdb=" N ILE E 558 " --> pdb=" O LEU E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA E 592 " --> pdb=" O ASP E 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE E 603 " --> pdb=" O LYS E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 623 removed outlier: 3.842A pdb=" N VAL E 623 " --> pdb=" O ASP E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN E 645 " --> pdb=" O ALA E 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 114 Processing helix chain 'F' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 161 Processing helix chain 'F' and resid 176 through 186 Processing helix chain 'F' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL F 262 " --> pdb=" O VAL F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU F 308 " --> pdb=" O ASN F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 370 Processing helix chain 'F' and resid 397 through 405 Processing helix chain 'F' and resid 553 through 558 removed outlier: 4.070A pdb=" N ILE F 558 " --> pdb=" O LEU F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA F 592 " --> pdb=" O ASP F 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 603 " --> pdb=" O LYS F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 623 removed outlier: 3.842A pdb=" N VAL F 623 " --> pdb=" O ASP F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN F 645 " --> pdb=" O ALA F 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 114 Processing helix chain 'G' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 161 Processing helix chain 'G' and resid 176 through 186 Processing helix chain 'G' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY G 261 " --> pdb=" O GLU G 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL G 262 " --> pdb=" O VAL G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU G 308 " --> pdb=" O ASN G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 370 Processing helix chain 'G' and resid 397 through 405 Processing helix chain 'G' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE G 558 " --> pdb=" O LEU G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 561 through 566 removed outlier: 4.090A pdb=" N PHE G 565 " --> pdb=" O LEU G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA G 592 " --> pdb=" O ASP G 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE G 603 " --> pdb=" O LYS G 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 623 removed outlier: 3.844A pdb=" N VAL G 623 " --> pdb=" O ASP G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN G 645 " --> pdb=" O ALA G 641 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 114 Processing helix chain 'H' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 161 Processing helix chain 'H' and resid 176 through 186 Processing helix chain 'H' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY H 261 " --> pdb=" O GLU H 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL H 262 " --> pdb=" O VAL H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU H 308 " --> pdb=" O ASN H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 370 Processing helix chain 'H' and resid 397 through 405 Processing helix chain 'H' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE H 558 " --> pdb=" O LEU H 554 " (cutoff:3.500A) Processing helix chain 'H' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE H 565 " --> pdb=" O LEU H 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA H 592 " --> pdb=" O ASP H 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE H 603 " --> pdb=" O LYS H 599 " (cutoff:3.500A) Processing helix chain 'H' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL H 623 " --> pdb=" O ASP H 620 " (cutoff:3.500A) Processing helix chain 'H' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN H 645 " --> pdb=" O ALA H 641 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 114 Processing helix chain 'I' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA I 126 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 161 Processing helix chain 'I' and resid 176 through 186 Processing helix chain 'I' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU I 232 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY I 261 " --> pdb=" O GLU I 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL I 262 " --> pdb=" O VAL I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU I 308 " --> pdb=" O ASN I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 370 Processing helix chain 'I' and resid 397 through 405 Processing helix chain 'I' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE I 558 " --> pdb=" O LEU I 554 " (cutoff:3.500A) Processing helix chain 'I' and resid 561 through 566 removed outlier: 4.090A pdb=" N PHE I 565 " --> pdb=" O LEU I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA I 592 " --> pdb=" O ASP I 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE I 603 " --> pdb=" O LYS I 599 " (cutoff:3.500A) Processing helix chain 'I' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL I 623 " --> pdb=" O ASP I 620 " (cutoff:3.500A) Processing helix chain 'I' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN I 645 " --> pdb=" O ALA I 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 114 Processing helix chain 'J' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA J 126 " --> pdb=" O LEU J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 161 Processing helix chain 'J' and resid 176 through 186 Processing helix chain 'J' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY J 261 " --> pdb=" O GLU J 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL J 262 " --> pdb=" O VAL J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU J 308 " --> pdb=" O ASN J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 370 Processing helix chain 'J' and resid 397 through 405 Processing helix chain 'J' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE J 558 " --> pdb=" O LEU J 554 " (cutoff:3.500A) Processing helix chain 'J' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE J 565 " --> pdb=" O LEU J 561 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA J 592 " --> pdb=" O ASP J 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE J 603 " --> pdb=" O LYS J 599 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL J 623 " --> pdb=" O ASP J 620 " (cutoff:3.500A) Processing helix chain 'J' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN J 645 " --> pdb=" O ALA J 641 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 114 Processing helix chain 'K' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA K 126 " --> pdb=" O LEU K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 161 Processing helix chain 'K' and resid 176 through 186 Processing helix chain 'K' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU K 232 " --> pdb=" O LEU K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL K 262 " --> pdb=" O VAL K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU K 308 " --> pdb=" O ASN K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 370 Processing helix chain 'K' and resid 397 through 405 Processing helix chain 'K' and resid 553 through 558 removed outlier: 4.070A pdb=" N ILE K 558 " --> pdb=" O LEU K 554 " (cutoff:3.500A) Processing helix chain 'K' and resid 561 through 566 removed outlier: 4.090A pdb=" N PHE K 565 " --> pdb=" O LEU K 561 " (cutoff:3.500A) Processing helix chain 'K' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA K 592 " --> pdb=" O ASP K 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE K 603 " --> pdb=" O LYS K 599 " (cutoff:3.500A) Processing helix chain 'K' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL K 623 " --> pdb=" O ASP K 620 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN K 645 " --> pdb=" O ALA K 641 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 114 Processing helix chain 'L' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA L 126 " --> pdb=" O LEU L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 161 Processing helix chain 'L' and resid 176 through 186 Processing helix chain 'L' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY L 261 " --> pdb=" O GLU L 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL L 262 " --> pdb=" O VAL L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU L 308 " --> pdb=" O ASN L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 370 Processing helix chain 'L' and resid 397 through 405 Processing helix chain 'L' and resid 553 through 558 removed outlier: 4.070A pdb=" N ILE L 558 " --> pdb=" O LEU L 554 " (cutoff:3.500A) Processing helix chain 'L' and resid 561 through 566 removed outlier: 4.090A pdb=" N PHE L 565 " --> pdb=" O LEU L 561 " (cutoff:3.500A) Processing helix chain 'L' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA L 592 " --> pdb=" O ASP L 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE L 603 " --> pdb=" O LYS L 599 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL L 623 " --> pdb=" O ASP L 620 " (cutoff:3.500A) Processing helix chain 'L' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN L 645 " --> pdb=" O ALA L 641 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 114 Processing helix chain 'M' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA M 126 " --> pdb=" O LEU M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 161 Processing helix chain 'M' and resid 176 through 186 Processing helix chain 'M' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU M 232 " --> pdb=" O LEU M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY M 261 " --> pdb=" O GLU M 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL M 262 " --> pdb=" O VAL M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU M 308 " --> pdb=" O ASN M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 370 Processing helix chain 'M' and resid 397 through 405 Processing helix chain 'M' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE M 558 " --> pdb=" O LEU M 554 " (cutoff:3.500A) Processing helix chain 'M' and resid 561 through 566 removed outlier: 4.090A pdb=" N PHE M 565 " --> pdb=" O LEU M 561 " (cutoff:3.500A) Processing helix chain 'M' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA M 592 " --> pdb=" O ASP M 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE M 603 " --> pdb=" O LYS M 599 " (cutoff:3.500A) Processing helix chain 'M' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL M 623 " --> pdb=" O ASP M 620 " (cutoff:3.500A) Processing helix chain 'M' and resid 636 through 646 removed outlier: 3.639A pdb=" N GLN M 645 " --> pdb=" O ALA M 641 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 114 Processing helix chain 'N' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA N 126 " --> pdb=" O LEU N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 161 Processing helix chain 'N' and resid 176 through 186 Processing helix chain 'N' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY N 261 " --> pdb=" O GLU N 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL N 262 " --> pdb=" O VAL N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU N 308 " --> pdb=" O ASN N 304 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 370 Processing helix chain 'N' and resid 397 through 405 Processing helix chain 'N' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE N 558 " --> pdb=" O LEU N 554 " (cutoff:3.500A) Processing helix chain 'N' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE N 565 " --> pdb=" O LEU N 561 " (cutoff:3.500A) Processing helix chain 'N' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA N 592 " --> pdb=" O ASP N 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE N 603 " --> pdb=" O LYS N 599 " (cutoff:3.500A) Processing helix chain 'N' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL N 623 " --> pdb=" O ASP N 620 " (cutoff:3.500A) Processing helix chain 'N' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN N 645 " --> pdb=" O ALA N 641 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 114 Processing helix chain 'O' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA O 126 " --> pdb=" O LEU O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 161 Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU O 232 " --> pdb=" O LEU O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY O 261 " --> pdb=" O GLU O 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL O 262 " --> pdb=" O VAL O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU O 308 " --> pdb=" O ASN O 304 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 370 Processing helix chain 'O' and resid 397 through 405 Processing helix chain 'O' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE O 558 " --> pdb=" O LEU O 554 " (cutoff:3.500A) Processing helix chain 'O' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE O 565 " --> pdb=" O LEU O 561 " (cutoff:3.500A) Processing helix chain 'O' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA O 592 " --> pdb=" O ASP O 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE O 603 " --> pdb=" O LYS O 599 " (cutoff:3.500A) Processing helix chain 'O' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL O 623 " --> pdb=" O ASP O 620 " (cutoff:3.500A) Processing helix chain 'O' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN O 645 " --> pdb=" O ALA O 641 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 135 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 171 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 246 Processing sheet with id=AA4, first strand: chain 'A' and resid 585 through 586 removed outlier: 6.595A pdb=" N ILE A 581 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL A 536 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU A 535 " --> pdb=" O MET B 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET B 443 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU A 537 " --> pdb=" O THR B 441 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 419 through 443 current: chain 'B' and resid 567 through 582 removed outlier: 6.595A pdb=" N ILE B 581 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL B 536 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 15.793A pdb=" N LEU B 535 " --> pdb=" O MET C 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET C 443 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 537 " --> pdb=" O THR C 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 581 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL C 536 " --> pdb=" O ILE C 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU C 535 " --> pdb=" O MET D 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET D 443 " --> pdb=" O LEU C 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU C 537 " --> pdb=" O THR D 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 581 " --> pdb=" O VAL E 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL E 536 " --> pdb=" O ILE E 581 " (cutoff:3.500A) removed outlier: 15.793A pdb=" N LEU E 535 " --> pdb=" O MET F 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET F 443 " --> pdb=" O LEU E 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU E 537 " --> pdb=" O THR F 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE F 581 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL F 536 " --> pdb=" O ILE F 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU F 535 " --> pdb=" O MET G 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET G 443 " --> pdb=" O LEU F 535 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU F 537 " --> pdb=" O THR G 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE G 581 " --> pdb=" O VAL G 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL G 536 " --> pdb=" O ILE G 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU G 535 " --> pdb=" O MET H 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET H 443 " --> pdb=" O LEU G 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU G 537 " --> pdb=" O THR H 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE H 581 " --> pdb=" O VAL H 536 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL H 536 " --> pdb=" O ILE H 581 " (cutoff:3.500A) removed outlier: 15.793A pdb=" N LEU H 535 " --> pdb=" O MET I 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET I 443 " --> pdb=" O LEU H 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU H 537 " --> pdb=" O THR I 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE I 581 " --> pdb=" O VAL I 536 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL I 536 " --> pdb=" O ILE I 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU I 535 " --> pdb=" O MET J 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET J 443 " --> pdb=" O LEU I 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU I 537 " --> pdb=" O THR J 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE J 581 " --> pdb=" O VAL J 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL J 536 " --> pdb=" O ILE J 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU J 535 " --> pdb=" O MET K 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET K 443 " --> pdb=" O LEU J 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU J 537 " --> pdb=" O THR K 441 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE K 581 " --> pdb=" O VAL K 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL K 536 " --> pdb=" O ILE K 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU K 535 " --> pdb=" O MET L 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET L 443 " --> pdb=" O LEU K 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU K 537 " --> pdb=" O THR L 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE L 581 " --> pdb=" O VAL L 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL L 536 " --> pdb=" O ILE L 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU L 535 " --> pdb=" O MET M 443 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N MET M 443 " --> pdb=" O LEU L 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU L 537 " --> pdb=" O THR M 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 585 through 586 Processing sheet with id=AA6, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AA7, first strand: chain 'D' and resid 585 through 586 removed outlier: 6.594A pdb=" N ILE D 581 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL D 536 " --> pdb=" O ILE D 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU D 535 " --> pdb=" O MET E 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET E 443 " --> pdb=" O LEU D 535 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU D 537 " --> pdb=" O THR E 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 585 through 586 Processing sheet with id=AA9, first strand: chain 'F' and resid 585 through 586 Processing sheet with id=AB1, first strand: chain 'G' and resid 585 through 586 Processing sheet with id=AB2, first strand: chain 'H' and resid 585 through 586 Processing sheet with id=AB3, first strand: chain 'I' and resid 585 through 586 Processing sheet with id=AB4, first strand: chain 'J' and resid 585 through 586 Processing sheet with id=AB5, first strand: chain 'K' and resid 585 through 586 Processing sheet with id=AB6, first strand: chain 'L' and resid 585 through 586 Processing sheet with id=AB7, first strand: chain 'M' and resid 585 through 586 removed outlier: 6.595A pdb=" N ILE M 581 " --> pdb=" O VAL M 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL M 536 " --> pdb=" O ILE M 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU M 535 " --> pdb=" O MET N 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET N 443 " --> pdb=" O LEU M 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU M 537 " --> pdb=" O THR N 441 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 585 through 586 removed outlier: 6.595A pdb=" N ILE N 581 " --> pdb=" O VAL N 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL N 536 " --> pdb=" O ILE N 581 " (cutoff:3.500A) removed outlier: 15.793A pdb=" N LEU N 535 " --> pdb=" O MET O 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET O 443 " --> pdb=" O LEU N 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU N 537 " --> pdb=" O THR O 441 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 585 through 586 removed outlier: 6.596A pdb=" N ILE O 581 " --> pdb=" O VAL O 536 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL O 536 " --> pdb=" O ILE O 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU O 535 " --> pdb=" O MET A 443 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N MET A 443 " --> pdb=" O LEU O 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU O 537 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 372 through 377 removed outlier: 3.965A pdb=" N THR O 375 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR N 375 " --> pdb=" O THR O 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR M 375 " --> pdb=" O THR N 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR L 375 " --> pdb=" O THR M 392 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR K 375 " --> pdb=" O THR L 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR J 375 " --> pdb=" O THR K 392 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR I 375 " --> pdb=" O THR J 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR H 375 " --> pdb=" O THR I 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR G 375 " --> pdb=" O THR H 392 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR F 375 " --> pdb=" O THR G 392 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR E 375 " --> pdb=" O THR F 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR D 375 " --> pdb=" O THR E 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR C 375 " --> pdb=" O THR D 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR B 375 " --> pdb=" O THR C 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 375 " --> pdb=" O THR B 392 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 448 through 455 removed outlier: 3.574A pdb=" N ASN A 499 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 504 " --> pdb=" O ARG A 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE A 518 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 455 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 453 " --> pdb=" O LYS A 520 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 499 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 504 " --> pdb=" O ARG B 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE B 518 " --> pdb=" O GLU C 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 455 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 453 " --> pdb=" O LYS B 520 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 499 " --> pdb=" O VAL C 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 504 " --> pdb=" O ARG C 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE C 518 " --> pdb=" O GLU D 455 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 455 " --> pdb=" O PHE C 518 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 453 " --> pdb=" O LYS C 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN D 499 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL D 504 " --> pdb=" O ARG D 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE D 518 " --> pdb=" O GLU E 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 455 " --> pdb=" O PHE D 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 453 " --> pdb=" O LYS D 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN E 499 " --> pdb=" O VAL E 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL E 504 " --> pdb=" O ARG E 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE E 518 " --> pdb=" O GLU F 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU F 455 " --> pdb=" O PHE E 518 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA F 453 " --> pdb=" O LYS E 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN F 499 " --> pdb=" O VAL F 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL F 504 " --> pdb=" O ARG F 521 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE F 518 " --> pdb=" O GLU G 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU G 455 " --> pdb=" O PHE F 518 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA G 453 " --> pdb=" O LYS F 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN G 499 " --> pdb=" O VAL G 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL G 504 " --> pdb=" O ARG G 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE G 518 " --> pdb=" O GLU H 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU H 455 " --> pdb=" O PHE G 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA H 453 " --> pdb=" O LYS G 520 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN H 499 " --> pdb=" O VAL H 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL H 504 " --> pdb=" O ARG H 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE H 518 " --> pdb=" O GLU I 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU I 455 " --> pdb=" O PHE H 518 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA I 453 " --> pdb=" O LYS H 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN I 499 " --> pdb=" O VAL I 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL I 504 " --> pdb=" O ARG I 521 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE I 518 " --> pdb=" O GLU J 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU J 455 " --> pdb=" O PHE I 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA J 453 " --> pdb=" O LYS I 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN J 499 " --> pdb=" O VAL J 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL J 504 " --> pdb=" O ARG J 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE J 518 " --> pdb=" O GLU K 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU K 455 " --> pdb=" O PHE J 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA K 453 " --> pdb=" O LYS J 520 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN K 499 " --> pdb=" O VAL K 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL K 504 " --> pdb=" O ARG K 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE K 518 " --> pdb=" O GLU L 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU L 455 " --> pdb=" O PHE K 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA L 453 " --> pdb=" O LYS K 520 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN L 499 " --> pdb=" O VAL L 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL L 504 " --> pdb=" O ARG L 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE L 518 " --> pdb=" O GLU M 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU M 455 " --> pdb=" O PHE L 518 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA M 453 " --> pdb=" O LYS L 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN M 499 " --> pdb=" O VAL M 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL M 504 " --> pdb=" O ARG M 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE M 518 " --> pdb=" O GLU N 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU N 455 " --> pdb=" O PHE M 518 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA N 453 " --> pdb=" O LYS M 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN N 499 " --> pdb=" O VAL N 487 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL N 504 " --> pdb=" O ARG N 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE N 518 " --> pdb=" O GLU O 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU O 455 " --> pdb=" O PHE N 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA O 453 " --> pdb=" O LYS N 520 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN O 499 " --> pdb=" O VAL O 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL O 504 " --> pdb=" O ARG O 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE O 518 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 455 " --> pdb=" O PHE O 518 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 453 " --> pdb=" O LYS O 520 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP B 135 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 166 through 171 Processing sheet with id=AC5, first strand: chain 'B' and resid 242 through 246 Processing sheet with id=AC6, first strand: chain 'C' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE C 139 " --> pdb=" O ASP C 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP C 135 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 166 through 171 Processing sheet with id=AC8, first strand: chain 'C' and resid 242 through 246 Processing sheet with id=AC9, first strand: chain 'D' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP D 135 " --> pdb=" O ILE D 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 166 through 171 Processing sheet with id=AD2, first strand: chain 'D' and resid 242 through 246 Processing sheet with id=AD3, first strand: chain 'E' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE E 139 " --> pdb=" O ASP E 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP E 135 " --> pdb=" O ILE E 139 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 166 through 171 Processing sheet with id=AD5, first strand: chain 'E' and resid 242 through 246 Processing sheet with id=AD6, first strand: chain 'F' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE F 139 " --> pdb=" O ASP F 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP F 135 " --> pdb=" O ILE F 139 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 166 through 171 Processing sheet with id=AD8, first strand: chain 'F' and resid 242 through 246 Processing sheet with id=AD9, first strand: chain 'G' and resid 100 through 104 removed outlier: 3.672A pdb=" N ILE G 139 " --> pdb=" O ASP G 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP G 135 " --> pdb=" O ILE G 139 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 166 through 171 Processing sheet with id=AE2, first strand: chain 'G' and resid 242 through 246 Processing sheet with id=AE3, first strand: chain 'H' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE H 139 " --> pdb=" O ASP H 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP H 135 " --> pdb=" O ILE H 139 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 166 through 171 Processing sheet with id=AE5, first strand: chain 'H' and resid 242 through 246 Processing sheet with id=AE6, first strand: chain 'I' and resid 100 through 104 removed outlier: 3.672A pdb=" N ILE I 139 " --> pdb=" O ASP I 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP I 135 " --> pdb=" O ILE I 139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 166 through 171 Processing sheet with id=AE8, first strand: chain 'I' and resid 242 through 246 Processing sheet with id=AE9, first strand: chain 'J' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE J 139 " --> pdb=" O ASP J 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP J 135 " --> pdb=" O ILE J 139 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 166 through 171 Processing sheet with id=AF2, first strand: chain 'J' and resid 242 through 246 Processing sheet with id=AF3, first strand: chain 'K' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE K 139 " --> pdb=" O ASP K 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP K 135 " --> pdb=" O ILE K 139 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 166 through 171 Processing sheet with id=AF5, first strand: chain 'K' and resid 242 through 246 Processing sheet with id=AF6, first strand: chain 'L' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE L 139 " --> pdb=" O ASP L 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP L 135 " --> pdb=" O ILE L 139 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 166 through 171 Processing sheet with id=AF8, first strand: chain 'L' and resid 242 through 246 Processing sheet with id=AF9, first strand: chain 'M' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE M 139 " --> pdb=" O ASP M 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP M 135 " --> pdb=" O ILE M 139 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 166 through 171 Processing sheet with id=AG2, first strand: chain 'M' and resid 242 through 246 Processing sheet with id=AG3, first strand: chain 'N' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE N 139 " --> pdb=" O ASP N 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP N 135 " --> pdb=" O ILE N 139 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 166 through 171 Processing sheet with id=AG5, first strand: chain 'N' and resid 242 through 246 Processing sheet with id=AG6, first strand: chain 'O' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE O 139 " --> pdb=" O ASP O 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP O 135 " --> pdb=" O ILE O 139 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 166 through 171 Processing sheet with id=AG8, first strand: chain 'O' and resid 242 through 246 4161 hydrogen bonds defined for protein. 11673 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: 23.40 Time building geometry restraints manager: 18.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11167 1.32 - 1.44: 11258 1.44 - 1.56: 33975 1.56 - 1.68: 0 1.68 - 1.80: 390 Bond restraints: 56790 Sorted by residual: bond pdb=" N PRO M 457 " pdb=" CD PRO M 457 " ideal model delta sigma weight residual 1.473 1.547 -0.074 1.40e-02 5.10e+03 2.82e+01 bond pdb=" N PRO E 457 " pdb=" CD PRO E 457 " ideal model delta sigma weight residual 1.473 1.547 -0.074 1.40e-02 5.10e+03 2.81e+01 bond pdb=" N PRO J 457 " pdb=" CD PRO J 457 " ideal model delta sigma weight residual 1.473 1.547 -0.074 1.40e-02 5.10e+03 2.81e+01 bond pdb=" N PRO C 457 " pdb=" CD PRO C 457 " ideal model delta sigma weight residual 1.473 1.547 -0.074 1.40e-02 5.10e+03 2.79e+01 bond pdb=" N PRO B 457 " pdb=" CD PRO B 457 " ideal model delta sigma weight residual 1.473 1.547 -0.074 1.40e-02 5.10e+03 2.79e+01 ... (remaining 56785 not shown) Histogram of bond angle deviations from ideal: 91.07 - 101.66: 210 101.66 - 112.26: 30538 112.26 - 122.86: 39543 122.86 - 133.45: 6419 133.45 - 144.05: 45 Bond angle restraints: 76755 Sorted by residual: angle pdb=" C VAL E 507 " pdb=" CA VAL E 507 " pdb=" CB VAL E 507 " ideal model delta sigma weight residual 110.28 91.07 19.21 1.58e+00 4.01e-01 1.48e+02 angle pdb=" C VAL B 507 " pdb=" CA VAL B 507 " pdb=" CB VAL B 507 " ideal model delta sigma weight residual 110.28 91.07 19.21 1.58e+00 4.01e-01 1.48e+02 angle pdb=" C VAL C 507 " pdb=" CA VAL C 507 " pdb=" CB VAL C 507 " ideal model delta sigma weight residual 110.28 91.07 19.21 1.58e+00 4.01e-01 1.48e+02 angle pdb=" C VAL I 507 " pdb=" CA VAL I 507 " pdb=" CB VAL I 507 " ideal model delta sigma weight residual 110.28 91.08 19.20 1.58e+00 4.01e-01 1.48e+02 angle pdb=" C VAL M 507 " pdb=" CA VAL M 507 " pdb=" CB VAL M 507 " ideal model delta sigma weight residual 110.28 91.08 19.20 1.58e+00 4.01e-01 1.48e+02 ... (remaining 76750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 32881 16.11 - 32.23: 1769 32.23 - 48.34: 360 48.34 - 64.46: 90 64.46 - 80.57: 90 Dihedral angle restraints: 35190 sinusoidal: 14010 harmonic: 21180 Sorted by residual: dihedral pdb=" C VAL B 507 " pdb=" N VAL B 507 " pdb=" CA VAL B 507 " pdb=" CB VAL B 507 " ideal model delta harmonic sigma weight residual -122.00 -101.30 -20.70 0 2.50e+00 1.60e-01 6.86e+01 dihedral pdb=" C VAL C 507 " pdb=" N VAL C 507 " pdb=" CA VAL C 507 " pdb=" CB VAL C 507 " ideal model delta harmonic sigma weight residual -122.00 -101.31 -20.69 0 2.50e+00 1.60e-01 6.85e+01 dihedral pdb=" C VAL E 507 " pdb=" N VAL E 507 " pdb=" CA VAL E 507 " pdb=" CB VAL E 507 " ideal model delta harmonic sigma weight residual -122.00 -101.33 -20.67 0 2.50e+00 1.60e-01 6.84e+01 ... (remaining 35187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 7586 0.081 - 0.162: 1588 0.162 - 0.243: 156 0.243 - 0.323: 30 0.323 - 0.404: 15 Chirality restraints: 9375 Sorted by residual: chirality pdb=" CA VAL B 507 " pdb=" N VAL B 507 " pdb=" C VAL B 507 " pdb=" CB VAL B 507 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA VAL H 507 " pdb=" N VAL H 507 " pdb=" C VAL H 507 " pdb=" CB VAL H 507 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA VAL C 507 " pdb=" N VAL C 507 " pdb=" C VAL C 507 " pdb=" CB VAL C 507 " both_signs ideal model delta sigma weight residual False 2.44 2.84 -0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 9372 not shown) Planarity restraints: 9975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER N 437 " 0.090 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO N 438 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO N 438 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO N 438 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 437 " 0.090 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO F 438 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO F 438 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO F 438 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 437 " 0.090 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO H 438 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO H 438 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO H 438 " 0.071 5.00e-02 4.00e+02 ... (remaining 9972 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 285 2.18 - 2.86: 20069 2.86 - 3.54: 77408 3.54 - 4.22: 126898 4.22 - 4.90: 224169 Nonbonded interactions: 448829 Sorted by model distance: nonbonded pdb=" CE1 PHE J 518 " pdb=" OE2 GLU K 455 " model vdw 1.501 3.340 nonbonded pdb=" CE1 PHE K 518 " pdb=" OE2 GLU L 455 " model vdw 1.502 3.340 nonbonded pdb=" OE2 GLU A 455 " pdb=" CE1 PHE O 518 " model vdw 1.502 3.340 nonbonded pdb=" CE1 PHE A 518 " pdb=" OE2 GLU B 455 " model vdw 1.502 3.340 nonbonded pdb=" CE1 PHE C 518 " pdb=" OE2 GLU D 455 " model vdw 1.502 3.340 ... (remaining 448824 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' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 4 Type Number sf(0) Gaussians S 195 5.16 5 C 35205 2.51 5 N 9840 2.21 5 O 11100 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 group one per residue 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 14.930 Check model and map are aligned: 0.650 Convert atoms to be neutral: 0.380 Process input model: 114.280 Find NCS groups from input model: 2.920 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.092 56790 Z= 0.559 Angle : 1.221 19.214 76755 Z= 0.697 Chirality : 0.066 0.404 9375 Planarity : 0.007 0.139 9975 Dihedral : 11.966 80.571 21420 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 38.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.38 % Favored : 95.41 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.09), residues: 7215 helix: -2.39 (0.10), residues: 1860 sheet: -1.12 (0.08), residues: 3090 loop : -0.89 (0.12), residues: 2265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1980 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1800 time to evaluate : 5.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 180 outliers final: 67 residues processed: 1965 average time/residue: 0.5313 time to fit residues: 1735.9638 Evaluate side-chains 1016 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 949 time to evaluate : 5.140 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 4 residues processed: 67 average time/residue: 0.6781 time to fit residues: 75.9419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 620 optimal weight: 4.9990 chunk 557 optimal weight: 0.8980 chunk 309 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 375 optimal weight: 0.6980 chunk 297 optimal weight: 20.0000 chunk 576 optimal weight: 0.6980 chunk 222 optimal weight: 2.9990 chunk 350 optimal weight: 3.9990 chunk 428 optimal weight: 0.2980 chunk 667 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS A 340 GLN A 424 ASN A 502 GLN ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN B 288 HIS B 340 GLN B 424 ASN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN B 506 ASN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN C 288 HIS ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN C 424 ASN C 502 GLN C 640 GLN D 288 HIS D 340 GLN D 424 ASN D 502 GLN D 640 GLN E 288 HIS E 300 GLN E 336 ASN E 340 GLN E 424 ASN E 502 GLN ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN F 288 HIS F 340 GLN F 424 ASN F 502 GLN ** F 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN G 288 HIS G 340 GLN G 354 ASN G 424 ASN G 502 GLN G 640 GLN H 288 HIS H 340 GLN H 424 ASN H 502 GLN H 640 GLN I 288 HIS I 340 GLN I 424 ASN I 502 GLN ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 640 GLN J 288 HIS J 340 GLN J 424 ASN J 502 GLN ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 640 GLN K 288 HIS K 424 ASN K 502 GLN ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 640 GLN L 288 HIS L 340 GLN L 424 ASN L 502 GLN L 640 GLN M 288 HIS M 340 GLN M 424 ASN M 502 GLN M 571 GLN M 640 GLN N 288 HIS N 340 GLN N 424 ASN N 502 GLN ** N 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 640 GLN O 288 HIS O 340 GLN O 424 ASN O 502 GLN ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 640 GLN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 56790 Z= 0.240 Angle : 0.766 10.959 76755 Z= 0.400 Chirality : 0.051 0.206 9375 Planarity : 0.006 0.091 9975 Dihedral : 6.002 25.111 7800 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.10 (0.09), residues: 7215 helix: -0.80 (0.11), residues: 2130 sheet: -0.53 (0.08), residues: 3135 loop : -0.48 (0.13), residues: 1950 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1292 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1271 time to evaluate : 5.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 0 residues processed: 1291 average time/residue: 0.4888 time to fit residues: 1081.1284 Evaluate side-chains 823 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 823 time to evaluate : 5.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 555 optimal weight: 7.9990 chunk 454 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 668 optimal weight: 3.9990 chunk 722 optimal weight: 2.9990 chunk 595 optimal weight: 8.9990 chunk 663 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 536 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN D 354 ASN D 361 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN E 361 ASN ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 ASN ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 ASN ** G 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 354 ASN ** H 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 522 GLN I 361 ASN ** I 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 354 ASN K 361 ASN ** K 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 361 ASN ** L 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 502 GLN ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 ASN ** M 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 522 GLN ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 361 ASN N 445 ASN ** N 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 607 GLN O 361 ASN ** O 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.7335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 56790 Z= 0.282 Angle : 0.747 10.617 76755 Z= 0.395 Chirality : 0.051 0.224 9375 Planarity : 0.005 0.096 9975 Dihedral : 5.489 24.581 7800 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.51 (0.09), residues: 7215 helix: -0.08 (0.11), residues: 2145 sheet: -0.26 (0.08), residues: 2985 loop : -0.35 (0.13), residues: 2085 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 988 time to evaluate : 5.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 0 residues processed: 1006 average time/residue: 0.4877 time to fit residues: 844.8604 Evaluate side-chains 633 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 633 time to evaluate : 5.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 3.9990 chunk 502 optimal weight: 2.9990 chunk 347 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 319 optimal weight: 7.9990 chunk 449 optimal weight: 6.9990 chunk 671 optimal weight: 0.0980 chunk 710 optimal weight: 10.0000 chunk 350 optimal weight: 9.9990 chunk 636 optimal weight: 0.0970 chunk 191 optimal weight: 2.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN C 445 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 445 ASN ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 ASN E 502 GLN ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN G 211 ASN ** G 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 445 ASN ** H 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 445 ASN ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 ASN ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 361 ASN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 445 ASN ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 640 GLN ** K 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 445 ASN ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 445 ASN L 640 GLN ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 445 ASN ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 211 ASN ** N 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 445 ASN ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.8944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 56790 Z= 0.306 Angle : 0.695 7.599 76755 Z= 0.371 Chirality : 0.049 0.176 9375 Planarity : 0.005 0.103 9975 Dihedral : 5.351 24.622 7800 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.30 (0.09), residues: 7215 helix: 0.60 (0.11), residues: 2145 sheet: -0.16 (0.08), residues: 3120 loop : -0.86 (0.13), residues: 1950 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 808 time to evaluate : 5.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 808 average time/residue: 0.4985 time to fit residues: 702.1338 Evaluate side-chains 570 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 570 time to evaluate : 5.136 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 591 optimal weight: 7.9990 chunk 403 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 528 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 606 optimal weight: 2.9990 chunk 491 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 362 optimal weight: 3.9990 chunk 637 optimal weight: 0.5980 chunk 179 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN C 300 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN E 211 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 ASN G 211 ASN ** G 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 GLN ** G 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 ASN ** H 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 ASN ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 GLN ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 640 GLN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 640 GLN N 211 ASN ** N 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 300 GLN O 354 ASN ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.9576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 56790 Z= 0.247 Angle : 0.650 8.563 76755 Z= 0.347 Chirality : 0.048 0.163 9375 Planarity : 0.004 0.071 9975 Dihedral : 5.093 23.077 7800 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.09), residues: 7215 helix: 0.68 (0.11), residues: 2205 sheet: 0.03 (0.08), residues: 3135 loop : -0.69 (0.13), residues: 1875 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 720 time to evaluate : 5.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 721 average time/residue: 0.4833 time to fit residues: 606.0321 Evaluate side-chains 545 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 544 time to evaluate : 5.212 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4612 time to fit residues: 7.8175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 239 optimal weight: 0.0060 chunk 639 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 417 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 711 optimal weight: 7.9990 chunk 590 optimal weight: 9.9990 chunk 329 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 235 optimal weight: 5.9990 chunk 373 optimal weight: 0.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 GLN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 ASN F 502 GLN G 211 ASN ** G 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 354 ASN ** H 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 ASN ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 300 GLN ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 1.0093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 56790 Z= 0.241 Angle : 0.640 6.802 76755 Z= 0.340 Chirality : 0.048 0.185 9375 Planarity : 0.004 0.060 9975 Dihedral : 4.986 22.978 7800 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.07 (0.09), residues: 7215 helix: 0.92 (0.11), residues: 2190 sheet: 0.09 (0.08), residues: 3135 loop : -0.80 (0.13), residues: 1890 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 678 time to evaluate : 5.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 681 average time/residue: 0.4903 time to fit residues: 583.1241 Evaluate side-chains 538 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 537 time to evaluate : 5.187 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4621 time to fit residues: 7.7870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 685 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 405 optimal weight: 0.4980 chunk 519 optimal weight: 9.9990 chunk 402 optimal weight: 0.6980 chunk 598 optimal weight: 2.9990 chunk 397 optimal weight: 10.0000 chunk 708 optimal weight: 0.3980 chunk 443 optimal weight: 9.9990 chunk 431 optimal weight: 6.9990 chunk 327 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN E 351 GLN ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 ASN F 300 GLN ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 635 HIS G 211 ASN G 242 ASN H 361 ASN H 445 ASN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 635 HIS ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 GLN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 635 HIS ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 502 GLN ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 1.0362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 56790 Z= 0.167 Angle : 0.612 7.328 76755 Z= 0.322 Chirality : 0.047 0.164 9375 Planarity : 0.004 0.059 9975 Dihedral : 4.716 24.045 7800 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.18 (0.09), residues: 7215 helix: 0.96 (0.11), residues: 2205 sheet: 0.18 (0.08), residues: 3135 loop : -0.77 (0.13), residues: 1875 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 678 time to evaluate : 5.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 680 average time/residue: 0.4755 time to fit residues: 567.9702 Evaluate side-chains 553 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 553 time to evaluate : 5.146 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 438 optimal weight: 0.0170 chunk 282 optimal weight: 0.8980 chunk 423 optimal weight: 0.5980 chunk 213 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 450 optimal weight: 0.0060 chunk 482 optimal weight: 0.7980 chunk 350 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 556 optimal weight: 4.9990 overall best weight: 0.4234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 ASN F 354 ASN F 361 ASN F 502 GLN G 211 ASN G 242 ASN ** G 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 ASN ** H 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 ASN ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 242 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 1.0551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 56790 Z= 0.156 Angle : 0.626 9.050 76755 Z= 0.327 Chirality : 0.047 0.180 9375 Planarity : 0.004 0.057 9975 Dihedral : 4.604 22.927 7800 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.31 (0.09), residues: 7215 helix: 1.05 (0.11), residues: 2205 sheet: 0.29 (0.09), residues: 3135 loop : -0.71 (0.13), residues: 1875 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 671 time to evaluate : 5.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 672 average time/residue: 0.4821 time to fit residues: 572.3315 Evaluate side-chains 565 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 565 time to evaluate : 5.221 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 8.9990 chunk 678 optimal weight: 4.9990 chunk 619 optimal weight: 0.7980 chunk 660 optimal weight: 0.8980 chunk 397 optimal weight: 1.9990 chunk 287 optimal weight: 5.9990 chunk 518 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 596 optimal weight: 6.9990 chunk 624 optimal weight: 4.9990 chunk 657 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 ASN F 361 ASN G 211 ASN G 242 ASN ** G 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 ASN ** H 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 ASN ** K 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 242 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN ** M 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 1.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 56790 Z= 0.215 Angle : 0.647 9.359 76755 Z= 0.342 Chirality : 0.048 0.192 9375 Planarity : 0.004 0.057 9975 Dihedral : 4.743 24.516 7800 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.72 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.26 (0.10), residues: 7215 helix: 0.99 (0.11), residues: 2205 sheet: 0.13 (0.08), residues: 3300 loop : -0.50 (0.14), residues: 1710 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 622 time to evaluate : 5.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 622 average time/residue: 0.4753 time to fit residues: 518.5733 Evaluate side-chains 528 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 5.115 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 0.9990 chunk 698 optimal weight: 10.0000 chunk 426 optimal weight: 4.9990 chunk 331 optimal weight: 0.7980 chunk 485 optimal weight: 4.9990 chunk 732 optimal weight: 0.0970 chunk 673 optimal weight: 4.9990 chunk 583 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 450 optimal weight: 0.0980 chunk 357 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 ASN ** G 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 ASN ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 242 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 502 GLN ** N 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 1.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 56790 Z= 0.164 Angle : 0.644 9.976 76755 Z= 0.337 Chirality : 0.048 0.181 9375 Planarity : 0.004 0.057 9975 Dihedral : 4.594 24.168 7800 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.27 (0.09), residues: 7215 helix: 0.96 (0.11), residues: 2205 sheet: 0.25 (0.09), residues: 3210 loop : -0.66 (0.14), residues: 1800 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 645 time to evaluate : 5.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 645 average time/residue: 0.4971 time to fit residues: 566.2746 Evaluate side-chains 546 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 546 time to evaluate : 5.530 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 5.9990 chunk 621 optimal weight: 0.7980 chunk 178 optimal weight: 6.9990 chunk 537 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 584 optimal weight: 1.9990 chunk 244 optimal weight: 0.0370 chunk 599 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN F 361 ASN G 242 ASN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 242 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN ** M 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 502 GLN ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.096199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.066831 restraints weight = 192706.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.068261 restraints weight = 119544.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.069316 restraints weight = 86345.509| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 1.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 56790 Z= 0.204 Angle : 0.651 9.955 76755 Z= 0.342 Chirality : 0.048 0.191 9375 Planarity : 0.004 0.067 9975 Dihedral : 4.686 23.608 7800 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.29 (0.10), residues: 7215 helix: 0.99 (0.11), residues: 2205 sheet: 0.20 (0.09), residues: 3270 loop : -0.56 (0.14), residues: 1740 =============================================================================== Job complete usr+sys time: 11756.51 seconds wall clock time: 207 minutes 33.21 seconds (12453.21 seconds total)