Starting phenix.real_space_refine (version: dev) on Mon Feb 27 04:43:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uvn_20908/02_2023/6uvn_20908.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uvn_20908/02_2023/6uvn_20908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uvn_20908/02_2023/6uvn_20908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uvn_20908/02_2023/6uvn_20908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uvn_20908/02_2023/6uvn_20908.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uvn_20908/02_2023/6uvn_20908.pdb" } resolution = 3.1 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "B ARG 99": "NH1" <-> "NH2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B ARG 538": "NH1" <-> "NH2" Residue "G ARG 31": "NH1" <-> "NH2" Residue "G ARG 40": "NH1" <-> "NH2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "G ARG 150": "NH1" <-> "NH2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G ARG 247": "NH1" <-> "NH2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "F ARG 31": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 150": "NH1" <-> "NH2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F GLU 257": "OE1" <-> "OE2" Residue "F ARG 289": "NH1" <-> "NH2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "H ARG 31": "NH1" <-> "NH2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "H ARG 101": "NH1" <-> "NH2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H ARG 150": "NH1" <-> "NH2" Residue "H ARG 213": "NH1" <-> "NH2" Residue "H ARG 247": "NH1" <-> "NH2" Residue "H ARG 289": "NH1" <-> "NH2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D GLU 66": "OE1" <-> "OE2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D ARG 150": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "C ARG 40": "NH1" <-> "NH2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "I GLU 15": "OE1" <-> "OE2" Residue "I ARG 32": "NH1" <-> "NH2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 121": "NH1" <-> "NH2" Residue "I ARG 133": "NH1" <-> "NH2" Residue "I PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 170": "NH1" <-> "NH2" Residue "I GLU 379": "OE1" <-> "OE2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J ARG 121": "NH1" <-> "NH2" Residue "J ARG 133": "NH1" <-> "NH2" Residue "J ARG 170": "NH1" <-> "NH2" Residue "J GLU 260": "OE1" <-> "OE2" Residue "J GLU 291": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29487 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1619 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "B" Number of atoms: 3921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3921 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 23, 'TRANS': 474} Chain breaks: 3 Chain: "G" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "F" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "E" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "H" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "D" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "C" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2495 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 16, 'TRANS': 291} Chain breaks: 2 Chain: "I" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3124 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain breaks: 2 Chain: "J" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3171 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 20, 'TRANS': 368} Chain breaks: 2 Chain: "M" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1275 Classifications: {'DNA': 2, 'RNA': 59} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 14, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 25, 'rna3p': 35} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 405 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'TRANS': 80} Chain breaks: 3 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'UNK:plan-1': 81} Unresolved non-hydrogen planarities: 81 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22533 SG CYS I 128 147.814 149.918 69.762 1.00117.96 S ATOM 22724 SG CYS I 150 146.594 150.159 66.366 1.00114.46 S ATOM 25657 SG CYS J 128 108.738 151.170 24.259 1.00139.86 S ATOM 25848 SG CYS J 150 111.025 151.827 27.144 1.00131.60 S Time building chain proxies: 17.24, per 1000 atoms: 0.58 Number of scatterers: 29487 At special positions: 0 Unit cell: (164.85, 175.35, 182.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 145 16.00 P 60 15.00 O 5636 8.00 N 5102 7.00 C 18542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS I 163 " - pdb=" SG CYS I 181 " distance=2.39 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: 13.13 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 401 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 128 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 150 " pdb="ZN ZN I 401 " - pdb=" ND1 HIS I 153 " pdb=" ZN J 401 " pdb="ZN ZN J 401 " - pdb=" ND1 HIS J 153 " pdb="ZN ZN J 401 " - pdb=" SG CYS J 128 " pdb="ZN ZN J 401 " - pdb=" SG CYS J 150 " 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6756 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 47 sheets defined 38.0% alpha, 16.2% beta 6 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 9.82 Creating SS restraints... Processing helix chain 'A' and resid 16 through 35 Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.710A pdb=" N ASP A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 105 through 108 Processing helix chain 'A' and resid 111 through 129 removed outlier: 3.850A pdb=" N ARG A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 9 Processing helix chain 'B' and resid 10 through 15 removed outlier: 4.659A pdb=" N ASP B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 15' Processing helix chain 'B' and resid 18 through 24 Processing helix chain 'B' and resid 36 through 47 removed outlier: 3.702A pdb=" N LEU B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 67 removed outlier: 3.789A pdb=" N LYS B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 77 Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.755A pdb=" N ARG B 82 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.703A pdb=" N PHE B 135 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.568A pdb=" N LEU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 153' Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.878A pdb=" N ALA B 178 " --> pdb=" O CYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 223 through 228 removed outlier: 3.520A pdb=" N ARG B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.683A pdb=" N THR B 498 " --> pdb=" O ASP B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.755A pdb=" N LYS B 517 " --> pdb=" O ASP B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 removed outlier: 3.562A pdb=" N ALA B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 555 Processing helix chain 'B' and resid 582 through 586 removed outlier: 3.679A pdb=" N TYR B 586 " --> pdb=" O LEU B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 613 removed outlier: 3.716A pdb=" N ILE B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 removed outlier: 4.026A pdb=" N ALA G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 48 through 52' Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.508A pdb=" N LEU G 118 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU G 120 " --> pdb=" O VAL G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 141 removed outlier: 3.558A pdb=" N ILE G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 189 through 203 removed outlier: 3.591A pdb=" N MET G 196 " --> pdb=" O ALA G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 272 Processing helix chain 'G' and resid 308 through 314 Processing helix chain 'G' and resid 315 through 323 Processing helix chain 'G' and resid 330 through 347 Processing helix chain 'F' and resid 48 through 52 removed outlier: 4.030A pdb=" N ALA F 52 " --> pdb=" O ALA F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 48 through 52' Processing helix chain 'F' and resid 64 through 70 removed outlier: 3.798A pdb=" N GLN F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.538A pdb=" N LEU F 118 " --> pdb=" O THR F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 141 removed outlier: 3.534A pdb=" N ASN F 138 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE F 139 " --> pdb=" O TYR F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 186 Processing helix chain 'F' and resid 189 through 203 removed outlier: 3.671A pdb=" N MET F 196 " --> pdb=" O ALA F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 272 Processing helix chain 'F' and resid 308 through 314 Processing helix chain 'F' and resid 315 through 325 Processing helix chain 'F' and resid 330 through 347 Processing helix chain 'E' and resid 48 through 52 removed outlier: 4.027A pdb=" N ALA E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 52' Processing helix chain 'E' and resid 66 through 70 removed outlier: 3.522A pdb=" N ALA E 69 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 128 through 141 removed outlier: 3.565A pdb=" N ASN E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 186 Processing helix chain 'E' and resid 190 through 203 removed outlier: 4.090A pdb=" N MET E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 272 Processing helix chain 'E' and resid 308 through 314 Processing helix chain 'E' and resid 315 through 325 removed outlier: 3.649A pdb=" N ALA E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 347 Processing helix chain 'H' and resid 48 through 52 removed outlier: 4.222A pdb=" N ALA H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 48 through 52' Processing helix chain 'H' and resid 64 through 70 removed outlier: 3.805A pdb=" N GLN H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 126 Processing helix chain 'H' and resid 128 through 141 removed outlier: 3.523A pdb=" N THR H 133 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN H 138 " --> pdb=" O ARG H 134 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE H 139 " --> pdb=" O TYR H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 186 Processing helix chain 'H' and resid 189 through 201 Processing helix chain 'H' and resid 263 through 272 Processing helix chain 'H' and resid 308 through 314 Processing helix chain 'H' and resid 315 through 325 Processing helix chain 'H' and resid 330 through 347 Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.764A pdb=" N ALA D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 52' Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.555A pdb=" N LEU D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 141 removed outlier: 3.539A pdb=" N ILE D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 186 removed outlier: 3.806A pdb=" N PHE D 184 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 185 " --> pdb=" O ARG D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 203 removed outlier: 3.753A pdb=" N MET D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 272 Processing helix chain 'D' and resid 308 through 314 Processing helix chain 'D' and resid 315 through 325 Processing helix chain 'D' and resid 330 through 347 Processing helix chain 'C' and resid 108 through 126 removed outlier: 3.834A pdb=" N THR C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 141 removed outlier: 3.884A pdb=" N ASN C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 187 removed outlier: 3.529A pdb=" N ASN C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 308 through 314 removed outlier: 3.853A pdb=" N ILE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 325 Processing helix chain 'C' and resid 330 through 347 Processing helix chain 'I' and resid 13 through 26 removed outlier: 3.995A pdb=" N LYS I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY I 26 " --> pdb=" O ALA I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 3.518A pdb=" N PHE I 33 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 52 removed outlier: 4.463A pdb=" N THR I 51 " --> pdb=" O ASN I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 59 removed outlier: 3.678A pdb=" N ILE I 59 " --> pdb=" O ILE I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 Processing helix chain 'I' and resid 128 through 136 Processing helix chain 'I' and resid 139 through 144 removed outlier: 3.626A pdb=" N TRP I 142 " --> pdb=" O SER I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 173 Processing helix chain 'I' and resid 194 through 205 removed outlier: 4.436A pdb=" N VAL I 200 " --> pdb=" O ALA I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 231 Processing helix chain 'I' and resid 236 through 244 removed outlier: 3.649A pdb=" N PHE I 240 " --> pdb=" O ASP I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 265 removed outlier: 3.743A pdb=" N HIS I 252 " --> pdb=" O PRO I 248 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 287 removed outlier: 3.522A pdb=" N PHE I 283 " --> pdb=" O LEU I 279 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE I 284 " --> pdb=" O GLY I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 Processing helix chain 'I' and resid 324 through 332 removed outlier: 3.512A pdb=" N VAL I 330 " --> pdb=" O LEU I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 345 Processing helix chain 'I' and resid 369 through 380 Processing helix chain 'I' and resid 387 through 392 removed outlier: 4.109A pdb=" N SER I 392 " --> pdb=" O SER I 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 26 removed outlier: 3.824A pdb=" N LYS J 24 " --> pdb=" O ARG J 20 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN J 25 " --> pdb=" O VAL J 21 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 44 removed outlier: 3.662A pdb=" N ILE J 44 " --> pdb=" O PHE J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 52 removed outlier: 4.331A pdb=" N THR J 51 " --> pdb=" O ASN J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 59 removed outlier: 3.529A pdb=" N ILE J 59 " --> pdb=" O ILE J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 82 Processing helix chain 'J' and resid 89 through 93 Processing helix chain 'J' and resid 128 through 136 Processing helix chain 'J' and resid 139 through 144 removed outlier: 3.535A pdb=" N TRP J 142 " --> pdb=" O SER J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 173 Processing helix chain 'J' and resid 194 through 205 removed outlier: 3.516A pdb=" N THR J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA J 205 " --> pdb=" O SER J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 231 removed outlier: 4.067A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY J 222 " --> pdb=" O SER J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 244 removed outlier: 3.575A pdb=" N PHE J 240 " --> pdb=" O ASP J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 265 removed outlier: 3.752A pdb=" N PHE J 251 " --> pdb=" O TRP J 247 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N HIS J 252 " --> pdb=" O PRO J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 287 removed outlier: 3.679A pdb=" N PHE J 283 " --> pdb=" O LEU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 309 Processing helix chain 'J' and resid 324 through 332 removed outlier: 4.438A pdb=" N VAL J 330 " --> pdb=" O LEU J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 345 Processing helix chain 'J' and resid 369 through 378 removed outlier: 3.636A pdb=" N LEU J 375 " --> pdb=" O ASP J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 390 Processing helix chain 'N' and resid 276 through 282 Processing helix chain 'N' and resid 284 through 300 removed outlier: 3.573A pdb=" N UNK N 288 " --> pdb=" O UNK N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 305 through 321 Processing helix chain 'N' and resid 334 through 346 Processing helix chain 'N' and resid 356 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 150 through 155 Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 146 removed outlier: 3.655A pdb=" N THR A 144 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 41 " --> pdb=" O THR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 5.683A pdb=" N GLU B 592 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR B 570 " --> pdb=" O GLU B 592 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE B 594 " --> pdb=" O VAL B 568 " (cutoff:3.500A) removed outlier: 15.380A pdb=" N SER B 566 " --> pdb=" O PRO B 627 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 568 " --> pdb=" O VAL B 625 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL B 625 " --> pdb=" O VAL B 568 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 139 through 142 Processing sheet with id=AA9, first strand: chain 'B' and resid 201 through 205 removed outlier: 4.185A pdb=" N LYS B 587 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 510 through 511 Processing sheet with id=AB2, first strand: chain 'B' and resid 510 through 511 removed outlier: 4.664A pdb=" N ASN B 392 " --> pdb=" O PHE B 479 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N PHE B 479 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER B 480 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL B 442 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE B 482 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE B 440 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN B 484 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE B 438 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 398 through 399 Processing sheet with id=AB4, first strand: chain 'G' and resid 105 through 106 Processing sheet with id=AB5, first strand: chain 'G' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 21 through 26 current: chain 'G' and resid 154 through 161 Processing sheet with id=AB6, first strand: chain 'G' and resid 32 through 33 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 87 through 97 current: chain 'G' and resid 251 through 254 Processing sheet with id=AB7, first strand: chain 'G' and resid 38 through 44 Processing sheet with id=AB8, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'F' and resid 105 through 106 Processing sheet with id=AC1, first strand: chain 'F' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 21 through 26 current: chain 'F' and resid 154 through 161 Processing sheet with id=AC2, first strand: chain 'F' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 87 through 97 current: chain 'F' and resid 251 through 254 Processing sheet with id=AC3, first strand: chain 'F' and resid 38 through 44 Processing sheet with id=AC4, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'E' and resid 105 through 106 Processing sheet with id=AC6, first strand: chain 'E' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 21 through 26 current: chain 'E' and resid 154 through 161 Processing sheet with id=AC7, first strand: chain 'E' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 87 through 97 current: chain 'E' and resid 251 through 254 Processing sheet with id=AC8, first strand: chain 'E' and resid 38 through 44 Processing sheet with id=AC9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'H' and resid 105 through 106 removed outlier: 3.595A pdb=" N LYS H 105 " --> pdb=" O ALA H 11 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 32 through 34 Processing sheet with id=AD3, first strand: chain 'H' and resid 32 through 34 removed outlier: 4.181A pdb=" N PHE H 23 " --> pdb=" O PRO H 260 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N VAL H 25 " --> pdb=" O ARG H 258 " (cutoff:3.500A) removed outlier: 13.589A pdb=" N ARG H 258 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 37 through 44 Processing sheet with id=AD5, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.543A pdb=" N GLN H 58 " --> pdb=" O ASP H 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 228 through 229 removed outlier: 4.563A pdb=" N VAL H 248 " --> pdb=" O VAL H 229 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 273 through 275 Processing sheet with id=AD8, first strand: chain 'D' and resid 105 through 106 Processing sheet with id=AD9, first strand: chain 'D' and resid 17 through 18 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 26 current: chain 'D' and resid 154 through 161 Processing sheet with id=AE1, first strand: chain 'D' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 87 through 97 current: chain 'D' and resid 251 through 254 Processing sheet with id=AE2, first strand: chain 'D' and resid 38 through 44 Processing sheet with id=AE3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'D' and resid 273 through 275 Processing sheet with id=AE5, first strand: chain 'C' and resid 105 through 106 Processing sheet with id=AE6, first strand: chain 'C' and resid 32 through 34 Processing sheet with id=AE7, first strand: chain 'C' and resid 32 through 34 removed outlier: 4.115A pdb=" N PHE C 23 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 10.779A pdb=" N VAL C 25 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 14.055A pdb=" N ARG C 258 " --> pdb=" O VAL C 25 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 273 through 275 Processing sheet with id=AE9, first strand: chain 'I' and resid 95 through 101 removed outlier: 6.422A pdb=" N THR I 97 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL I 109 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N MET I 99 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA I 107 " --> pdb=" O MET I 99 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR I 105 " --> pdb=" O TYR I 101 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 95 through 101 removed outlier: 6.845A pdb=" N THR J 97 " --> pdb=" O VAL J 109 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL J 109 " --> pdb=" O THR J 97 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N MET J 99 " --> pdb=" O ALA J 107 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA J 107 " --> pdb=" O MET J 99 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR J 105 " --> pdb=" O TYR J 101 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 322 through 323 1083 hydrogen bonds defined for protein. 2985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 11.84 Time building geometry restraints manager: 14.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7220 1.33 - 1.45: 6879 1.45 - 1.57: 15926 1.57 - 1.69: 120 1.69 - 1.81: 206 Bond restraints: 30351 Sorted by residual: bond pdb=" CA ASP J 371 " pdb=" C ASP J 371 " ideal model delta sigma weight residual 1.523 1.468 0.054 1.41e-02 5.03e+03 1.49e+01 bond pdb=" N TYR C 278 " pdb=" CA TYR C 278 " ideal model delta sigma weight residual 1.456 1.487 -0.031 9.40e-03 1.13e+04 1.05e+01 bond pdb=" N VAL I 259 " pdb=" CA VAL I 259 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.14e+00 bond pdb=" C HIS C 217 " pdb=" N LEU C 218 " ideal model delta sigma weight residual 1.327 1.285 0.042 1.39e-02 5.18e+03 8.96e+00 bond pdb=" N VAL H 55 " pdb=" CA VAL H 55 " ideal model delta sigma weight residual 1.457 1.492 -0.036 1.19e-02 7.06e+03 8.93e+00 ... (remaining 30346 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.38: 838 105.38 - 112.58: 16231 112.58 - 119.77: 9871 119.77 - 126.97: 13961 126.97 - 134.17: 582 Bond angle restraints: 41483 Sorted by residual: angle pdb=" N PRO B 391 " pdb=" CA PRO B 391 " pdb=" C PRO B 391 " ideal model delta sigma weight residual 113.47 122.01 -8.54 1.43e+00 4.89e-01 3.56e+01 angle pdb=" N LYS C 143 " pdb=" CA LYS C 143 " pdb=" C LYS C 143 " ideal model delta sigma weight residual 114.56 107.74 6.82 1.27e+00 6.20e-01 2.89e+01 angle pdb=" N THR B 413 " pdb=" CA THR B 413 " pdb=" C THR B 413 " ideal model delta sigma weight residual 111.71 105.56 6.15 1.15e+00 7.56e-01 2.86e+01 angle pdb=" N PRO I 290 " pdb=" CA PRO I 290 " pdb=" C PRO I 290 " ideal model delta sigma weight residual 112.47 102.01 10.46 2.06e+00 2.36e-01 2.58e+01 angle pdb=" N PRO J 290 " pdb=" CA PRO J 290 " pdb=" CB PRO J 290 " ideal model delta sigma weight residual 103.25 98.19 5.06 1.05e+00 9.07e-01 2.33e+01 ... (remaining 41478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.38: 17214 28.38 - 56.75: 642 56.75 - 85.13: 53 85.13 - 113.50: 9 113.50 - 141.88: 1 Dihedral angle restraints: 17919 sinusoidal: 7530 harmonic: 10389 Sorted by residual: dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual 200.00 58.12 141.88 1 1.50e+01 4.44e-03 7.62e+01 dihedral pdb=" O4' U M 42 " pdb=" C1' U M 42 " pdb=" N1 U M 42 " pdb=" C2 U M 42 " ideal model delta sinusoidal sigma weight residual -160.00 -64.32 -95.68 1 1.50e+01 4.44e-03 4.69e+01 dihedral pdb=" CA ASP D 296 " pdb=" C ASP D 296 " pdb=" N VAL D 297 " pdb=" CA VAL D 297 " ideal model delta harmonic sigma weight residual -180.00 -150.80 -29.20 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 17916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3681 0.062 - 0.123: 836 0.123 - 0.184: 78 0.184 - 0.246: 7 0.246 - 0.307: 6 Chirality restraints: 4608 Sorted by residual: chirality pdb=" CA LEU I 289 " pdb=" N LEU I 289 " pdb=" C LEU I 289 " pdb=" CB LEU I 289 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA PRO J 290 " pdb=" N PRO J 290 " pdb=" C PRO J 290 " pdb=" CB PRO J 290 " both_signs ideal model delta sigma weight residual False 2.72 3.00 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA ILE B 393 " pdb=" N ILE B 393 " pdb=" C ILE B 393 " pdb=" CB ILE B 393 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 4605 not shown) Planarity restraints: 5088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 50 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C SER H 50 " -0.060 2.00e-02 2.50e+03 pdb=" O SER H 50 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU H 51 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U M 33 " 0.041 2.00e-02 2.50e+03 2.02e-02 9.18e+00 pdb=" N1 U M 33 " -0.040 2.00e-02 2.50e+03 pdb=" C2 U M 33 " -0.008 2.00e-02 2.50e+03 pdb=" O2 U M 33 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U M 33 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U M 33 " 0.008 2.00e-02 2.50e+03 pdb=" O4 U M 33 " 0.013 2.00e-02 2.50e+03 pdb=" C5 U M 33 " -0.005 2.00e-02 2.50e+03 pdb=" C6 U M 33 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS I 161 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C CYS I 161 " -0.047 2.00e-02 2.50e+03 pdb=" O CYS I 161 " 0.018 2.00e-02 2.50e+03 pdb=" N SER I 162 " 0.015 2.00e-02 2.50e+03 ... (remaining 5085 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1003 2.67 - 3.23: 30776 3.23 - 3.79: 49537 3.79 - 4.34: 68318 4.34 - 4.90: 109726 Nonbonded interactions: 259360 Sorted by model distance: nonbonded pdb=" O VAL H 55 " pdb=" OG SER H 56 " model vdw 2.114 2.440 nonbonded pdb=" OH TYR G 53 " pdb=" OD2 ASP F 308 " model vdw 2.196 2.440 nonbonded pdb=" OH TYR F 53 " pdb=" OD2 ASP E 308 " model vdw 2.200 2.440 nonbonded pdb=" NH1 ARG E 289 " pdb=" OD1 ASN E 343 " model vdw 2.202 2.520 nonbonded pdb=" O TRP D 277 " pdb=" NH2 ARG D 301 " model vdw 2.204 2.520 ... (remaining 259355 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 'C' selection = (chain 'D' and (resid 4 through 43 or resid 73 through 353)) selection = (chain 'E' and (resid 4 through 43 or resid 73 through 353)) selection = (chain 'F' and (resid 4 through 43 or resid 73 through 353)) selection = (chain 'G' and (resid 4 through 43 or resid 73 through 353)) selection = (chain 'H' and (resid 4 through 43 or resid 73 through 353)) } ncs_group { reference = (chain 'I' and (resid 1 through 162 or resid 164 through 394 or resid 401)) selection = (chain 'J' and (resid 1 through 354 or resid 362 through 394 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 60 5.49 5 S 145 5.16 5 C 18542 2.51 5 N 5102 2.21 5 O 5636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.530 Check model and map are aligned: 0.480 Process input model: 92.080 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.310 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 105.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.010 0.079 30351 Z= 0.619 Angle : 0.843 10.458 41483 Z= 0.485 Chirality : 0.050 0.307 4608 Planarity : 0.005 0.051 5088 Dihedral : 14.349 141.875 11160 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.09 % Favored : 91.77 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.12), residues: 3413 helix: -2.45 (0.12), residues: 1141 sheet: -2.01 (0.21), residues: 555 loop : -2.85 (0.13), residues: 1717 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 3.604 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 234 average time/residue: 0.4899 time to fit residues: 176.0053 Evaluate side-chains 153 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 3.283 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3406 time to fit residues: 9.2644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 8.9990 chunk 267 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 276 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 320 optimal weight: 9.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN B 120 HIS B 171 GLN B 224 HIS B 392 ASN B 420 HIS B 446 HIS ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 621 ASN B 626 GLN G 38 ASN G 221 ASN G 250 GLN G 318 HIS G 331 GLN G 335 ASN G 338 HIS G 352 HIS ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN F 245 ASN F 250 GLN F 335 ASN F 338 HIS E 75 GLN E 182 GLN E 335 ASN E 352 HIS H 74 HIS H 80 HIS H 182 GLN H 331 GLN H 335 ASN H 338 HIS D 182 GLN D 335 ASN D 338 HIS D 352 HIS ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 113 GLN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 HIS I 60 ASN I 66 ASN I 225 HIS I 262 ASN I 381 GLN J 46 HIS J 47 ASN J 153 HIS J 225 HIS J 381 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 30351 Z= 0.199 Angle : 0.600 12.730 41483 Z= 0.309 Chirality : 0.042 0.204 4608 Planarity : 0.005 0.074 5088 Dihedral : 9.980 141.310 4524 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -2.56 (0.13), residues: 3413 helix: -1.03 (0.14), residues: 1163 sheet: -1.18 (0.23), residues: 493 loop : -2.35 (0.14), residues: 1757 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 184 time to evaluate : 3.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 26 residues processed: 229 average time/residue: 0.3994 time to fit residues: 151.9693 Evaluate side-chains 176 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 3.481 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2679 time to fit residues: 17.5978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 266 optimal weight: 0.8980 chunk 218 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 321 optimal weight: 4.9990 chunk 346 optimal weight: 50.0000 chunk 286 optimal weight: 3.9990 chunk 318 optimal weight: 30.0000 chunk 109 optimal weight: 0.9990 chunk 257 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 ASN B 171 GLN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN E 331 GLN ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN D 80 HIS D 217 HIS D 221 ASN C 75 GLN C 335 ASN J 80 GLN J 207 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 30351 Z= 0.381 Angle : 0.645 11.567 41483 Z= 0.329 Chirality : 0.044 0.232 4608 Planarity : 0.005 0.063 5088 Dihedral : 9.853 139.736 4524 Min Nonbonded Distance : 1.507 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.83 % Favored : 93.14 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -2.14 (0.14), residues: 3413 helix: -0.55 (0.15), residues: 1166 sheet: -1.08 (0.23), residues: 524 loop : -2.17 (0.14), residues: 1723 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 171 time to evaluate : 3.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 31 residues processed: 221 average time/residue: 0.4028 time to fit residues: 149.6026 Evaluate side-chains 186 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 3.532 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2661 time to fit residues: 20.3812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 317 optimal weight: 4.9990 chunk 241 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 chunk 153 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 322 optimal weight: 4.9990 chunk 341 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 305 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN B 581 ASN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 HIS D 70 GLN D 75 GLN C 75 GLN C 138 ASN I 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 30351 Z= 0.186 Angle : 0.555 11.542 41483 Z= 0.283 Chirality : 0.041 0.219 4608 Planarity : 0.004 0.060 5088 Dihedral : 9.652 138.414 4524 Min Nonbonded Distance : 1.624 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.71 (0.14), residues: 3413 helix: -0.18 (0.15), residues: 1185 sheet: -0.81 (0.23), residues: 519 loop : -1.95 (0.14), residues: 1709 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 181 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 21 residues processed: 214 average time/residue: 0.3941 time to fit residues: 142.3400 Evaluate side-chains 172 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 3.556 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2651 time to fit residues: 15.4928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 284 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 254 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 235 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 306 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 30351 Z= 0.290 Angle : 0.587 11.185 41483 Z= 0.297 Chirality : 0.042 0.220 4608 Planarity : 0.004 0.059 5088 Dihedral : 9.653 138.372 4524 Min Nonbonded Distance : 1.617 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.60 (0.14), residues: 3413 helix: -0.06 (0.15), residues: 1184 sheet: -0.81 (0.23), residues: 535 loop : -1.89 (0.14), residues: 1694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 165 time to evaluate : 3.891 Fit side-chains outliers start: 48 outliers final: 25 residues processed: 208 average time/residue: 0.4142 time to fit residues: 144.2008 Evaluate side-chains 175 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 3.389 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2704 time to fit residues: 17.4300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 114 optimal weight: 2.9990 chunk 307 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 84 optimal weight: 0.0980 chunk 341 optimal weight: 8.9990 chunk 283 optimal weight: 20.0000 chunk 158 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 112 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS H 187 ASN C 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 30351 Z= 0.221 Angle : 0.569 13.419 41483 Z= 0.286 Chirality : 0.041 0.246 4608 Planarity : 0.004 0.063 5088 Dihedral : 9.580 137.666 4524 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.43 (0.14), residues: 3413 helix: 0.10 (0.16), residues: 1185 sheet: -0.78 (0.23), residues: 521 loop : -1.78 (0.15), residues: 1707 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 170 time to evaluate : 3.570 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 18 residues processed: 202 average time/residue: 0.4206 time to fit residues: 140.7297 Evaluate side-chains 169 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 3.739 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2805 time to fit residues: 14.1214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 329 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 287 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 340 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS D 189 ASN C 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 30351 Z= 0.226 Angle : 0.573 12.682 41483 Z= 0.287 Chirality : 0.041 0.341 4608 Planarity : 0.004 0.070 5088 Dihedral : 9.550 137.517 4524 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.31 (0.14), residues: 3413 helix: 0.21 (0.16), residues: 1182 sheet: -0.70 (0.23), residues: 539 loop : -1.72 (0.15), residues: 1692 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 3.588 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 179 average time/residue: 0.4157 time to fit residues: 126.1428 Evaluate side-chains 169 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 3.484 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2976 time to fit residues: 13.9056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 210 optimal weight: 0.4980 chunk 135 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 267 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS G 80 HIS C 75 GLN I 153 HIS I 262 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 30351 Z= 0.217 Angle : 0.572 14.107 41483 Z= 0.285 Chirality : 0.041 0.341 4608 Planarity : 0.004 0.067 5088 Dihedral : 9.534 137.880 4524 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.21 (0.14), residues: 3413 helix: 0.28 (0.16), residues: 1187 sheet: -0.65 (0.23), residues: 547 loop : -1.67 (0.15), residues: 1679 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 4.105 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 184 average time/residue: 0.4131 time to fit residues: 126.6619 Evaluate side-chains 162 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 3.224 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2646 time to fit residues: 7.2945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 309 optimal weight: 3.9990 chunk 325 optimal weight: 7.9990 chunk 297 optimal weight: 8.9990 chunk 317 optimal weight: 9.9990 chunk 190 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 299 optimal weight: 4.9990 chunk 315 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS G 250 GLN E 221 ASN C 75 GLN C 138 ASN I 46 HIS I 262 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.092 30351 Z= 0.576 Angle : 0.726 13.353 41483 Z= 0.366 Chirality : 0.048 0.312 4608 Planarity : 0.005 0.065 5088 Dihedral : 9.767 139.810 4524 Min Nonbonded Distance : 1.480 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -1.54 (0.14), residues: 3413 helix: -0.01 (0.15), residues: 1170 sheet: -0.84 (0.22), residues: 553 loop : -1.83 (0.15), residues: 1690 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 3.535 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 169 average time/residue: 0.4011 time to fit residues: 114.3555 Evaluate side-chains 164 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 3.569 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2639 time to fit residues: 11.1579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 208 optimal weight: 5.9990 chunk 335 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 233 optimal weight: 0.9980 chunk 351 optimal weight: 50.0000 chunk 323 optimal weight: 0.8980 chunk 280 optimal weight: 9.9990 chunk 29 optimal weight: 0.3980 chunk 216 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN I 135 ASN I 262 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 30351 Z= 0.184 Angle : 0.582 14.790 41483 Z= 0.293 Chirality : 0.041 0.263 4608 Planarity : 0.004 0.068 5088 Dihedral : 9.630 140.767 4524 Min Nonbonded Distance : 1.513 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -1.30 (0.14), residues: 3413 helix: 0.21 (0.15), residues: 1188 sheet: -0.75 (0.23), residues: 539 loop : -1.69 (0.15), residues: 1686 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 159 time to evaluate : 3.740 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 165 average time/residue: 0.4356 time to fit residues: 118.2587 Evaluate side-chains 150 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 3.377 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2913 time to fit residues: 6.7124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 222 optimal weight: 0.1980 chunk 298 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 258 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 288 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.075564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060067 restraints weight = 95010.720| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.73 r_work: 0.3175 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 30351 Z= 0.286 Angle : 0.605 14.418 41483 Z= 0.303 Chirality : 0.043 0.289 4608 Planarity : 0.005 0.066 5088 Dihedral : 9.580 139.854 4524 Min Nonbonded Distance : 1.535 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -1.26 (0.14), residues: 3413 helix: 0.26 (0.16), residues: 1175 sheet: -0.69 (0.23), residues: 548 loop : -1.69 (0.15), residues: 1690 =============================================================================== Job complete usr+sys time: 5010.02 seconds wall clock time: 94 minutes 59.36 seconds (5699.36 seconds total)