Starting phenix.real_space_refine on Wed Nov 15 23:57:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyd_29565/11_2023/8fyd_29565.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyd_29565/11_2023/8fyd_29565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyd_29565/11_2023/8fyd_29565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyd_29565/11_2023/8fyd_29565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyd_29565/11_2023/8fyd_29565.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyd_29565/11_2023/8fyd_29565.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 154 5.49 5 S 32 5.16 5 C 8107 2.51 5 N 2481 2.21 5 O 2838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "E GLU 285": "OE1" <-> "OE2" Residue "F GLU 14": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 13612 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1005 Classifications: {'DNA': 49} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 48} Chain: "A" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2295 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "C" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2163 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2261 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 10, 'TRANS': 277} Chain breaks: 1 Chain: "F" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2188 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "G" Number of atoms: 1330 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 64, 1308 Classifications: {'DNA': 64} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 63} Conformer: "B" Number of residues, atoms: 64, 1308 Classifications: {'DNA': 64} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 63} bond proxies already assigned to first conformer: 1440 Chain: "H" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "I" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 265 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DG G 29 " occ=0.61 ... (42 atoms not shown) pdb=" C4 B DG G 29 " occ=0.39 Time building chain proxies: 7.69, per 1000 atoms: 0.56 Number of scatterers: 13612 At special positions: 0 Unit cell: (115.96, 95.89, 154.985, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 154 15.00 O 2838 8.00 N 2481 7.00 C 8107 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: 6.98 Conformation dependent library (CDL) restraints added in 2.5 seconds 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2446 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 7 sheets defined 52.8% alpha, 12.8% beta 61 base pairs and 119 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 68 through 76 removed outlier: 3.629A pdb=" N ASP B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 89 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.253A pdb=" N ASN B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 130 removed outlier: 3.519A pdb=" N TYR B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 162 removed outlier: 3.730A pdb=" N ARG B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 205 removed outlier: 4.271A pdb=" N LEU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 231 removed outlier: 3.879A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.793A pdb=" N ALA B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 removed outlier: 3.536A pdb=" N LYS B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 271 " --> pdb=" O LYS B 267 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.930A pdb=" N ARG C 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 68 through 77 removed outlier: 3.551A pdb=" N THR C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.670A pdb=" N ASN C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 removed outlier: 3.808A pdb=" N ARG C 129 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 163 removed outlier: 3.553A pdb=" N ARG C 144 " --> pdb=" O MET C 140 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER C 145 " --> pdb=" O GLN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 204 removed outlier: 3.829A pdb=" N GLN C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.519A pdb=" N TYR C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.949A pdb=" N ILE C 237 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 266 removed outlier: 3.518A pdb=" N ASP C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 278 Processing helix chain 'D' and resid 12 through 19 removed outlier: 3.537A pdb=" N ARG D 16 " --> pdb=" O PRO D 12 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 17 " --> pdb=" O GLN D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 36 through 51 removed outlier: 3.551A pdb=" N ARG D 40 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 77 removed outlier: 3.556A pdb=" N LEU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.611A pdb=" N ARG E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 114 removed outlier: 4.354A pdb=" N ASN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 139 through 162 removed outlier: 3.549A pdb=" N HIS E 146 " --> pdb=" O GLN E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 205 removed outlier: 3.518A pdb=" N ALA E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 231 removed outlier: 3.525A pdb=" N ASP E 227 " --> pdb=" O TYR E 223 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ALA E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 245 Processing helix chain 'E' and resid 251 through 265 removed outlier: 3.912A pdb=" N ALA E 262 " --> pdb=" O ARG E 258 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP E 265 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 removed outlier: 3.550A pdb=" N LYS E 274 " --> pdb=" O LYS E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 303 Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'F' and resid 11 through 15 Processing helix chain 'F' and resid 17 through 21 removed outlier: 4.018A pdb=" N ARG F 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 55 Processing helix chain 'F' and resid 67 through 78 removed outlier: 3.938A pdb=" N VAL F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.747A pdb=" N ASN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 130 removed outlier: 4.169A pdb=" N TYR F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN F 127 " --> pdb=" O ARG F 123 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 163 removed outlier: 3.586A pdb=" N ARG F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS F 160 " --> pdb=" O ARG F 156 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 205 removed outlier: 3.885A pdb=" N GLN F 184 " --> pdb=" O ASP F 180 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA F 185 " --> pdb=" O PRO F 181 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 229 removed outlier: 3.588A pdb=" N ASP F 227 " --> pdb=" O TYR F 223 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 244 removed outlier: 3.517A pdb=" N ILE F 237 " --> pdb=" O ILE F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 267 removed outlier: 3.893A pdb=" N LEU F 254 " --> pdb=" O ASP F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 280 removed outlier: 3.679A pdb=" N VAL F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 5.910A pdb=" N GLU A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL A 32 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A 27 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 56 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 71 " --> pdb=" O MET A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.608A pdb=" N ARG E 34 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 94 removed outlier: 5.979A pdb=" N LEU B 58 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 84 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU B 60 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL B 57 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N THR B 23 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 59 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA B 22 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 309 through 310 removed outlier: 3.840A pdb=" N LYS B 31 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 65 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 32 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 67 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG B 34 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG C 34 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG C 49 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE D 88 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 27 removed outlier: 6.353A pdb=" N THR C 23 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU C 59 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 25 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 80 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.211A pdb=" N GLU D 25 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL D 32 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA D 27 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N MET D 3 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 61 " --> pdb=" O MET D 3 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA D 56 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D 73 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 60 " --> pdb=" O ASP D 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 289 through 293 removed outlier: 6.571A pdb=" N ALA E 22 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU E 293 " --> pdb=" O ALA E 22 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE E 24 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL E 57 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR E 23 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU E 59 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE E 25 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU E 58 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL E 84 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU E 60 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU E 81 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY F 85 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU F 58 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL F 84 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU F 60 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE F 25 " --> pdb=" O VAL F 57 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 157 hydrogen bonds 314 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 4.80 Time building geometry restraints manager: 7.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3797 1.34 - 1.46: 3112 1.46 - 1.57: 6912 1.57 - 1.69: 308 1.69 - 1.81: 62 Bond restraints: 14191 Sorted by residual: bond pdb=" O3' DC J 21 " pdb=" P DT J 22 " ideal model delta sigma weight residual 1.607 1.638 -0.031 1.50e-02 4.44e+03 4.38e+00 bond pdb=" O3' DG J 20 " pdb=" P DC J 21 " ideal model delta sigma weight residual 1.607 1.638 -0.031 1.50e-02 4.44e+03 4.32e+00 bond pdb=" O3' DT G 30 " pdb=" P DC G 31 " ideal model delta sigma weight residual 1.607 1.629 -0.022 1.50e-02 4.44e+03 2.19e+00 bond pdb=" O3' DA J 32 " pdb=" P DA J 33 " ideal model delta sigma weight residual 1.607 1.626 -0.019 1.50e-02 4.44e+03 1.64e+00 bond pdb=" C3' DG G 8 " pdb=" O3' DG G 8 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.59e+00 ... (remaining 14186 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.37: 1191 106.37 - 113.30: 7623 113.30 - 120.24: 5226 120.24 - 127.17: 5433 127.17 - 134.11: 401 Bond angle restraints: 19874 Sorted by residual: angle pdb=" CA GLN F 87 " pdb=" CB GLN F 87 " pdb=" CG GLN F 87 " ideal model delta sigma weight residual 114.10 119.91 -5.81 2.00e+00 2.50e-01 8.45e+00 angle pdb=" C GLU C 232 " pdb=" N ILE C 233 " pdb=" CA ILE C 233 " ideal model delta sigma weight residual 122.97 120.14 2.83 9.80e-01 1.04e+00 8.35e+00 angle pdb=" CA MET F 125 " pdb=" CB MET F 125 " pdb=" CG MET F 125 " ideal model delta sigma weight residual 114.10 119.79 -5.69 2.00e+00 2.50e-01 8.09e+00 angle pdb=" O3' DA J 37 " pdb=" C3' DA J 37 " pdb=" C2' DA J 37 " ideal model delta sigma weight residual 111.50 107.47 4.03 1.50e+00 4.44e-01 7.20e+00 angle pdb=" C3' DT G 30 " pdb=" C2' DT G 30 " pdb=" C1' DT G 30 " ideal model delta sigma weight residual 101.60 105.61 -4.01 1.50e+00 4.44e-01 7.14e+00 ... (remaining 19869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 7279 35.88 - 71.75: 659 71.75 - 107.63: 19 107.63 - 143.50: 3 143.50 - 179.38: 4 Dihedral angle restraints: 7964 sinusoidal: 4148 harmonic: 3816 Sorted by residual: dihedral pdb=" C4' DA J 32 " pdb=" C3' DA J 32 " pdb=" O3' DA J 32 " pdb=" P DA J 33 " ideal model delta sinusoidal sigma weight residual -140.00 39.38 -179.38 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA J 31 " pdb=" C3' DA J 31 " pdb=" O3' DA J 31 " pdb=" P DA J 32 " ideal model delta sinusoidal sigma weight residual -140.00 38.42 -178.42 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG G 38 " pdb=" C3' DG G 38 " pdb=" O3' DG G 38 " pdb=" P DC G 39 " ideal model delta sinusoidal sigma weight residual -140.00 34.60 -174.60 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1695 0.039 - 0.078: 407 0.078 - 0.116: 104 0.116 - 0.155: 25 0.155 - 0.194: 2 Chirality restraints: 2233 Sorted by residual: chirality pdb=" C1' DC J 21 " pdb=" O4' DC J 21 " pdb=" C2' DC J 21 " pdb=" N1 DC J 21 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" P DC J 21 " pdb=" OP1 DC J 21 " pdb=" OP2 DC J 21 " pdb=" O5' DC J 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.50 -0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA VAL B 303 " pdb=" N VAL B 303 " pdb=" C VAL B 303 " pdb=" CB VAL B 303 " both_signs ideal model delta sigma weight residual False 2.44 2.29 0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 2230 not shown) Planarity restraints: 2009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 8 " 0.028 2.00e-02 2.50e+03 1.17e-02 4.11e+00 pdb=" N9 DG J 8 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG J 8 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG J 8 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG J 8 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG J 8 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG J 8 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG J 8 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG J 8 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG J 8 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG J 8 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG J 8 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 37 " 0.024 2.00e-02 2.50e+03 1.12e-02 3.48e+00 pdb=" N9 DA J 37 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA J 37 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA J 37 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA J 37 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA J 37 " 0.007 2.00e-02 2.50e+03 pdb=" N6 DA J 37 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA J 37 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA J 37 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA J 37 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA J 37 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 1 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO A 2 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 2 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 2 " -0.025 5.00e-02 4.00e+02 ... (remaining 2006 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1115 2.74 - 3.28: 14284 3.28 - 3.82: 25857 3.82 - 4.36: 29081 4.36 - 4.90: 45125 Nonbonded interactions: 115462 Sorted by model distance: nonbonded pdb=" OH TYR B 91 " pdb=" OG SER B 94 " model vdw 2.196 2.440 nonbonded pdb=" O ASN F 33 " pdb=" OG1 THR F 40 " model vdw 2.235 2.440 nonbonded pdb=" NE2 GLN E 277 " pdb=" O ILE E 288 " model vdw 2.247 2.520 nonbonded pdb=" OG SER B 159 " pdb=" O VAL B 164 " model vdw 2.256 2.440 nonbonded pdb=" NH2 ARG A 46 " pdb=" OG SER C 10 " model vdw 2.259 2.520 ... (remaining 115457 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 'D' } ncs_group { reference = (chain 'B' and (resid 20 through 129 or resid 134 through 279)) selection = (chain 'C' and (resid 20 through 129 or resid 134 through 279)) selection = (chain 'E' and resid 20 through 279) selection = (chain 'F' and (resid 20 through 129 or resid 134 through 279)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.39 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.780 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 45.750 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 : 0.003 0.038 14191 Z= 0.184 Angle : 0.582 7.149 19874 Z= 0.326 Chirality : 0.038 0.194 2233 Planarity : 0.004 0.044 2009 Dihedral : 22.269 179.381 5518 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1311 helix: 0.80 (0.21), residues: 597 sheet: -0.24 (0.37), residues: 191 loop : -0.83 (0.27), residues: 523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.443 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2622 time to fit residues: 101.7990 Evaluate side-chains 203 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 0.0010 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 GLN B 146 HIS ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14191 Z= 0.210 Angle : 0.622 7.996 19874 Z= 0.341 Chirality : 0.041 0.169 2233 Planarity : 0.004 0.044 2009 Dihedral : 25.318 175.928 3046 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.76 % Allowed : 12.77 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.23), residues: 1311 helix: 0.97 (0.20), residues: 626 sheet: -0.30 (0.38), residues: 181 loop : -0.81 (0.28), residues: 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 237 time to evaluate : 1.443 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 247 average time/residue: 0.2394 time to fit residues: 87.5396 Evaluate side-chains 205 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 1.374 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1245 time to fit residues: 4.3661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 129 optimal weight: 0.0010 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 0.0170 overall best weight: 0.6028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 190 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN F 114 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14191 Z= 0.193 Angle : 0.608 10.805 19874 Z= 0.330 Chirality : 0.040 0.173 2233 Planarity : 0.004 0.041 2009 Dihedral : 25.257 179.761 3046 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.48 % Allowed : 16.74 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1311 helix: 0.91 (0.21), residues: 626 sheet: -0.43 (0.38), residues: 185 loop : -0.77 (0.28), residues: 500 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 220 time to evaluate : 1.465 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 229 average time/residue: 0.2546 time to fit residues: 85.8273 Evaluate side-chains 215 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 207 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1252 time to fit residues: 3.5584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS B 163 ASN ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 190 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14191 Z= 0.220 Angle : 0.609 8.558 19874 Z= 0.331 Chirality : 0.040 0.144 2233 Planarity : 0.004 0.040 2009 Dihedral : 25.224 179.502 3046 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.04 % Allowed : 18.59 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1311 helix: 0.92 (0.21), residues: 629 sheet: -0.44 (0.38), residues: 187 loop : -0.77 (0.28), residues: 495 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 time to evaluate : 1.341 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 237 average time/residue: 0.2368 time to fit residues: 83.8048 Evaluate side-chains 212 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 200 time to evaluate : 1.469 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1608 time to fit residues: 5.0460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 118 optimal weight: 0.6980 chunk 96 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 overall best weight: 2.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN B 146 HIS B 163 ASN B 184 GLN ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 190 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN F 114 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14191 Z= 0.271 Angle : 0.636 8.978 19874 Z= 0.345 Chirality : 0.041 0.181 2233 Planarity : 0.004 0.040 2009 Dihedral : 25.241 179.997 3046 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.94 % Allowed : 20.81 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1311 helix: 0.89 (0.21), residues: 630 sheet: -0.43 (0.37), residues: 195 loop : -0.84 (0.28), residues: 486 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 208 time to evaluate : 1.428 Fit side-chains outliers start: 21 outliers final: 9 residues processed: 216 average time/residue: 0.2464 time to fit residues: 78.2842 Evaluate side-chains 202 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1246 time to fit residues: 3.7635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 139 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN B 184 GLN ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 190 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14191 Z= 0.276 Angle : 0.656 10.481 19874 Z= 0.354 Chirality : 0.041 0.193 2233 Planarity : 0.005 0.071 2009 Dihedral : 25.295 179.829 3046 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.57 % Allowed : 22.11 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.23), residues: 1311 helix: 0.89 (0.21), residues: 629 sheet: -0.50 (0.37), residues: 195 loop : -0.91 (0.28), residues: 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 202 time to evaluate : 1.616 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 212 average time/residue: 0.2408 time to fit residues: 75.8761 Evaluate side-chains 202 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 1.362 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1268 time to fit residues: 4.6426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.0070 chunk 77 optimal weight: 0.3980 chunk 138 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.0804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 HIS C 190 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14191 Z= 0.214 Angle : 0.646 12.812 19874 Z= 0.347 Chirality : 0.040 0.197 2233 Planarity : 0.004 0.049 2009 Dihedral : 25.242 179.612 3046 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.02 % Allowed : 23.50 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1311 helix: 0.94 (0.21), residues: 631 sheet: -0.46 (0.37), residues: 190 loop : -0.90 (0.28), residues: 490 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 212 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 218 average time/residue: 0.2433 time to fit residues: 78.7726 Evaluate side-chains 199 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 193 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2033 time to fit residues: 3.5622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 0.0770 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 0.0670 chunk 12 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14191 Z= 0.198 Angle : 0.666 16.710 19874 Z= 0.353 Chirality : 0.041 0.228 2233 Planarity : 0.004 0.047 2009 Dihedral : 25.157 179.511 3046 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.30 % Allowed : 23.59 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.23), residues: 1311 helix: 0.90 (0.21), residues: 629 sheet: -0.42 (0.36), residues: 200 loop : -0.89 (0.29), residues: 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 219 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 225 average time/residue: 0.2394 time to fit residues: 80.0362 Evaluate side-chains 211 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 202 time to evaluate : 1.431 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1635 time to fit residues: 4.2972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 129 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 116 optimal weight: 7.9990 chunk 122 optimal weight: 0.0040 chunk 128 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 HIS C 190 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14191 Z= 0.205 Angle : 0.685 13.121 19874 Z= 0.363 Chirality : 0.041 0.204 2233 Planarity : 0.004 0.046 2009 Dihedral : 25.124 179.597 3046 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.46 % Allowed : 24.70 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1311 helix: 0.92 (0.21), residues: 628 sheet: -0.54 (0.36), residues: 200 loop : -0.84 (0.29), residues: 483 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 216 time to evaluate : 1.393 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 219 average time/residue: 0.2421 time to fit residues: 78.9190 Evaluate side-chains 206 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.461 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 114 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 0.0970 chunk 90 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 163 ASN ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14191 Z= 0.201 Angle : 0.698 14.600 19874 Z= 0.367 Chirality : 0.042 0.213 2233 Planarity : 0.004 0.047 2009 Dihedral : 25.092 179.950 3046 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.74 % Allowed : 25.62 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1311 helix: 0.82 (0.21), residues: 626 sheet: -0.44 (0.36), residues: 196 loop : -0.86 (0.29), residues: 489 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 218 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 219 average time/residue: 0.2442 time to fit residues: 79.3351 Evaluate side-chains 206 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 199 time to evaluate : 1.417 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1697 time to fit residues: 3.5092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.128670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.087087 restraints weight = 52137.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.090081 restraints weight = 24753.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.092000 restraints weight = 16113.967| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14191 Z= 0.262 Angle : 0.707 12.467 19874 Z= 0.374 Chirality : 0.042 0.314 2233 Planarity : 0.004 0.051 2009 Dihedral : 25.117 179.973 3046 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.28 % Allowed : 25.99 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1311 helix: 0.80 (0.21), residues: 629 sheet: -0.60 (0.36), residues: 195 loop : -0.88 (0.28), residues: 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2704.70 seconds wall clock time: 49 minutes 59.80 seconds (2999.80 seconds total)