Starting phenix.real_space_refine (version: dev) on Sun Feb 26 17:01:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tax_25789/02_2023/7tax_25789.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tax_25789/02_2023/7tax_25789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tax_25789/02_2023/7tax_25789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tax_25789/02_2023/7tax_25789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tax_25789/02_2023/7tax_25789.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tax_25789/02_2023/7tax_25789.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 459 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 99": "OE1" <-> "OE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F GLU 175": "OE1" <-> "OE2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F GLU 231": "OE1" <-> "OE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "G GLU 210": "OE1" <-> "OE2" Residue "H GLU 231": "OE1" <-> "OE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J GLU 157": "OE1" <-> "OE2" Residue "J PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 54": "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: 27855 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 196 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "K" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "Y" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "X" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 17.02, per 1000 atoms: 0.61 Number of scatterers: 27855 At special positions: 0 Unit cell: (130.2, 178.5, 152.25, 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 33 16.00 P 98 15.00 O 5455 8.00 N 5054 7.00 C 17215 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: 12.44 Conformation dependent library (CDL) restraints added in 4.2 seconds 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6226 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 55 sheets defined 35.1% alpha, 21.0% beta 18 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 8.03 Creating SS restraints... Processing helix chain 'A' and resid 9 through 33 removed outlier: 3.518A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.508A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 61 removed outlier: 3.743A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.667A pdb=" N GLU A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.808A pdb=" N TRP A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 195 through 212 Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 294 through 309 removed outlier: 4.018A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 341 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.551A pdb=" N ALA A 349 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 364 removed outlier: 4.021A pdb=" N LEU A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TRP A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.176A pdb=" N THR A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 Processing helix chain 'A' and resid 385 through 398 removed outlier: 3.934A pdb=" N ASN A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.904A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.801A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.638A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.586A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.773A pdb=" N LEU C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.949A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 322 through 332 removed outlier: 3.547A pdb=" N LEU D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 51 through 58 removed outlier: 5.265A pdb=" N GLN E 56 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU E 57 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP E 58 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 92 removed outlier: 3.549A pdb=" N SER E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 208 through 223 Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 322 through 332 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 58 removed outlier: 3.555A pdb=" N SER F 55 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN F 56 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU F 57 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 208 through 223 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 316 through 320 Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 92 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 293 through 297 removed outlier: 3.673A pdb=" N LEU G 296 " --> pdb=" O GLU G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 322 through 332 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.629A pdb=" N SER H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 322 through 332 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 82 through 91 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 150 through 163 Processing helix chain 'I' and resid 164 through 172 removed outlier: 6.503A pdb=" N ARG I 169 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 302 through 304 No H-bonds generated for 'chain 'I' and resid 302 through 304' Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 47 through 70 removed outlier: 3.519A pdb=" N PHE J 55 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 136 Processing helix chain 'J' and resid 140 through 147 Processing helix chain 'J' and resid 163 through 168 Processing helix chain 'J' and resid 180 through 188 Processing helix chain 'J' and resid 191 through 197 Processing helix chain 'J' and resid 211 through 222 Processing helix chain 'K' and resid 47 through 70 removed outlier: 3.515A pdb=" N ASP K 53 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE K 58 " --> pdb=" O GLU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 136 Processing helix chain 'K' and resid 140 through 147 Processing helix chain 'K' and resid 163 through 168 Processing helix chain 'K' and resid 180 through 189 Processing helix chain 'K' and resid 191 through 199 Processing helix chain 'K' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.423A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 182 removed outlier: 4.351A pdb=" N GLY A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 240 removed outlier: 4.541A pdb=" N PHE B 81 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 265 through 267 removed outlier: 5.727A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 61 removed outlier: 3.852A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE B 61 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER B 108 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 68 removed outlier: 4.898A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB4, first strand: chain 'D' and resid 31 through 33 removed outlier: 3.838A pdb=" N PHE D 355 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.969A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL D 177 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP D 196 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 179 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG D 194 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE D 181 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA D 192 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS D 183 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AB9, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.764A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC2, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AC3, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.804A pdb=" N PHE E 355 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.185A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA E 176 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL E 177 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASP E 196 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL E 179 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG E 194 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC6, first strand: chain 'E' and resid 63 through 70 removed outlier: 3.627A pdb=" N GLY E 70 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN E 94 " --> pdb=" O GLY E 70 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA E 101 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC8, first strand: chain 'E' and resid 306 through 307 removed outlier: 3.723A pdb=" N LYS E 312 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.530A pdb=" N VAL F 118 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA F 176 " --> pdb=" O ARG F 237 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL F 177 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ASP F 196 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL F 179 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARG F 194 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD3, first strand: chain 'F' and resid 63 through 70 removed outlier: 3.519A pdb=" N GLN F 96 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY F 70 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN F 94 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA F 101 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD5, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.695A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 31 through 33 Processing sheet with id=AD7, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.210A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD9, first strand: chain 'G' and resid 63 through 70 removed outlier: 3.585A pdb=" N GLY G 70 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 285 through 287 Processing sheet with id=AE2, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AE3, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.692A pdb=" N PHE H 355 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 188 through 196 removed outlier: 5.000A pdb=" N VAL H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG H 185 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG H 191 " --> pdb=" O HIS H 183 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.763A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.763A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER H 262 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR H 97 " --> pdb=" O SER H 262 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR H 264 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP H 99 " --> pdb=" O THR H 264 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AE8, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.754A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.511A pdb=" N ALA I 127 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.282A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG I 191 " --> pdb=" O HIS I 183 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AF3, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.964A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 243 through 244 removed outlier: 4.560A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA J 38 " --> pdb=" O LEU J 30 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR J 32 " --> pdb=" O GLU J 36 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU J 36 " --> pdb=" O TYR J 32 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF6, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.700A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 85 through 90 removed outlier: 5.232A pdb=" N LEU J 119 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER J 99 " --> pdb=" O GLY J 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 4 through 6 removed outlier: 6.256A pdb=" N HIS K 26 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR K 41 " --> pdb=" O HIS K 26 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP K 28 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE K 39 " --> pdb=" O TRP K 28 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU K 30 " --> pdb=" O MET K 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 85 through 91 Processing sheet with id=AG1, first strand: chain 'K' and resid 99 through 100 1159 hydrogen bonds defined for protein. 3156 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 10.35 Time building geometry restraints manager: 13.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4483 1.30 - 1.43: 7939 1.43 - 1.56: 15980 1.56 - 1.68: 195 1.68 - 1.81: 52 Bond restraints: 28649 Sorted by residual: bond pdb=" CA ALA G 271 " pdb=" C ALA G 271 " ideal model delta sigma weight residual 1.521 1.455 0.066 1.19e-02 7.06e+03 3.06e+01 bond pdb=" C HIS G 159 " pdb=" O HIS G 159 " ideal model delta sigma weight residual 1.237 1.175 0.061 1.19e-02 7.06e+03 2.66e+01 bond pdb=" CA HIS G 159 " pdb=" C HIS G 159 " ideal model delta sigma weight residual 1.524 1.471 0.052 1.29e-02 6.01e+03 1.63e+01 bond pdb=" CA ARG G 269 " pdb=" C ARG G 269 " ideal model delta sigma weight residual 1.530 1.474 0.055 1.44e-02 4.82e+03 1.48e+01 bond pdb=" C ALA G 158 " pdb=" O ALA G 158 " ideal model delta sigma weight residual 1.236 1.189 0.048 1.25e-02 6.40e+03 1.45e+01 ... (remaining 28644 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.08: 1432 107.08 - 113.84: 15913 113.84 - 120.59: 11134 120.59 - 127.34: 10433 127.34 - 134.09: 474 Bond angle restraints: 39386 Sorted by residual: angle pdb=" N LEU G 161 " pdb=" CA LEU G 161 " pdb=" C LEU G 161 " ideal model delta sigma weight residual 114.04 102.35 11.69 1.24e+00 6.50e-01 8.89e+01 angle pdb=" O SER G 267 " pdb=" C SER G 267 " pdb=" N VAL G 268 " ideal model delta sigma weight residual 123.33 130.37 -7.04 1.21e+00 6.83e-01 3.39e+01 angle pdb=" C LEU G 161 " pdb=" N ALA G 162 " pdb=" CA ALA G 162 " ideal model delta sigma weight residual 120.68 111.67 9.01 1.70e+00 3.46e-01 2.81e+01 angle pdb=" N ILE D 286 " pdb=" CA ILE D 286 " pdb=" C ILE D 286 " ideal model delta sigma weight residual 113.20 108.23 4.97 9.60e-01 1.09e+00 2.68e+01 angle pdb=" CA SER G 267 " pdb=" C SER G 267 " pdb=" N VAL G 268 " ideal model delta sigma weight residual 116.01 108.52 7.49 1.51e+00 4.39e-01 2.46e+01 ... (remaining 39381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 16477 35.90 - 71.81: 367 71.81 - 107.71: 29 107.71 - 143.62: 1 143.62 - 179.52: 5 Dihedral angle restraints: 16879 sinusoidal: 7233 harmonic: 9646 Sorted by residual: dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 55.78 144.22 1 1.50e+01 4.44e-03 7.73e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 57.83 142.17 1 1.50e+01 4.44e-03 7.64e+01 dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual 232.00 52.48 179.52 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 16876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3645 0.051 - 0.103: 635 0.103 - 0.154: 140 0.154 - 0.205: 10 0.205 - 0.257: 2 Chirality restraints: 4432 Sorted by residual: chirality pdb=" CA ASP G 270 " pdb=" N ASP G 270 " pdb=" C ASP G 270 " pdb=" CB ASP G 270 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB THR B 318 " pdb=" CA THR B 318 " pdb=" OG1 THR B 318 " pdb=" CG2 THR B 318 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB THR A 301 " pdb=" CA THR A 301 " pdb=" OG1 THR A 301 " pdb=" CG2 THR A 301 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 4429 not shown) Planarity restraints: 4823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.051 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PRO A 72 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER G 267 " 0.013 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C SER G 267 " -0.051 2.00e-02 2.50e+03 pdb=" O SER G 267 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL G 268 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 364 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO A 365 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " -0.041 5.00e-02 4.00e+02 ... (remaining 4820 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4673 2.77 - 3.30: 25724 3.30 - 3.83: 48928 3.83 - 4.37: 59225 4.37 - 4.90: 98107 Nonbonded interactions: 236657 Sorted by model distance: nonbonded pdb=" OH TYR A 179 " pdb=" OD2 ASP B 272 " model vdw 2.236 2.440 nonbonded pdb=" O VAL K 170 " pdb=" OG1 THR K 177 " model vdw 2.243 2.440 nonbonded pdb=" O GLY J 172 " pdb=" OG SER J 175 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR F 324 " pdb=" O SER G 73 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR H 324 " pdb=" O SER I 73 " model vdw 2.268 2.440 ... (remaining 236652 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 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } ncs_group { reference = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 98 5.49 5 S 33 5.16 5 C 17215 2.51 5 N 5054 2.21 5 O 5455 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=0.37 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.030 Extract box with map and model: 10.010 Check model and map are aligned: 0.400 Process input model: 81.310 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.290 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:14.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 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 0.066 28649 Z= 0.207 Angle : 0.668 11.694 39386 Z= 0.369 Chirality : 0.042 0.257 4432 Planarity : 0.005 0.077 4823 Dihedral : 15.136 179.523 10653 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 3322 helix: -0.02 (0.14), residues: 1078 sheet: 0.76 (0.21), residues: 540 loop : -1.58 (0.14), residues: 1704 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 866 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 4 residues processed: 866 average time/residue: 1.1975 time to fit residues: 1234.3669 Evaluate side-chains 513 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 509 time to evaluate : 2.891 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 3 average time/residue: 0.3724 time to fit residues: 5.8337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 2.9990 chunk 254 optimal weight: 0.6980 chunk 141 optimal weight: 0.0470 chunk 86 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 263 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 196 optimal weight: 0.9990 chunk 305 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 62 GLN A 129 ASN ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN B 89 ASN B 104 HIS B 168 GLN C 19 GLN D 170 ASN D 281 ASN E 91 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN F 242 GLN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 GLN H 96 GLN H 242 GLN H 348 ASN I 94 ASN I 146 ASN I 281 ASN J 26 HIS ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 28649 Z= 0.236 Angle : 0.668 9.169 39386 Z= 0.349 Chirality : 0.042 0.309 4432 Planarity : 0.005 0.057 4823 Dihedral : 13.689 178.869 4764 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 3.49 % 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: -0.51 (0.14), residues: 3322 helix: 0.70 (0.15), residues: 1066 sheet: 0.70 (0.21), residues: 567 loop : -1.43 (0.14), residues: 1689 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 567 time to evaluate : 3.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 28 residues processed: 626 average time/residue: 1.1508 time to fit residues: 866.0099 Evaluate side-chains 455 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 427 time to evaluate : 3.348 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 19 residues processed: 12 average time/residue: 0.3092 time to fit residues: 10.7905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 253 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 305 optimal weight: 2.9990 chunk 330 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 303 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 245 optimal weight: 0.0870 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN D 170 ASN E 91 GLN E 146 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 GLN F 160 ASN F 183 HIS F 242 GLN F 343 HIS ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN J 27 GLN ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.7246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 28649 Z= 0.307 Angle : 0.727 13.238 39386 Z= 0.373 Chirality : 0.045 0.248 4432 Planarity : 0.005 0.054 4823 Dihedral : 13.635 178.426 4764 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 5.14 % 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: -0.53 (0.14), residues: 3322 helix: 0.54 (0.15), residues: 1058 sheet: 0.74 (0.21), residues: 568 loop : -1.35 (0.15), residues: 1696 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 452 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 32 residues processed: 539 average time/residue: 1.2485 time to fit residues: 797.2345 Evaluate side-chains 368 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 336 time to evaluate : 3.109 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 24 residues processed: 9 average time/residue: 0.3071 time to fit residues: 9.0778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 145 optimal weight: 0.5980 chunk 205 optimal weight: 0.6980 chunk 306 optimal weight: 5.9990 chunk 324 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 290 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 82 ASN B 282 ASN D 170 ASN D 183 HIS D 343 HIS E 102 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS F 242 GLN G 94 ASN G 146 ASN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 GLN J 19 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.7885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 28649 Z= 0.203 Angle : 0.607 9.798 39386 Z= 0.310 Chirality : 0.041 0.215 4432 Planarity : 0.004 0.039 4823 Dihedral : 13.500 178.066 4764 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 4.14 % 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: -0.24 (0.14), residues: 3322 helix: 1.00 (0.15), residues: 1063 sheet: 0.82 (0.21), residues: 564 loop : -1.31 (0.14), residues: 1695 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 350 time to evaluate : 3.275 Fit side-chains revert: symmetry clash outliers start: 108 outliers final: 41 residues processed: 430 average time/residue: 1.3520 time to fit residues: 686.6818 Evaluate side-chains 337 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 296 time to evaluate : 3.266 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 33 residues processed: 12 average time/residue: 0.3110 time to fit residues: 10.8005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 277 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 0.9990 chunk 291 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 256 ASN ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 282 ASN D 102 ASN D 170 ASN E 146 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 146 ASN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.8658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 28649 Z= 0.219 Angle : 0.606 10.346 39386 Z= 0.309 Chirality : 0.041 0.199 4432 Planarity : 0.004 0.040 4823 Dihedral : 13.424 179.590 4764 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 4.37 % 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: -0.19 (0.14), residues: 3322 helix: 1.06 (0.15), residues: 1076 sheet: 0.75 (0.21), residues: 576 loop : -1.28 (0.15), residues: 1670 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 322 time to evaluate : 3.202 Fit side-chains outliers start: 114 outliers final: 49 residues processed: 404 average time/residue: 1.2824 time to fit residues: 614.6866 Evaluate side-chains 336 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 287 time to evaluate : 3.366 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 35 residues processed: 16 average time/residue: 0.4958 time to fit residues: 16.0348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.4980 chunk 292 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 325 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 256 ASN A 283 HIS A 324 GLN ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN B 64 HIS B 194 GLN B 220 ASN B 282 ASN D 170 ASN E 146 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN G 102 ASN H 163 ASN ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.9646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 28649 Z= 0.291 Angle : 0.666 12.790 39386 Z= 0.336 Chirality : 0.043 0.210 4432 Planarity : 0.004 0.043 4823 Dihedral : 13.567 179.311 4764 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 4.75 % 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: -0.21 (0.14), residues: 3322 helix: 0.99 (0.15), residues: 1072 sheet: 0.70 (0.21), residues: 556 loop : -1.21 (0.15), residues: 1694 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 290 time to evaluate : 3.208 Fit side-chains revert: symmetry clash outliers start: 124 outliers final: 50 residues processed: 378 average time/residue: 1.3831 time to fit residues: 617.2049 Evaluate side-chains 301 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 251 time to evaluate : 3.156 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 39 residues processed: 12 average time/residue: 0.4128 time to fit residues: 11.7911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 323 optimal weight: 0.0570 chunk 202 optimal weight: 0.4980 chunk 197 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS A 255 ASN A 256 ASN A 416 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 282 ASN D 170 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN G 94 ASN G 96 GLN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 GLN I 183 HIS ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.9793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 28649 Z= 0.185 Angle : 0.589 10.360 39386 Z= 0.297 Chirality : 0.040 0.209 4432 Planarity : 0.004 0.042 4823 Dihedral : 13.431 178.297 4764 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer Outliers : 3.45 % 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: -0.06 (0.14), residues: 3322 helix: 1.24 (0.16), residues: 1070 sheet: 0.80 (0.21), residues: 544 loop : -1.20 (0.15), residues: 1708 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 292 time to evaluate : 3.487 Fit side-chains outliers start: 90 outliers final: 48 residues processed: 360 average time/residue: 1.3160 time to fit residues: 563.6073 Evaluate side-chains 297 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 249 time to evaluate : 3.035 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 40 residues processed: 10 average time/residue: 0.3308 time to fit residues: 10.4682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 97 optimal weight: 0.0070 chunk 63 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 220 optimal weight: 0.0870 chunk 160 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 254 optimal weight: 5.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 282 ASN D 170 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 96 GLN G 242 GLN I 96 GLN J 27 GLN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 HIS K 208 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.9898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 28649 Z= 0.171 Angle : 0.587 10.672 39386 Z= 0.296 Chirality : 0.041 0.319 4432 Planarity : 0.004 0.043 4823 Dihedral : 13.359 177.749 4764 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 2.91 % 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: -0.06 (0.14), residues: 3322 helix: 1.31 (0.16), residues: 1070 sheet: 0.77 (0.21), residues: 574 loop : -1.28 (0.15), residues: 1678 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 280 time to evaluate : 3.257 Fit side-chains outliers start: 76 outliers final: 48 residues processed: 342 average time/residue: 1.2912 time to fit residues: 525.5664 Evaluate side-chains 302 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 254 time to evaluate : 3.692 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 41 residues processed: 10 average time/residue: 0.5010 time to fit residues: 11.7530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 0.5980 chunk 310 optimal weight: 20.0000 chunk 283 optimal weight: 0.9980 chunk 301 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 272 optimal weight: 0.6980 chunk 285 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 273 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN D 170 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 348 ASN I 96 GLN I 102 ASN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 1.0096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 28649 Z= 0.201 Angle : 0.599 11.554 39386 Z= 0.300 Chirality : 0.041 0.309 4432 Planarity : 0.004 0.043 4823 Dihedral : 13.340 178.490 4764 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 2.72 % 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 (0.14), residues: 3322 helix: 1.34 (0.16), residues: 1072 sheet: 0.88 (0.21), residues: 557 loop : -1.29 (0.15), residues: 1693 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 265 time to evaluate : 4.915 Fit side-chains outliers start: 71 outliers final: 52 residues processed: 319 average time/residue: 1.3635 time to fit residues: 521.8125 Evaluate side-chains 307 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 255 time to evaluate : 3.051 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 43 residues processed: 12 average time/residue: 0.4982 time to fit residues: 13.5754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.6980 chunk 319 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 221 optimal weight: 0.9980 chunk 334 optimal weight: 7.9990 chunk 308 optimal weight: 0.2980 chunk 266 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN D 170 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 GLN I 102 ASN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 1.0268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 28649 Z= 0.187 Angle : 0.602 11.851 39386 Z= 0.300 Chirality : 0.041 0.297 4432 Planarity : 0.004 0.045 4823 Dihedral : 13.267 178.322 4764 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 1.96 % 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: 0.00 (0.14), residues: 3322 helix: 1.39 (0.16), residues: 1072 sheet: 0.90 (0.21), residues: 558 loop : -1.28 (0.15), residues: 1692 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 261 time to evaluate : 3.254 Fit side-chains outliers start: 51 outliers final: 40 residues processed: 306 average time/residue: 1.2885 time to fit residues: 469.9277 Evaluate side-chains 283 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 243 time to evaluate : 3.225 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 38 residues processed: 4 average time/residue: 0.3288 time to fit residues: 6.5130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.5980 chunk 283 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 274 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 273 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN F 96 GLN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 248 GLN I 96 GLN J 206 ASN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.139594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.085579 restraints weight = 53387.347| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.74 r_work: 0.2946 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3840 r_free = 0.3840 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 1.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 28649 Z= 0.309 Angle : 0.667 11.760 39386 Z= 0.336 Chirality : 0.044 0.299 4432 Planarity : 0.004 0.051 4823 Dihedral : 13.426 179.113 4764 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 2.34 % 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: -0.16 (0.14), residues: 3322 helix: 1.12 (0.16), residues: 1077 sheet: 0.69 (0.22), residues: 543 loop : -1.22 (0.15), residues: 1702 =============================================================================== Job complete usr+sys time: 11066.67 seconds wall clock time: 198 minutes 2.04 seconds (11882.04 seconds total)