Starting phenix.real_space_refine on Mon Jun 23 09:08:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t3j_25660/06_2025/7t3j_25660.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3j_25660/06_2025/7t3j_25660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t3j_25660/06_2025/7t3j_25660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3j_25660/06_2025/7t3j_25660.map" model { file = "/net/cci-nas-00/data/ceres_data/7t3j_25660/06_2025/7t3j_25660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3j_25660/06_2025/7t3j_25660.cif" } resolution = 3.2 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 33 5.16 5 C 16843 2.51 5 N 4913 2.21 5 O 5227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.61s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27076 Number of models: 1 Model: "" Number of chains: 12 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: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 17.94, per 1000 atoms: 0.66 Number of scatterers: 27076 At special positions: 0 Unit cell: (128.1, 161.7, 175.35, 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 60 15.00 O 5227 8.00 N 4913 7.00 C 16843 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 - 3.00 Amino acid : True - 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: 6.63 Conformation dependent library (CDL) restraints added in 3.5 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 53 sheets defined 34.8% alpha, 20.6% beta 5 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 13.09 Creating SS restraints... Processing helix chain 'A' and resid 9 through 33 removed outlier: 3.944A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 49 through 58 removed outlier: 4.128A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.899A pdb=" N LYS A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 148 through 161 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: 3.910A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 removed outlier: 3.506A pdb=" N ILE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.519A pdb=" N ASP A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.774A pdb=" N LEU A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 397 Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.686A pdb=" N LEU A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.728A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.744A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.536A pdb=" N LEU B 118 " --> pdb=" O GLY B 115 " (cutoff:3.500A) 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: 3.902A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.597A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.899A pdb=" N GLY B 312 " --> pdb=" O PRO B 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.991A 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 removed outlier: 3.528A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 77' Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.730A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 118 " --> pdb=" O ARG C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.837A pdb=" N VAL C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA C 136 " --> pdb=" O ASP C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 132 through 136' Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 150 through 163 removed outlier: 3.610A pdb=" N ALA D 154 " --> pdb=" O PHE D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.512A pdb=" N ILE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) 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: 3.521A pdb=" N LEU D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 51 through 55 Processing helix chain 'E' and resid 82 through 91 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 306 removed outlier: 3.530A pdb=" N GLY E 305 " --> pdb=" O GLU E 302 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER E 306 " --> pdb=" O PRO E 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 302 through 306' Processing helix chain 'E' and resid 322 through 332 removed outlier: 3.532A pdb=" N LEU E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 55 removed outlier: 3.796A pdb=" N SER F 55 " --> pdb=" O ARG F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 91 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 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 322 through 332 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 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 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 82 through 92 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 171 removed outlier: 6.331A 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: 3.522A pdb=" N PHE J 55 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 5.280A 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 removed outlier: 3.754A pdb=" N ILE J 143 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 147 " --> pdb=" O THR J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 152 removed outlier: 3.537A pdb=" N VAL J 151 " --> pdb=" O PRO J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 169 Processing helix chain 'J' and resid 180 through 189 Processing helix chain 'J' and resid 191 through 200 Processing helix chain 'J' and resid 211 through 222 Processing helix chain 'K' and resid 47 through 70 removed outlier: 4.666A pdb=" N ASP K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 5.192A 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 142 through 147 removed outlier: 3.872A pdb=" N LEU K 146 " --> pdb=" O TRP K 142 " (cutoff:3.500A) 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 200 removed outlier: 3.567A pdb=" N PHE K 195 " --> pdb=" O SER K 191 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR K 198 " --> pdb=" O ASN K 194 " (cutoff:3.500A) 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 94 through 95 removed outlier: 5.658A pdb=" N GLY B 285 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLY B 287 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 240 removed outlier: 4.221A pdb=" N PHE B 81 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 267 removed outlier: 5.780A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 61 removed outlier: 3.891A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE B 61 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER B 108 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 68 removed outlier: 4.821A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 220 through 222 removed outlier: 4.696A pdb=" N ASN B 220 " --> pdb=" O ARG B 242 " (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 41 through 43 Processing sheet with id=AB3, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AB6, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.880A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 177 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP D 196 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL D 179 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG D 194 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 181 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA D 192 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.717A 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 46 through 47 Processing sheet with id=AB9, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AC1, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.771A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC3, first strand: chain 'D' and resid 306 through 307 removed outlier: 3.575A pdb=" N LYS D 312 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.806A pdb=" N PHE E 355 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.829A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL E 179 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG E 194 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'E' and resid 63 through 70 removed outlier: 4.513A pdb=" N ALA E 101 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC9, first strand: chain 'F' and resid 31 through 32 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.911A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL F 177 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP F 196 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL F 179 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG F 194 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.451A 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 64 through 70 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: 3.672A 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: 3.899A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.485A 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: 4.377A 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 'H' and resid 127 through 128 removed outlier: 3.983A pdb=" N PHE H 355 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 188 through 196 removed outlier: 6.472A pdb=" N HIS H 183 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA H 192 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE H 181 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG H 194 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL H 179 " --> pdb=" O ARG H 194 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASP H 196 " --> pdb=" O VAL H 177 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL H 177 " --> pdb=" O ASP H 196 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.823A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.823A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS H 261 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR H 97 " --> pdb=" O LYS H 261 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS H 263 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU H 265 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ALA H 101 " --> pdb=" O LEU H 265 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AE7, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.944A pdb=" N VAL H 307 " --> pdb=" O LYS H 312 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.698A pdb=" N GLY I 353 " --> pdb=" O PHE I 33 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.523A pdb=" N ARG I 117 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL I 177 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP I 196 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL I 179 " --> pdb=" O ARG I 194 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG I 194 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE I 181 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA I 192 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS I 183 " --> pdb=" O ALA I 190 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.523A pdb=" N ARG I 117 " --> pdb=" O ASP I 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.945A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 243 through 244 removed outlier: 4.575A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR J 12 " --> pdb=" O TYR J 31 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR J 31 " --> pdb=" O THR J 12 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA J 14 " --> pdb=" O THR J 29 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR J 29 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG J 16 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN J 27 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N HIS J 26 " --> pdb=" O THR J 41 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR J 41 " --> pdb=" O HIS J 26 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP J 28 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE J 39 " --> pdb=" O TRP J 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU J 30 " --> pdb=" O MET J 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF5, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.524A pdb=" N VAL I 307 " --> pdb=" O LYS I 312 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'J' and resid 85 through 91 removed outlier: 3.603A pdb=" N ASP J 73 " --> pdb=" O VAL J 91 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU J 119 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER J 99 " --> pdb=" O GLY J 120 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 4 through 6 removed outlier: 6.198A pdb=" N HIS K 26 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR K 41 " --> pdb=" O HIS K 26 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TRP K 28 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE K 39 " --> pdb=" O TRP K 28 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU K 30 " --> pdb=" O MET K 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 85 through 90 removed outlier: 5.362A pdb=" N LEU K 119 " --> pdb=" O THR K 113 " (cutoff:3.500A) 1123 hydrogen bonds defined for protein. 3072 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 12.30 Time building geometry restraints manager: 7.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7141 1.33 - 1.45: 5339 1.45 - 1.57: 15125 1.57 - 1.69: 120 1.69 - 1.81: 52 Bond restraints: 27777 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.39e+00 bond pdb=" CB ARG A 302 " pdb=" CG ARG A 302 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.83e+00 bond pdb=" CA LYS A 71 " pdb=" C LYS A 71 " ideal model delta sigma weight residual 1.524 1.544 -0.020 1.26e-02 6.30e+03 2.62e+00 bond pdb=" CB GLN K 27 " pdb=" CG GLN K 27 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.61e+00 bond pdb=" C HIS C 93 " pdb=" N PRO C 94 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.61e+00 ... (remaining 27772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 37388 2.44 - 4.88: 558 4.88 - 7.32: 79 7.32 - 9.76: 18 9.76 - 12.21: 2 Bond angle restraints: 38045 Sorted by residual: angle pdb=" C LYS G 77 " pdb=" N THR G 78 " pdb=" CA THR G 78 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" CB MET K 1 " pdb=" CG MET K 1 " pdb=" SD MET K 1 " ideal model delta sigma weight residual 112.70 124.91 -12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C PRO B 205 " pdb=" N GLU B 206 " pdb=" CA GLU B 206 " ideal model delta sigma weight residual 121.54 128.86 -7.32 1.91e+00 2.74e-01 1.47e+01 angle pdb=" N PRO D 246 " pdb=" CD PRO D 246 " pdb=" CG PRO D 246 " ideal model delta sigma weight residual 103.20 97.50 5.70 1.50e+00 4.44e-01 1.44e+01 angle pdb=" CB PRO D 246 " pdb=" CG PRO D 246 " pdb=" CD PRO D 246 " ideal model delta sigma weight residual 106.10 94.00 12.10 3.20e+00 9.77e-02 1.43e+01 ... (remaining 38040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 16160 35.77 - 71.54: 512 71.54 - 107.31: 42 107.31 - 143.08: 1 143.08 - 178.85: 6 Dihedral angle restraints: 16721 sinusoidal: 7075 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 52.46 147.54 1 1.50e+01 4.44e-03 7.87e+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 52.68 147.32 1 1.50e+01 4.44e-03 7.86e+01 dihedral pdb=" O4' C M 37 " pdb=" C1' C M 37 " pdb=" N1 C M 37 " pdb=" C2 C M 37 " ideal model delta sinusoidal sigma weight residual 232.00 53.15 178.85 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 16718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3696 0.065 - 0.131: 534 0.131 - 0.196: 40 0.196 - 0.261: 7 0.261 - 0.327: 3 Chirality restraints: 4280 Sorted by residual: chirality pdb=" CB ILE E 72 " pdb=" CA ILE E 72 " pdb=" CG1 ILE E 72 " pdb=" CG2 ILE E 72 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB ILE K 6 " pdb=" CA ILE K 6 " pdb=" CG1 ILE K 6 " pdb=" CG2 ILE K 6 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB THR E 97 " pdb=" CA THR E 97 " pdb=" OG1 THR E 97 " pdb=" CG2 THR E 97 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 4277 not shown) Planarity restraints: 4785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 82 " 0.085 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO F 83 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO F 83 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO F 83 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO A 72 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 162 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.46e+00 pdb=" N PRO C 163 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 163 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 163 " 0.042 5.00e-02 4.00e+02 ... (remaining 4782 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4988 2.77 - 3.30: 24372 3.30 - 3.84: 48736 3.84 - 4.37: 57947 4.37 - 4.90: 96063 Nonbonded interactions: 232106 Sorted by model distance: nonbonded pdb=" OE1 GLN K 27 " pdb=" OG1 THR K 41 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR G 290 " pdb=" O GLY G 297 " model vdw 2.244 3.040 nonbonded pdb=" O ALA J 141 " pdb=" OG1 THR J 144 " model vdw 2.266 3.040 nonbonded pdb=" OG SER B 24 " pdb=" O PHE B 31 " model vdw 2.282 3.040 nonbonded pdb=" O VAL C 100 " pdb=" OG SER C 179 " model vdw 2.298 3.040 ... (remaining 232101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.430 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: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 73.580 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.140 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.004 0.072 27777 Z= 0.176 Angle : 0.740 12.205 38045 Z= 0.396 Chirality : 0.046 0.327 4280 Planarity : 0.007 0.127 4785 Dihedral : 17.151 178.855 10495 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.58 % Allowed : 17.10 % Favored : 82.32 % 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: -1.91 (0.13), residues: 3322 helix: -1.34 (0.12), residues: 1056 sheet: 0.44 (0.23), residues: 522 loop : -1.77 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 193 HIS 0.008 0.001 HIS D 159 PHE 0.015 0.002 PHE K 212 TYR 0.045 0.002 TYR D 304 ARG 0.014 0.000 ARG B 14 Details of bonding type rmsd hydrogen bonds : bond 0.15379 ( 1107) hydrogen bonds : angle 7.36843 ( 3094) covalent geometry : bond 0.00362 (27777) covalent geometry : angle 0.73956 (38045) *********************** 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 251 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.7735 (mpt-90) cc_final: 0.7517 (mmp-170) REVERT: G 51 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: I 203 ARG cc_start: 0.7349 (ptp-110) cc_final: 0.7057 (ttm110) REVERT: J 113 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8950 (p) REVERT: K 62 PHE cc_start: 0.8702 (t80) cc_final: 0.8476 (t80) outliers start: 15 outliers final: 4 residues processed: 245 average time/residue: 0.4110 time to fit residues: 158.6259 Evaluate side-chains 223 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 217 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain J residue 123 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 0.8980 chunk 253 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 170 optimal weight: 0.0040 chunk 135 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 303 optimal weight: 6.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN C 29 HIS ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.108758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.088175 restraints weight = 66721.580| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.00 r_work: 0.3261 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27777 Z= 0.143 Angle : 0.525 6.755 38045 Z= 0.277 Chirality : 0.039 0.215 4280 Planarity : 0.005 0.073 4785 Dihedral : 14.349 177.104 4616 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.46 % Allowed : 15.95 % Favored : 82.59 % 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: -0.86 (0.14), residues: 3322 helix: 0.22 (0.15), residues: 1057 sheet: 0.70 (0.23), residues: 503 loop : -1.49 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 362 HIS 0.006 0.001 HIS D 227 PHE 0.013 0.001 PHE I 114 TYR 0.013 0.001 TYR A 187 ARG 0.013 0.000 ARG A 14 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 1107) hydrogen bonds : angle 5.36486 ( 3094) covalent geometry : bond 0.00312 (27777) covalent geometry : angle 0.52477 (38045) *********************** 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 275 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6451 (ttp-170) cc_final: 0.5543 (tpm170) REVERT: D 216 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6585 (mt-10) REVERT: G 51 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: G 94 ASN cc_start: 0.8725 (p0) cc_final: 0.8481 (p0) REVERT: G 212 ASP cc_start: 0.7873 (m-30) cc_final: 0.7537 (m-30) REVERT: I 203 ARG cc_start: 0.7946 (ptp-110) cc_final: 0.7566 (ttm110) outliers start: 38 outliers final: 20 residues processed: 262 average time/residue: 0.4151 time to fit residues: 170.0852 Evaluate side-chains 232 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 159 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 162 optimal weight: 0.9980 chunk 300 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS A 324 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 114 HIS ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 348 ASN J 194 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.107102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.086105 restraints weight = 72663.814| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.10 r_work: 0.3213 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27777 Z= 0.168 Angle : 0.536 7.739 38045 Z= 0.279 Chirality : 0.040 0.203 4280 Planarity : 0.004 0.059 4785 Dihedral : 14.250 176.973 4609 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.42 % Allowed : 15.87 % Favored : 81.71 % 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: -0.49 (0.14), residues: 3322 helix: 0.75 (0.15), residues: 1058 sheet: 0.76 (0.23), residues: 495 loop : -1.36 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 159 HIS 0.013 0.001 HIS B 114 PHE 0.012 0.001 PHE I 114 TYR 0.016 0.002 TYR F 290 ARG 0.003 0.000 ARG H 237 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 1107) hydrogen bonds : angle 5.15481 ( 3094) covalent geometry : bond 0.00373 (27777) covalent geometry : angle 0.53605 (38045) *********************** 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 287 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 224 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6217 (ttp-170) cc_final: 0.5180 (tpm170) REVERT: E 52 ARG cc_start: 0.6978 (mtm180) cc_final: 0.6693 (mtm180) REVERT: F 216 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: G 51 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8239 (mp10) REVERT: G 87 ASP cc_start: 0.8438 (m-30) cc_final: 0.8003 (m-30) REVERT: G 94 ASN cc_start: 0.8746 (p0) cc_final: 0.8528 (p0) outliers start: 63 outliers final: 35 residues processed: 271 average time/residue: 0.4093 time to fit residues: 174.0279 Evaluate side-chains 246 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 224 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 318 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 225 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN H 281 ASN ** H 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 ASN K 26 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.105949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.084607 restraints weight = 72934.733| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.13 r_work: 0.3186 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27777 Z= 0.179 Angle : 0.548 6.836 38045 Z= 0.285 Chirality : 0.041 0.310 4280 Planarity : 0.004 0.058 4785 Dihedral : 14.247 176.747 4609 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.88 % Allowed : 16.07 % Favored : 81.06 % 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: -0.37 (0.14), residues: 3322 helix: 0.95 (0.15), residues: 1065 sheet: 0.58 (0.23), residues: 520 loop : -1.31 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 362 HIS 0.015 0.001 HIS A 203 PHE 0.011 0.001 PHE I 114 TYR 0.017 0.002 TYR F 290 ARG 0.003 0.000 ARG D 156 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 1107) hydrogen bonds : angle 5.04109 ( 3094) covalent geometry : bond 0.00402 (27777) covalent geometry : angle 0.54795 (38045) *********************** 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 299 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 224 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6155 (ttp-170) cc_final: 0.5134 (tpm170) REVERT: A 121 LEU cc_start: 0.7072 (mt) cc_final: 0.6766 (mt) REVERT: A 228 TRP cc_start: 0.8546 (t-100) cc_final: 0.8340 (t-100) REVERT: A 366 LEU cc_start: 0.7254 (tp) cc_final: 0.6979 (tp) REVERT: E 52 ARG cc_start: 0.7039 (mtm180) cc_final: 0.6729 (mtm180) REVERT: F 216 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: G 51 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8339 (mp10) REVERT: G 87 ASP cc_start: 0.8460 (m-30) cc_final: 0.8068 (m-30) REVERT: G 94 ASN cc_start: 0.8621 (p0) cc_final: 0.8397 (p0) REVERT: K 57 ASP cc_start: 0.7968 (p0) cc_final: 0.7696 (m-30) outliers start: 75 outliers final: 44 residues processed: 287 average time/residue: 0.4103 time to fit residues: 183.9436 Evaluate side-chains 255 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 181 optimal weight: 3.9990 chunk 122 optimal weight: 0.0040 chunk 212 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 308 optimal weight: 20.0000 chunk 223 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 HIS J 194 ASN K 26 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.104695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.083530 restraints weight = 75604.920| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.26 r_work: 0.3148 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27777 Z= 0.219 Angle : 0.579 8.744 38045 Z= 0.300 Chirality : 0.042 0.267 4280 Planarity : 0.005 0.061 4785 Dihedral : 14.291 176.577 4609 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.91 % Allowed : 16.49 % Favored : 80.60 % 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: -0.38 (0.14), residues: 3322 helix: 0.95 (0.15), residues: 1066 sheet: 0.55 (0.23), residues: 522 loop : -1.31 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 49 HIS 0.012 0.001 HIS K 26 PHE 0.011 0.002 PHE G 114 TYR 0.018 0.002 TYR E 290 ARG 0.005 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 1107) hydrogen bonds : angle 5.07359 ( 3094) covalent geometry : bond 0.00495 (27777) covalent geometry : angle 0.57911 (38045) *********************** 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 297 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 221 time to evaluate : 4.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.7067 (t80) REVERT: A 58 ARG cc_start: 0.6311 (ttp-170) cc_final: 0.5220 (tpm170) REVERT: A 121 LEU cc_start: 0.7166 (mt) cc_final: 0.6894 (mt) REVERT: A 228 TRP cc_start: 0.8555 (t-100) cc_final: 0.8343 (t-100) REVERT: A 366 LEU cc_start: 0.7265 (tp) cc_final: 0.7008 (tp) REVERT: E 52 ARG cc_start: 0.7089 (mtm180) cc_final: 0.6739 (mtm180) REVERT: F 216 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: F 240 ASP cc_start: 0.7945 (p0) cc_final: 0.7724 (p0) REVERT: F 319 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8420 (pt0) REVERT: G 51 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8411 (mp10) REVERT: G 87 ASP cc_start: 0.8496 (m-30) cc_final: 0.8074 (m-30) REVERT: G 94 ASN cc_start: 0.8591 (p0) cc_final: 0.8386 (p0) outliers start: 76 outliers final: 54 residues processed: 283 average time/residue: 0.5096 time to fit residues: 226.0049 Evaluate side-chains 263 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 285 optimal weight: 4.9990 chunk 309 optimal weight: 0.5980 chunk 325 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 276 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 265 optimal weight: 0.8980 chunk 312 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 ASN K 26 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.106259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.084959 restraints weight = 75899.497| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.16 r_work: 0.3188 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27777 Z= 0.136 Angle : 0.522 6.668 38045 Z= 0.271 Chirality : 0.040 0.246 4280 Planarity : 0.004 0.057 4785 Dihedral : 14.233 177.116 4609 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.76 % Allowed : 17.02 % Favored : 80.21 % 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 (0.15), residues: 3322 helix: 1.23 (0.16), residues: 1066 sheet: 0.60 (0.23), residues: 528 loop : -1.27 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 49 HIS 0.010 0.001 HIS A 203 PHE 0.010 0.001 PHE J 195 TYR 0.014 0.001 TYR D 304 ARG 0.004 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 1107) hydrogen bonds : angle 4.89094 ( 3094) covalent geometry : bond 0.00304 (27777) covalent geometry : angle 0.52153 (38045) *********************** 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 298 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 226 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.6996 (t80) REVERT: A 58 ARG cc_start: 0.6394 (ttp-170) cc_final: 0.6132 (ttp-170) REVERT: A 121 LEU cc_start: 0.7232 (mt) cc_final: 0.6945 (mt) REVERT: A 228 TRP cc_start: 0.8536 (t-100) cc_final: 0.8313 (t-100) REVERT: A 366 LEU cc_start: 0.7304 (tp) cc_final: 0.7051 (tp) REVERT: B 170 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8088 (ptm-80) REVERT: C 46 ASP cc_start: 0.5500 (p0) cc_final: 0.5088 (p0) REVERT: D 44 MET cc_start: 0.6960 (mpp) cc_final: 0.6535 (ptp) REVERT: F 216 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: F 319 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8374 (pt0) REVERT: G 51 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8348 (mp10) REVERT: G 87 ASP cc_start: 0.8465 (m-30) cc_final: 0.8061 (m-30) REVERT: G 94 ASN cc_start: 0.8595 (p0) cc_final: 0.8370 (p0) REVERT: G 159 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.7968 (m-70) REVERT: K 57 ASP cc_start: 0.7998 (p0) cc_final: 0.7675 (m-30) outliers start: 72 outliers final: 48 residues processed: 281 average time/residue: 0.4030 time to fit residues: 177.9689 Evaluate side-chains 262 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 146 ASN Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 153 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 283 optimal weight: 0.8980 chunk 214 optimal weight: 0.8980 chunk 327 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 314 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS H 343 HIS J 194 ASN K 26 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.106766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.085693 restraints weight = 72721.398| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.08 r_work: 0.3212 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27777 Z= 0.123 Angle : 0.514 7.003 38045 Z= 0.266 Chirality : 0.039 0.242 4280 Planarity : 0.004 0.059 4785 Dihedral : 14.154 177.255 4609 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.61 % Allowed : 17.68 % Favored : 79.72 % 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: -0.09 (0.15), residues: 3322 helix: 1.36 (0.16), residues: 1067 sheet: 0.60 (0.22), residues: 538 loop : -1.24 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 362 HIS 0.015 0.001 HIS K 26 PHE 0.010 0.001 PHE J 195 TYR 0.014 0.001 TYR D 304 ARG 0.004 0.000 ARG G 269 Details of bonding type rmsd hydrogen bonds : bond 0.03227 ( 1107) hydrogen bonds : angle 4.78877 ( 3094) covalent geometry : bond 0.00275 (27777) covalent geometry : angle 0.51440 (38045) *********************** 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 285 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 217 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.7050 (t80) REVERT: A 58 ARG cc_start: 0.6347 (ttp-170) cc_final: 0.6120 (ttp-170) REVERT: A 121 LEU cc_start: 0.7208 (mt) cc_final: 0.6936 (mt) REVERT: A 228 TRP cc_start: 0.8541 (t-100) cc_final: 0.8317 (t-100) REVERT: A 366 LEU cc_start: 0.7226 (tp) cc_final: 0.6972 (tp) REVERT: B 170 ARG cc_start: 0.8321 (ttp80) cc_final: 0.8043 (ptm-80) REVERT: C 46 ASP cc_start: 0.5455 (p0) cc_final: 0.5082 (p0) REVERT: D 44 MET cc_start: 0.6980 (mpp) cc_final: 0.6657 (ptp) REVERT: E 212 ASP cc_start: 0.7525 (m-30) cc_final: 0.7296 (m-30) REVERT: F 64 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7660 (ptm-80) REVERT: F 216 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: F 283 LEU cc_start: 0.8586 (mt) cc_final: 0.8276 (mt) REVERT: F 319 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8367 (pt0) REVERT: G 51 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8325 (mp10) REVERT: G 87 ASP cc_start: 0.8457 (m-30) cc_final: 0.8052 (m-30) REVERT: G 94 ASN cc_start: 0.8564 (p0) cc_final: 0.8347 (p0) REVERT: G 159 HIS cc_start: 0.8442 (OUTLIER) cc_final: 0.7950 (m-70) REVERT: J 37 MET cc_start: 0.8939 (mtm) cc_final: 0.8617 (mtm) outliers start: 68 outliers final: 54 residues processed: 273 average time/residue: 0.4190 time to fit residues: 177.7050 Evaluate side-chains 273 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 198 optimal weight: 0.6980 chunk 221 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 290 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 209 optimal weight: 0.8980 chunk 189 optimal weight: 0.0770 chunk 304 optimal weight: 7.9990 chunk 176 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN D 183 HIS E 260 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 HIS J 194 ASN K 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.107885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.086586 restraints weight = 66429.684| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.10 r_work: 0.3241 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27777 Z= 0.107 Angle : 0.504 7.318 38045 Z= 0.260 Chirality : 0.039 0.234 4280 Planarity : 0.004 0.091 4785 Dihedral : 14.087 179.475 4609 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.30 % Allowed : 18.06 % Favored : 79.64 % 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: 0.03 (0.15), residues: 3322 helix: 1.53 (0.16), residues: 1066 sheet: 0.65 (0.22), residues: 538 loop : -1.22 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 362 HIS 0.010 0.001 HIS A 203 PHE 0.011 0.001 PHE J 195 TYR 0.013 0.001 TYR H 290 ARG 0.007 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 1107) hydrogen bonds : angle 4.65279 ( 3094) covalent geometry : bond 0.00236 (27777) covalent geometry : angle 0.50365 (38045) *********************** 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 293 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 233 time to evaluate : 4.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.6986 (t80) REVERT: A 58 ARG cc_start: 0.6390 (ttp-170) cc_final: 0.6169 (ttp-170) REVERT: A 120 PHE cc_start: 0.7671 (t80) cc_final: 0.7347 (t80) REVERT: A 121 LEU cc_start: 0.7287 (mt) cc_final: 0.6980 (mt) REVERT: A 228 TRP cc_start: 0.8524 (t-100) cc_final: 0.8310 (t-100) REVERT: A 366 LEU cc_start: 0.7342 (tp) cc_final: 0.7098 (tp) REVERT: B 170 ARG cc_start: 0.8311 (ttp80) cc_final: 0.8047 (ptm-80) REVERT: C 46 ASP cc_start: 0.5159 (p0) cc_final: 0.4740 (p0) REVERT: D 44 MET cc_start: 0.7008 (mpp) cc_final: 0.6677 (ptp) REVERT: E 105 SER cc_start: 0.7540 (m) cc_final: 0.6974 (t) REVERT: E 212 ASP cc_start: 0.7485 (m-30) cc_final: 0.7277 (m-30) REVERT: F 64 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7643 (ptm-80) REVERT: F 216 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: F 283 LEU cc_start: 0.8482 (mt) cc_final: 0.8149 (mt) REVERT: G 87 ASP cc_start: 0.8419 (m-30) cc_final: 0.7979 (m-30) REVERT: G 94 ASN cc_start: 0.8548 (p0) cc_final: 0.8324 (p0) REVERT: J 37 MET cc_start: 0.8884 (mtm) cc_final: 0.8585 (mtm) REVERT: K 57 ASP cc_start: 0.8004 (p0) cc_final: 0.7669 (m-30) REVERT: K 126 ASN cc_start: 0.7478 (m-40) cc_final: 0.7276 (m110) outliers start: 60 outliers final: 45 residues processed: 278 average time/residue: 0.4883 time to fit residues: 211.3878 Evaluate side-chains 262 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 275 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS J 194 ASN K 26 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.106656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085471 restraints weight = 76021.729| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.14 r_work: 0.3197 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27777 Z= 0.152 Angle : 0.529 6.635 38045 Z= 0.273 Chirality : 0.040 0.225 4280 Planarity : 0.004 0.059 4785 Dihedral : 14.072 177.296 4606 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.34 % Allowed : 18.10 % Favored : 79.56 % 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 (0.15), residues: 3322 helix: 1.47 (0.16), residues: 1066 sheet: 0.62 (0.22), residues: 532 loop : -1.21 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 362 HIS 0.015 0.001 HIS K 25 PHE 0.010 0.001 PHE K 212 TYR 0.016 0.001 TYR D 304 ARG 0.008 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 1107) hydrogen bonds : angle 4.71635 ( 3094) covalent geometry : bond 0.00344 (27777) covalent geometry : angle 0.52852 (38045) *********************** 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 278 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 217 time to evaluate : 3.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.7014 (t80) REVERT: A 120 PHE cc_start: 0.7692 (t80) cc_final: 0.7352 (t80) REVERT: A 121 LEU cc_start: 0.7331 (mt) cc_final: 0.7032 (mt) REVERT: A 228 TRP cc_start: 0.8542 (t-100) cc_final: 0.8334 (t-100) REVERT: A 281 MET cc_start: 0.5865 (mmm) cc_final: 0.5455 (tpt) REVERT: A 366 LEU cc_start: 0.7281 (tp) cc_final: 0.7076 (tp) REVERT: B 170 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8081 (ptm-80) REVERT: C 46 ASP cc_start: 0.5251 (p0) cc_final: 0.4753 (p0) REVERT: D 44 MET cc_start: 0.7037 (mpp) cc_final: 0.6831 (ptp) REVERT: D 302 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7259 (mm-30) REVERT: E 105 SER cc_start: 0.7627 (m) cc_final: 0.7035 (t) REVERT: E 212 ASP cc_start: 0.7519 (m-30) cc_final: 0.7297 (m-30) REVERT: F 64 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7654 (ptm-80) REVERT: F 216 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: F 283 LEU cc_start: 0.8548 (mt) cc_final: 0.8221 (mt) REVERT: G 87 ASP cc_start: 0.8455 (m-30) cc_final: 0.8075 (m-30) REVERT: G 94 ASN cc_start: 0.8578 (p0) cc_final: 0.8359 (p0) REVERT: K 57 ASP cc_start: 0.8036 (p0) cc_final: 0.7715 (m-30) outliers start: 61 outliers final: 52 residues processed: 264 average time/residue: 0.5273 time to fit residues: 218.4469 Evaluate side-chains 267 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 212 time to evaluate : 4.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 263 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 191 optimal weight: 0.4980 chunk 1 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 332 optimal weight: 20.0000 chunk 117 optimal weight: 0.8980 chunk 14 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN F 319 GLN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS I 186 GLN J 26 HIS J 194 ASN K 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.084637 restraints weight = 58504.582| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.95 r_work: 0.3194 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27777 Z= 0.190 Angle : 0.563 7.983 38045 Z= 0.291 Chirality : 0.041 0.221 4280 Planarity : 0.004 0.058 4785 Dihedral : 14.092 176.198 4606 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.42 % Allowed : 18.29 % Favored : 79.29 % 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: -0.09 (0.15), residues: 3322 helix: 1.36 (0.16), residues: 1063 sheet: 0.60 (0.22), residues: 532 loop : -1.23 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 49 HIS 0.025 0.002 HIS K 25 PHE 0.011 0.001 PHE G 114 TYR 0.017 0.002 TYR D 304 ARG 0.013 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 1107) hydrogen bonds : angle 4.81793 ( 3094) covalent geometry : bond 0.00432 (27777) covalent geometry : angle 0.56343 (38045) ********************** 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 273 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 4.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6948 (t80) REVERT: A 120 PHE cc_start: 0.7685 (t80) cc_final: 0.7330 (t80) REVERT: A 121 LEU cc_start: 0.7342 (mt) cc_final: 0.7052 (mt) REVERT: A 281 MET cc_start: 0.5545 (mmm) cc_final: 0.5318 (tpt) REVERT: B 170 ARG cc_start: 0.8333 (ttp80) cc_final: 0.8050 (ptm-80) REVERT: C 46 ASP cc_start: 0.5012 (p0) cc_final: 0.4511 (p0) REVERT: D 302 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7199 (mm-30) REVERT: E 212 ASP cc_start: 0.7376 (m-30) cc_final: 0.7057 (m-30) REVERT: F 64 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7640 (ptm-80) REVERT: F 216 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: G 87 ASP cc_start: 0.8430 (m-30) cc_final: 0.8028 (m-30) REVERT: G 94 ASN cc_start: 0.8508 (p0) cc_final: 0.8293 (p0) REVERT: K 57 ASP cc_start: 0.8014 (p0) cc_final: 0.7671 (m-30) outliers start: 63 outliers final: 55 residues processed: 259 average time/residue: 0.4698 time to fit residues: 194.1111 Evaluate side-chains 257 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 199 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 15 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 176 optimal weight: 0.4980 chunk 227 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS I 186 GLN J 194 ASN K 26 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.106662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.085343 restraints weight = 75963.292| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.16 r_work: 0.3195 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27777 Z= 0.130 Angle : 0.530 6.899 38045 Z= 0.274 Chirality : 0.040 0.216 4280 Planarity : 0.004 0.058 4785 Dihedral : 14.073 176.658 4606 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.22 % Allowed : 18.44 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3322 helix: 1.45 (0.16), residues: 1063 sheet: 0.62 (0.23), residues: 532 loop : -1.21 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 228 HIS 0.015 0.001 HIS K 25 PHE 0.011 0.001 PHE J 195 TYR 0.017 0.001 TYR D 304 ARG 0.008 0.000 ARG K 35 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 1107) hydrogen bonds : angle 4.73682 ( 3094) covalent geometry : bond 0.00292 (27777) covalent geometry : angle 0.53030 (38045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18148.04 seconds wall clock time: 322 minutes 41.68 seconds (19361.68 seconds total)