Starting phenix.real_space_refine (version: dev) on Sat Feb 25 01:39:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/02_2023/7jzw_22582.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/02_2023/7jzw_22582.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/02_2023/7jzw_22582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/02_2023/7jzw_22582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/02_2023/7jzw_22582.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/02_2023/7jzw_22582.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 12": "OE1" <-> "OE2" Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 55": "OD1" <-> "OD2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ASP 76": "OD1" <-> "OD2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "C ASP 6": "OD1" <-> "OD2" Residue "C ASP 12": "OD1" <-> "OD2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ASP 272": "OD1" <-> "OD2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "E ASP 208": "OD1" <-> "OD2" Residue "E PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "D ASP 130": "OD1" <-> "OD2" Residue "D ASP 135": "OD1" <-> "OD2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D ASP 240": "OD1" <-> "OD2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 270": "OD1" <-> "OD2" Residue "D TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 294": "OD1" <-> "OD2" Residue "D ASP 334": "OD1" <-> "OD2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F ASP 53": "OD1" <-> "OD2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ASP 208": "OD1" <-> "OD2" Residue "F GLU 216": "OE1" <-> "OE2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 253": "OD1" <-> "OD2" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 322": "OD1" <-> "OD2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 38": "OD1" <-> "OD2" Residue "G ASP 82": "OD1" <-> "OD2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "G ASP 208": "OD1" <-> "OD2" Residue "G GLU 216": "OE1" <-> "OE2" Residue "G PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 240": "OD1" <-> "OD2" Residue "G ASP 270": "OD1" <-> "OD2" Residue "G TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 292": "OD1" <-> "OD2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H ASP 38": "OD1" <-> "OD2" Residue "H ASP 82": "OD1" <-> "OD2" Residue "H ARG 169": "NH1" <-> "NH2" Residue "H ASP 292": "OD1" <-> "OD2" Residue "H GLU 293": "OE1" <-> "OE2" Residue "H GLU 302": "OE1" <-> "OE2" Residue "H ASP 322": "OD1" <-> "OD2" Residue "H GLU 335": "OE1" <-> "OE2" Residue "I PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 65": "OE1" <-> "OE2" Residue "I ASP 82": "OD1" <-> "OD2" Residue "I ASP 130": "OD1" <-> "OD2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 169": "NH1" <-> "NH2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "I GLU 216": "OE1" <-> "OE2" Residue "I GLU 249": "OE1" <-> "OE2" Residue "I GLU 302": "OE1" <-> "OE2" Residue "I ASP 322": "OD1" <-> "OD2" Residue "I GLU 335": "OE1" <-> "OE2" Residue "J ASP 10": "OD1" <-> "OD2" Residue "J ASP 31": "OD1" <-> "OD2" Residue "J GLU 32": "OE1" <-> "OE2" Residue "J GLU 50": "OE1" <-> "OE2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J GLU 92": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 24266 Number of models: 1 Model: "" Number of chains: 11 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': 78} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 364 Unresolved non-hydrogen dihedrals: 232 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': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 192 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: {'PCIS': 1, 'PTRANS': 14, '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: {'PCIS': 1, 'PTRANS': 14, '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: "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: "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: "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: "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: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2554 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 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: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 760 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 14.53, per 1000 atoms: 0.60 Number of scatterers: 24266 At special positions: 0 Unit cell: (130.2, 157.5, 148.05, 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 29 16.00 P 60 15.00 O 4715 8.00 N 4422 7.00 C 15040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.62 Conformation dependent library (CDL) restraints added in 3.6 seconds 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5548 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 56 sheets defined 32.4% alpha, 22.8% beta 6 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 6.54 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.417A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 removed outlier: 3.663A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.600A pdb=" N GLU A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.500A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.785A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.658A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.819A pdb=" N GLU A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 removed outlier: 4.444A pdb=" N GLN A 273 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.515A pdb=" N SER A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 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 364 through 368 removed outlier: 4.044A pdb=" N ARG A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.590A pdb=" N ARG A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 381' Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.667A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.781A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 431 removed outlier: 4.376A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.902A pdb=" N LEU C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.889A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'B' and resid 33 through 49 removed outlier: 3.904A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.648A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.581A pdb=" N LEU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 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 322 through 331 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 152 through 163 Processing helix chain 'D' and resid 209 through 224 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 322 through 332 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.633A pdb=" N SER F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 209 through 223 removed outlier: 3.588A pdb=" N ALA F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 322 through 332 removed outlier: 3.504A pdb=" N LEU F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 209 through 223 removed outlier: 3.565A pdb=" N ALA G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 293 through 297 Processing helix chain 'G' and resid 322 through 331 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.739A pdb=" N SER H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 322 through 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 51 through 55 Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 152 through 163 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 5 through 14 removed outlier: 3.539A pdb=" N ILE J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR J 12 " --> pdb=" O ASP J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 78 Processing helix chain 'J' and resid 79 through 100 removed outlier: 3.690A pdb=" N VAL J 83 " --> pdb=" O ARG J 79 " (cutoff:3.500A) 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 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.211A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.211A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 254 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLY B 285 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY B 287 " --> pdb=" O PRO B 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA7, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.534A pdb=" N HIS C 3 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.534A pdb=" N HIS C 3 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.509A pdb=" N VAL C 184 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB2, first strand: chain 'B' and resid 54 through 60 removed outlier: 4.079A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.198A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AB5, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AB6, first strand: chain 'B' and resid 304 through 306 Processing sheet with id=AB7, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AB8, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.212A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 189 through 192 removed outlier: 6.553A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 63 through 70 Processing sheet with id=AC2, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC3, first strand: chain 'E' and resid 306 through 307 removed outlier: 3.519A pdb=" N VAL E 307 " --> pdb=" O LYS E 312 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS E 312 " --> pdb=" O VAL E 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AC5, first strand: chain 'D' and resid 38 through 39 removed outlier: 4.093A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA D 176 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL D 177 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP D 196 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 179 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG D 194 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE D 181 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA D 192 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HIS D 183 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D 188 " --> pdb=" O ARG D 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'D' and resid 63 through 66 removed outlier: 4.598A pdb=" N ALA D 101 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 248 through 249 removed outlier: 4.603A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AD1, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AD2, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AD3, first strand: chain 'F' and resid 38 through 39 removed outlier: 4.181A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG F 191 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD5, first strand: chain 'F' and resid 63 through 70 removed outlier: 3.671A pdb=" N GLY F 70 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN F 94 " --> pdb=" O GLY F 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD7, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.670A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 127 through 128 Processing sheet with id=AD9, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.040A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 189 through 192 removed outlier: 3.670A pdb=" N ARG G 191 " --> pdb=" O HIS G 183 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 63 through 70 removed outlier: 3.611A pdb=" N GLY G 70 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AE4, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.569A pdb=" N GLY H 353 " --> pdb=" O PHE H 33 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 38 through 39 removed outlier: 4.142A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 188 through 192 removed outlier: 6.731A pdb=" N HIS H 183 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA H 192 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE H 181 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 63 through 66 removed outlier: 4.576A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 69 through 70 removed outlier: 3.697A pdb=" N GLY H 70 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'H' and resid 248 through 249 removed outlier: 4.702A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AF2, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.653A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AF4, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.528A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL I 177 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASP I 196 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL I 179 " --> pdb=" O ARG I 194 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG I 194 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE I 181 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA I 192 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N HIS I 183 " --> pdb=" O ALA I 190 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AF6, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.729A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.729A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LYS I 261 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR I 97 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS I 263 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF9, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.665A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 17 through 21 removed outlier: 12.893A pdb=" N TRP J 28 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N VAL J 47 " --> pdb=" O TRP J 28 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE J 30 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY J 55 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 17 through 21 1050 hydrogen bonds defined for protein. 2925 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 9.00 Time building geometry restraints manager: 10.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5046 1.32 - 1.44: 5968 1.44 - 1.56: 13702 1.56 - 1.68: 120 1.68 - 1.80: 44 Bond restraints: 24880 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.337 1.382 -0.046 9.80e-03 1.04e+04 2.16e+01 bond pdb=" O3' A M 36 " pdb=" P C M 37 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.26e+01 bond pdb=" N LEU A 70 " pdb=" CA LEU A 70 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.32e-02 5.74e+03 8.10e+00 bond pdb=" N GLN H 186 " pdb=" CA GLN H 186 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.19e+00 bond pdb=" CG LEU D 229 " pdb=" CD1 LEU D 229 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.90e+00 ... (remaining 24875 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.35: 993 106.35 - 113.29: 13482 113.29 - 120.23: 9214 120.23 - 127.17: 9946 127.17 - 134.11: 441 Bond angle restraints: 34076 Sorted by residual: angle pdb=" O ARG H 185 " pdb=" C ARG H 185 " pdb=" N GLN H 186 " ideal model delta sigma weight residual 122.23 129.29 -7.06 1.33e+00 5.65e-01 2.82e+01 angle pdb=" C ARG F 185 " pdb=" N GLN F 186 " pdb=" CA GLN F 186 " ideal model delta sigma weight residual 120.82 128.71 -7.89 1.50e+00 4.44e-01 2.77e+01 angle pdb=" C GLN A 124 " pdb=" N TYR A 125 " pdb=" CA TYR A 125 " ideal model delta sigma weight residual 120.79 127.65 -6.86 1.39e+00 5.18e-01 2.44e+01 angle pdb=" C ARG I 185 " pdb=" N GLN I 186 " pdb=" CA GLN I 186 " ideal model delta sigma weight residual 120.38 126.93 -6.55 1.37e+00 5.33e-01 2.28e+01 angle pdb=" C ARG H 185 " pdb=" N GLN H 186 " pdb=" CA GLN H 186 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.25e+01 ... (remaining 34071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 14400 35.59 - 71.19: 365 71.19 - 106.78: 24 106.78 - 142.37: 1 142.37 - 177.96: 5 Dihedral angle restraints: 14795 sinusoidal: 6203 harmonic: 8592 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 53.90 146.10 1 1.50e+01 4.44e-03 7.81e+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 65.69 134.31 1 1.50e+01 4.44e-03 7.25e+01 dihedral pdb=" O4' C M 38 " pdb=" C1' C M 38 " pdb=" N1 C M 38 " pdb=" C2 C M 38 " ideal model delta sinusoidal sigma weight residual -128.00 49.96 -177.96 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 14792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3034 0.063 - 0.127: 682 0.127 - 0.190: 113 0.190 - 0.254: 6 0.254 - 0.317: 4 Chirality restraints: 3839 Sorted by residual: chirality pdb=" CB THR B 318 " pdb=" CA THR B 318 " pdb=" OG1 THR B 318 " pdb=" CG2 THR B 318 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE B 219 " pdb=" CA ILE B 219 " pdb=" CG1 ILE B 219 " pdb=" CG2 ILE B 219 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C1' U M 33 " pdb=" O4' U M 33 " pdb=" C2' U M 33 " pdb=" N1 U M 33 " both_signs ideal model delta sigma weight residual False 2.47 2.21 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3836 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.053 5.00e-02 4.00e+02 7.88e-02 9.95e+00 pdb=" N PRO A 72 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 73 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO C 74 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 103 " 0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO D 104 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 104 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 104 " 0.038 5.00e-02 4.00e+02 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4954 2.77 - 3.30: 21528 3.30 - 3.83: 42348 3.83 - 4.37: 51903 4.37 - 4.90: 87079 Nonbonded interactions: 207812 Sorted by model distance: nonbonded pdb=" OH TYR F 324 " pdb=" O SER G 73 " model vdw 2.237 2.440 nonbonded pdb=" OH TYR E 324 " pdb=" O SER F 73 " model vdw 2.237 2.440 nonbonded pdb=" OH TYR G 324 " pdb=" O SER H 73 " model vdw 2.255 2.440 nonbonded pdb=" OH TYR H 324 " pdb=" O SER I 73 " model vdw 2.256 2.440 nonbonded pdb=" O SER E 73 " pdb=" OH TYR D 324 " model vdw 2.266 2.440 ... (remaining 207807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 29 5.16 5 C 15040 2.51 5 N 4422 2.21 5 O 4715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 5.870 Check model and map are aligned: 0.350 Process input model: 67.570 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.210 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.080 24880 Z= 0.635 Angle : 0.973 10.119 34076 Z= 0.541 Chirality : 0.055 0.317 3839 Planarity : 0.007 0.079 4272 Dihedral : 16.209 177.963 9247 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.93 % Favored : 93.04 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.12), residues: 2959 helix: -2.82 (0.11), residues: 933 sheet: -1.31 (0.22), residues: 482 loop : -2.85 (0.12), residues: 1544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 285 time to evaluate : 2.720 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 288 average time/residue: 0.5372 time to fit residues: 217.3518 Evaluate side-chains 204 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 2.697 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2125 time to fit residues: 4.3854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 174 optimal weight: 0.5980 chunk 271 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN C 29 HIS ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 24880 Z= 0.179 Angle : 0.546 11.232 34076 Z= 0.288 Chirality : 0.040 0.201 3839 Planarity : 0.004 0.056 4272 Dihedral : 12.039 179.465 3987 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.75 % Favored : 94.22 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.13), residues: 2959 helix: -0.81 (0.15), residues: 950 sheet: -0.50 (0.23), residues: 460 loop : -2.44 (0.13), residues: 1549 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 2.957 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 251 average time/residue: 0.4962 time to fit residues: 179.2803 Evaluate side-chains 219 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 205 time to evaluate : 2.911 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3416 time to fit residues: 11.6115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 225 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 242 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 218 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN C 154 HIS ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN D 102 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN G 148 GLN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 319 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 24880 Z= 0.200 Angle : 0.531 11.588 34076 Z= 0.275 Chirality : 0.040 0.187 3839 Planarity : 0.004 0.052 4272 Dihedral : 11.784 179.140 3987 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.19 % Favored : 93.78 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.63 (0.14), residues: 2959 helix: 0.18 (0.16), residues: 954 sheet: -0.41 (0.23), residues: 492 loop : -2.22 (0.14), residues: 1513 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 215 time to evaluate : 2.716 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 234 average time/residue: 0.4831 time to fit residues: 166.0214 Evaluate side-chains 215 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 200 time to evaluate : 2.684 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2755 time to fit residues: 10.7375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 0.6980 chunk 204 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 258 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS E 91 GLN E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 242 GLN D 102 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 24880 Z= 0.189 Angle : 0.511 11.253 34076 Z= 0.265 Chirality : 0.039 0.183 3839 Planarity : 0.003 0.052 4272 Dihedral : 11.618 179.208 3987 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.98 % Favored : 93.98 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.15 (0.15), residues: 2959 helix: 0.74 (0.17), residues: 958 sheet: -0.17 (0.23), residues: 486 loop : -2.04 (0.14), residues: 1515 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 221 time to evaluate : 2.791 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 236 average time/residue: 0.4634 time to fit residues: 160.8203 Evaluate side-chains 214 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 203 time to evaluate : 2.812 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2407 time to fit residues: 8.8139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 0.4980 chunk 164 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 246 optimal weight: 0.6980 chunk 199 optimal weight: 0.1980 chunk 0 optimal weight: 40.0000 chunk 147 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN G 91 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 24880 Z= 0.182 Angle : 0.500 12.057 34076 Z= 0.259 Chirality : 0.039 0.182 3839 Planarity : 0.003 0.050 4272 Dihedral : 11.523 179.115 3987 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.02 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.89 (0.15), residues: 2959 helix: 1.05 (0.17), residues: 958 sheet: -0.02 (0.23), residues: 486 loop : -1.95 (0.14), residues: 1515 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 216 time to evaluate : 2.599 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 229 average time/residue: 0.4800 time to fit residues: 160.7648 Evaluate side-chains 198 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 189 time to evaluate : 2.727 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2444 time to fit residues: 7.6156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 2.9990 chunk 260 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 289 optimal weight: 5.9990 chunk 240 optimal weight: 0.0770 chunk 133 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN F 242 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.043 24880 Z= 0.448 Angle : 0.620 13.072 34076 Z= 0.318 Chirality : 0.044 0.192 3839 Planarity : 0.004 0.055 4272 Dihedral : 11.771 179.438 3987 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.27 % Favored : 92.70 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.09 (0.15), residues: 2959 helix: 0.85 (0.17), residues: 956 sheet: -0.29 (0.22), residues: 514 loop : -2.02 (0.15), residues: 1489 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 2.763 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 220 average time/residue: 0.5104 time to fit residues: 163.5526 Evaluate side-chains 207 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 196 time to evaluate : 2.667 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2786 time to fit residues: 8.8805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 164 optimal weight: 0.4980 chunk 211 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 288 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 175 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN F 159 HIS ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 24880 Z= 0.184 Angle : 0.511 12.202 34076 Z= 0.265 Chirality : 0.039 0.181 3839 Planarity : 0.003 0.052 4272 Dihedral : 11.581 179.476 3987 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.02 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.77 (0.15), residues: 2959 helix: 1.20 (0.17), residues: 959 sheet: 0.03 (0.23), residues: 474 loop : -1.91 (0.15), residues: 1526 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 200 time to evaluate : 2.779 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 210 average time/residue: 0.5113 time to fit residues: 155.0444 Evaluate side-chains 194 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 187 time to evaluate : 3.001 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3731 time to fit residues: 7.9374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 196 optimal weight: 0.7980 chunk 142 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 GLN D 348 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 24880 Z= 0.191 Angle : 0.510 12.129 34076 Z= 0.264 Chirality : 0.039 0.180 3839 Planarity : 0.003 0.052 4272 Dihedral : 11.486 179.127 3987 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.81 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.64 (0.15), residues: 2959 helix: 1.35 (0.17), residues: 956 sheet: 0.09 (0.23), residues: 474 loop : -1.85 (0.15), residues: 1529 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 198 time to evaluate : 2.821 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 204 average time/residue: 0.5060 time to fit residues: 149.6490 Evaluate side-chains 192 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 2.885 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2072 time to fit residues: 5.1502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 251 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 210 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 chunk 253 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 24880 Z= 0.243 Angle : 0.530 12.346 34076 Z= 0.273 Chirality : 0.040 0.182 3839 Planarity : 0.004 0.052 4272 Dihedral : 11.501 178.497 3987 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.81 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.63 (0.15), residues: 2959 helix: 1.35 (0.17), residues: 956 sheet: 0.02 (0.23), residues: 492 loop : -1.82 (0.15), residues: 1511 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 2.808 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 197 average time/residue: 0.5423 time to fit residues: 153.3612 Evaluate side-chains 192 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 3.118 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2511 time to fit residues: 6.0435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 0.7980 chunk 283 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 197 optimal weight: 0.0980 chunk 297 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 237 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 24880 Z= 0.160 Angle : 0.497 12.104 34076 Z= 0.257 Chirality : 0.039 0.181 3839 Planarity : 0.003 0.052 4272 Dihedral : 11.376 179.632 3987 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.46 (0.15), residues: 2959 helix: 1.53 (0.17), residues: 957 sheet: 0.16 (0.23), residues: 474 loop : -1.75 (0.15), residues: 1528 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 2.738 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 203 average time/residue: 0.5301 time to fit residues: 154.2875 Evaluate side-chains 192 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 2.661 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3454 time to fit residues: 4.0821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 0.8980 chunk 252 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 218 optimal weight: 0.0020 chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 237 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 43 optimal weight: 0.0070 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.094666 restraints weight = 48848.217| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.58 r_work: 0.2925 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 24880 Z= 0.144 Angle : 0.491 12.082 34076 Z= 0.253 Chirality : 0.039 0.180 3839 Planarity : 0.003 0.052 4272 Dihedral : 11.288 179.636 3987 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.33 (0.15), residues: 2959 helix: 1.66 (0.17), residues: 957 sheet: 0.22 (0.23), residues: 474 loop : -1.69 (0.15), residues: 1528 =============================================================================== Job complete usr+sys time: 4608.65 seconds wall clock time: 85 minutes 28.08 seconds (5128.08 seconds total)