Starting phenix.real_space_refine (version: dev) on Sun Feb 19 11:48:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/02_2023/6wkw_21811_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/02_2023/6wkw_21811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/02_2023/6wkw_21811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/02_2023/6wkw_21811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/02_2023/6wkw_21811_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/02_2023/6wkw_21811_updated.pdb" } resolution = 3.6 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= 0.007 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 "D ASP 53": "OD1" <-> "OD2" Residue "D PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 61": "OD1" <-> "OD2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 91": "OD1" <-> "OD2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 109": "OD1" <-> "OD2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 287": "OE1" <-> "OE2" Residue "D PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C GLU 351": "OE1" <-> "OE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B ASP 255": "OD1" <-> "OD2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 296": "OD1" <-> "OD2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 47": "OE1" <-> "OE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10037 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 2403 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 329, 2396 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 319} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 104 Conformer: "B" Number of residues, atoms: 329, 2396 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 319} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 104 bond proxies already assigned to first conformer: 2425 Chain: "C" Number of atoms: 2502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2495 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 320} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 330, 2495 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 320} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 2527 Chain: "B" Number of atoms: 2463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2456 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 7, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 76 Conformer: "B" Number of residues, atoms: 330, 2456 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 7, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 76 bond proxies already assigned to first conformer: 2488 Chain: "A" Number of atoms: 2493 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2484 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 53 Conformer: "B" Number of residues, atoms: 330, 2484 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 53 bond proxies already assigned to first conformer: 2516 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N HIS C 250 " occ=0.88 ... (8 atoms not shown) pdb=" NE2 HIS C 250 " occ=0.88 residue: pdb=" N TYR A 234 " occ=0.77 ... (10 atoms not shown) pdb=" OH TYR A 234 " occ=0.77 residue: pdb=" N AGLN A 328 " occ=0.55 ... (16 atoms not shown) pdb=" NE2BGLN A 328 " occ=0.45 Time building chain proxies: 10.72, per 1000 atoms: 1.07 Number of scatterers: 10037 At special positions: 0 Unit cell: (104.4, 94.83, 81.78, 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 49 16.00 P 8 15.00 O 1914 8.00 N 1779 7.00 C 6287 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.94 Conformation dependent library (CDL) restraints added in 3.0 seconds 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2462 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 15 sheets defined 29.2% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 71 through 74 No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 89 through 92 No H-bonds generated for 'chain 'D' and resid 89 through 92' Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 134 through 146 removed outlier: 3.596A pdb=" N HIS D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 165 through 171 removed outlier: 3.796A pdb=" N ARG D 169 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.908A pdb=" N VAL D 195 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 235 removed outlier: 4.166A pdb=" N TYR D 234 " --> pdb=" O GLN D 230 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN D 235 " --> pdb=" O ASP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 278 through 287 removed outlier: 4.623A pdb=" N GLN D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU D 287 " --> pdb=" O GLN D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 344 removed outlier: 4.375A pdb=" N ARG D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 337 " --> pdb=" O MET D 333 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 113 through 116 No H-bonds generated for 'chain 'C' and resid 113 through 116' Processing helix chain 'C' and resid 134 through 146 removed outlier: 3.744A pdb=" N LEU C 143 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 157 Processing helix chain 'C' and resid 165 through 168 No H-bonds generated for 'chain 'C' and resid 165 through 168' Processing helix chain 'C' and resid 190 through 196 removed outlier: 4.294A pdb=" N VAL C 195 " --> pdb=" O THR C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 255 through 260 removed outlier: 3.639A pdb=" N LYS C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 255 through 260' Processing helix chain 'C' and resid 273 through 275 No H-bonds generated for 'chain 'C' and resid 273 through 275' Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 330 through 346 removed outlier: 3.836A pdb=" N GLU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 51 No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 72 through 75 No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 89 through 92 No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 113 through 119 removed outlier: 4.209A pdb=" N GLU B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 removed outlier: 3.958A pdb=" N ASP B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 146 No H-bonds generated for 'chain 'B' and resid 143 through 146' Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 165 through 171 removed outlier: 4.013A pdb=" N GLU B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 198 removed outlier: 3.564A pdb=" N ARG B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 278 through 286 removed outlier: 3.839A pdb=" N GLN B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 346 removed outlier: 4.732A pdb=" N ARG B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 344 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.908A pdb=" N ASN A 74 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.940A pdb=" N GLU A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LYS A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 94' Processing helix chain 'A' and resid 113 through 118 removed outlier: 4.148A pdb=" N GLU A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 3.603A pdb=" N ALA A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 156 removed outlier: 3.598A pdb=" N GLN A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 removed outlier: 3.583A pdb=" N ARG A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 removed outlier: 3.676A pdb=" N VAL A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 220 No H-bonds generated for 'chain 'A' and resid 217 through 220' Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.553A pdb=" N GLN A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 329 through 343 removed outlier: 3.836A pdb=" N GLU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing sheet with id= A, first strand: chain 'D' and resid 100 through 103 removed outlier: 7.156A pdb=" N ALA D 122 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ARG D 103 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS D 124 " --> pdb=" O ARG D 103 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'D' and resid 266 through 268 removed outlier: 3.504A pdb=" N CYS D 238 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER D 205 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU D 185 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE D 207 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLN D 224 " --> pdb=" O PHE D 208 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 293 through 295 Processing sheet with id= D, first strand: chain 'C' and resid 36 through 38 removed outlier: 3.838A pdb=" N LEU C 38 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 100 through 103 removed outlier: 6.716A pdb=" N ALA C 122 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ARG C 103 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS C 124 " --> pdb=" O ARG C 103 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 182 through 185 removed outlier: 6.184A pdb=" N SER C 205 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU C 185 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 207 " --> pdb=" O LEU C 185 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 238 through 241 removed outlier: 6.537A pdb=" N PHE C 266 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N LEU C 241 " --> pdb=" O PHE C 266 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL C 268 " --> pdb=" O LEU C 241 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 293 through 295 Processing sheet with id= I, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.374A pdb=" N ALA B 122 " --> pdb=" O ILE B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.523A pdb=" N TYR B 209 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N CYS B 238 " --> pdb=" O GLY B 184 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE B 186 " --> pdb=" O CYS B 238 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER B 240 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE B 266 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU B 241 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL B 268 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 293 through 295 Processing sheet with id= L, first strand: chain 'A' and resid 35 through 38 removed outlier: 6.332A pdb=" N THR A 56 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU A 38 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA A 58 " --> pdb=" O LEU A 38 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.716A pdb=" N VAL A 100 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N MET A 81 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 102 " --> pdb=" O MET A 81 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 239 through 241 removed outlier: 6.384A pdb=" N GLY A 184 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 207 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLN A 224 " --> pdb=" O PHE A 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'A' and resid 293 through 295 154 hydrogen bonds defined for protein. 456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1716 1.29 - 1.42: 2560 1.42 - 1.55: 5842 1.55 - 1.67: 28 1.67 - 1.80: 76 Bond restraints: 10222 Sorted by residual: bond pdb=" C3B NAD C 401 " pdb=" C4B NAD C 401 " ideal model delta sigma weight residual 1.523 1.229 0.294 2.00e-02 2.50e+03 2.16e+02 bond pdb=" C3B NAD D 401 " pdb=" C4B NAD D 401 " ideal model delta sigma weight residual 1.523 1.231 0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C3B NAD B 401 " pdb=" C4B NAD B 401 " ideal model delta sigma weight residual 1.523 1.233 0.290 2.00e-02 2.50e+03 2.11e+02 bond pdb=" C3B NAD A 401 " pdb=" C4B NAD A 401 " ideal model delta sigma weight residual 1.523 1.234 0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C1B NAD A 401 " pdb=" C2B NAD A 401 " ideal model delta sigma weight residual 1.534 1.268 0.266 2.00e-02 2.50e+03 1.76e+02 ... (remaining 10217 not shown) Histogram of bond angle deviations from ideal: 98.90 - 106.32: 236 106.32 - 113.74: 5943 113.74 - 121.17: 5110 121.17 - 128.59: 2587 128.59 - 136.02: 71 Bond angle restraints: 13947 Sorted by residual: angle pdb=" N VAL D 46 " pdb=" CA VAL D 46 " pdb=" C VAL D 46 " ideal model delta sigma weight residual 112.12 107.48 4.64 8.40e-01 1.42e+00 3.05e+01 angle pdb=" N VAL B 46 " pdb=" CA VAL B 46 " pdb=" C VAL B 46 " ideal model delta sigma weight residual 113.53 108.27 5.26 9.80e-01 1.04e+00 2.88e+01 angle pdb=" N ILE B 345 " pdb=" CA ILE B 345 " pdb=" C ILE B 345 " ideal model delta sigma weight residual 112.90 107.89 5.01 9.60e-01 1.09e+00 2.72e+01 angle pdb=" N GLY B 274 " pdb=" CA GLY B 274 " pdb=" C GLY B 274 " ideal model delta sigma weight residual 115.63 108.05 7.58 1.49e+00 4.50e-01 2.59e+01 angle pdb=" N LEU B 331 " pdb=" CA LEU B 331 " pdb=" C LEU B 331 " ideal model delta sigma weight residual 114.31 108.11 6.20 1.29e+00 6.01e-01 2.31e+01 ... (remaining 13942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5401 17.43 - 34.85: 496 34.85 - 52.28: 82 52.28 - 69.71: 17 69.71 - 87.14: 12 Dihedral angle restraints: 6008 sinusoidal: 2189 harmonic: 3819 Sorted by residual: dihedral pdb=" CA ILE A 349 " pdb=" C ILE A 349 " pdb=" N PRO A 350 " pdb=" CA PRO A 350 " ideal model delta harmonic sigma weight residual -180.00 -131.82 -48.18 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" CA VAL B 77 " pdb=" C VAL B 77 " pdb=" N GLY B 78 " pdb=" CA GLY B 78 " ideal model delta harmonic sigma weight residual -180.00 -146.60 -33.40 0 5.00e+00 4.00e-02 4.46e+01 dihedral pdb=" CA LEU C 38 " pdb=" C LEU C 38 " pdb=" N LEU C 39 " pdb=" CA LEU C 39 " ideal model delta harmonic sigma weight residual 180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 6005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1357 0.074 - 0.147: 262 0.147 - 0.221: 12 0.221 - 0.295: 6 0.295 - 0.369: 4 Chirality restraints: 1641 Sorted by residual: chirality pdb=" C3D NAD B 401 " pdb=" C2D NAD B 401 " pdb=" C4D NAD B 401 " pdb=" O3D NAD B 401 " both_signs ideal model delta sigma weight residual False -2.73 -2.36 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C3D NAD D 401 " pdb=" C2D NAD D 401 " pdb=" C4D NAD D 401 " pdb=" O3D NAD D 401 " both_signs ideal model delta sigma weight residual False -2.73 -2.36 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C3D NAD A 401 " pdb=" C2D NAD A 401 " pdb=" C4D NAD A 401 " pdb=" O3D NAD A 401 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 1638 not shown) Planarity restraints: 1809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 349 " 0.064 5.00e-02 4.00e+02 9.66e-02 1.49e+01 pdb=" N PRO A 350 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 350 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 350 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 188 " 0.026 2.00e-02 2.50e+03 2.37e-02 9.82e+00 pdb=" CG PHE C 188 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE C 188 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 188 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 188 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 188 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 188 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 357 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C VAL B 357 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL B 357 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN B 358 " 0.012 2.00e-02 2.50e+03 ... (remaining 1806 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 209 2.63 - 3.20: 9626 3.20 - 3.77: 15132 3.77 - 4.33: 22095 4.33 - 4.90: 36423 Nonbonded interactions: 83485 Sorted by model distance: nonbonded pdb=" OD2 ASP B 40 " pdb=" OG1 THR B 84 " model vdw 2.066 2.440 nonbonded pdb=" OD1 ASN B 246 " pdb=" ND2 ASN B 249 " model vdw 2.103 2.520 nonbonded pdb=" ND1 HIS A 251 " pdb=" OD1 ASP A 277 " model vdw 2.107 2.520 nonbonded pdb=" OE1 GLU B 132 " pdb=" NH2 ARG B 198 " model vdw 2.119 2.520 nonbonded pdb=" OD1 ASP A 296 " pdb=" OG1 THR A 319 " model vdw 2.143 2.440 ... (remaining 83480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 33 and (name N or name CA or name C or name O or name CB \ )) or resid 34 through 43 or (resid 44 and (name N or name CA or name C or name \ O or name CB )) or resid 45 through 47 or (resid 48 and (name N or name CA or na \ me C or name O or name CB )) or resid 49 through 53 or (resid 54 through 56 and \ (name N or name CA or name C or name O or name CB )) or resid 57 through 62 or ( \ resid 63 through 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 68 or (resid 70 through 72 and (name N or name CA or name C or \ name O or name CB )) or resid 73 or (resid 74 and (name N or name CA or name C o \ r name O or name CB or name CG )) or (resid 75 through 76 and (name N or name CA \ or name C or name O or name CB )) or resid 77 through 91 or (resid 92 through 9 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 98 or (resid \ 99 and (name N or name CA or name C or name O or name CB )) or resid 100 throug \ h 160 or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG )) or resid 162 through 163 or (resid 164 and (name N or name CA or name C \ or name O or name CB )) or resid 165 through 213 or (resid 214 and (name N or na \ me CA or name C or name O or name CB )) or resid 215 through 233 or (resid 234 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 235 \ through 246 or (resid 247 and (name N or name CA or name C or name O or name CB \ )) or resid 248 through 249 or resid 251 through 254 or (resid 255 and (name N o \ r name CA or name C or name O or name CB )) or resid 256 through 258 or (resid 2 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 260 through \ 285 or (resid 286 and (name N or name CA or name C or name O or name CB )) or r \ esid 287 through 288 or (resid 289 and (name N or name CA or name C or name O or \ name CB )) or resid 290 or (resid 291 and (name N or name CA or name C or name \ O or name CB )) or resid 292 through 306 or (resid 307 and (name N or name CA or \ name C or name O or name CB )) or resid 308 through 310 or (resid 311 through 3 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 314 through \ 327 or resid 329 through 334 or (resid 335 and (name N or name CA or name C or \ name O or name CB or name CG )) or resid 336 through 341 or (resid 342 and (name \ N or name CA or name C or name O or name CB )) or resid 343 through 344 or (res \ id 345 through 346 and (name N or name CA or name C or name O or name CB )) or r \ esid 347 or (resid 348 and (name N or name CA or name C or name O or name CB )) \ or resid 349 through 350 or (resid 351 and (name N or name CA or name C or name \ O or name CB )) or resid 352 through 353 or (resid 354 and (name N or name CA or \ name C or name O or name CB )) or resid 355 through 358 or (resid 359 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 360 or (resi \ d 361 and (name N or name CA or name C or name O or name CB )) or resid 401)) selection = (chain 'B' and (resid 33 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 47 or (resid 48 and (name N or nam \ e CA or name C or name O or name CB )) or resid 49 through 53 or (resid 54 throu \ gh 56 and (name N or name CA or name C or name O or name CB )) or resid 57 throu \ gh 65 or (resid 66 and (name N or name CA or name C or name O or name CB )) or r \ esid 67 through 68 or (resid 70 through 72 and (name N or name CA or name C or n \ ame O or name CB )) or resid 73 or (resid 74 and (name N or name CA or name C or \ name O or name CB or name CG )) or resid 75 through 91 or (resid 92 through 97 \ and (name N or name CA or name C or name O or name CB )) or resid 98 through 156 \ or (resid 157 and (name N or name CA or name C or name O or name CB or name CG \ )) or resid 158 through 160 or (resid 161 and (name N or name CA or name C or na \ me O or name CB or name CG )) or resid 162 through 163 or (resid 164 and (name N \ or name CA or name C or name O or name CB )) or resid 165 through 169 or (resid \ 170 and (name N or name CA or name C or name O or name CB )) or resid 171 throu \ gh 206 or (resid 207 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2)) or resid 208 through 216 or (resid 217 and (name N or name \ CA or name C or name O or name CB or name CG1 or name CG2)) or resid 218 through \ 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) or r \ esid 225 through 229 or (resid 230 and (name N or name CA or name C or name O or \ name CB )) or resid 231 through 246 or (resid 247 and (name N or name CA or nam \ e C or name O or name CB )) or resid 248 through 249 or resid 251 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB )) or resid 25 \ 6 through 278 or (resid 279 through 280 and (name N or name CA or name C or name \ O or name CB )) or resid 281 through 285 or (resid 286 and (name N or name CA o \ r name C or name O or name CB )) or resid 287 through 310 or (resid 311 through \ 313 and (name N or name CA or name C or name O or name CB )) or resid 314 throug \ h 327 or resid 329 through 334 or (resid 335 and (name N or name CA or name C or \ name O or name CB or name CG )) or resid 336 through 344 or (resid 345 through \ 346 and (name N or name CA or name C or name O or name CB )) or resid 347 throug \ h 350 or (resid 351 and (name N or name CA or name C or name O or name CB )) or \ resid 352 through 353 or (resid 354 and (name N or name CA or name C or name O o \ r name CB )) or resid 355 through 360 or (resid 361 and (name N or name CA or na \ me C or name O or name CB )) or resid 401)) selection = (chain 'C' and ((resid 33 and (name N or name CA or name C or name O or name CB \ )) or resid 34 through 41 or (resid 42 and (name N or name CA or name C or name \ O or name CB )) or resid 43 or (resid 44 and (name N or name CA or name C or nam \ e O or name CB )) or resid 45 through 47 or (resid 48 and (name N or name CA or \ name C or name O or name CB )) or resid 49 through 51 or (resid 52 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 53 or (resid 54 \ through 56 and (name N or name CA or name C or name O or name CB )) or resid 57 \ through 62 or (resid 63 through 64 and (name N or name CA or name C or name O or \ name CB )) or resid 65 or (resid 66 and (name N or name CA or name C or name O \ or name CB )) or resid 67 through 68 or (resid 70 through 72 and (name N or name \ CA or name C or name O or name CB )) or resid 73 or (resid 74 and (name N or na \ me CA or name C or name O or name CB or name CG )) or (resid 75 through 76 and ( \ name N or name CA or name C or name O or name CB )) or resid 77 through 89 or (r \ esid 90 and (name N or name CA or name C or name O or name CB )) or resid 91 or \ (resid 92 through 97 and (name N or name CA or name C or name O or name CB )) or \ resid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) \ or resid 100 through 113 or (resid 114 through 116 and (name N or name CA or nam \ e C or name O or name CB )) or resid 117 through 156 or (resid 157 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 158 through 206 \ or (resid 207 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 208 through 213 or (resid 214 and (name N or name CA or n \ ame C or name O or name CB )) or resid 215 through 216 or (resid 217 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2)) or resid 21 \ 8 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 229 or (resid 230 and (name N or name CA or name C or \ name O or name CB )) or resid 231 through 246 or (resid 247 and (name N or name \ CA or name C or name O or name CB )) or resid 248 through 249 or resid 251 throu \ gh 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) or \ resid 256 through 258 or (resid 259 and (name N or name CA or name C or name O \ or name CB )) or resid 260 through 285 or (resid 286 and (name N or name CA or n \ ame C or name O or name CB )) or resid 287 through 288 or (resid 289 and (name N \ or name CA or name C or name O or name CB )) or resid 290 through 326 or (resid \ 327 and (name N or name CA or name C or name O or name CB )) or resid 329 throu \ gh 334 or (resid 335 and (name N or name CA or name C or name O or name CB or na \ me CG )) or resid 336 through 341 or (resid 342 and (name N or name CA or name C \ or name O or name CB )) or resid 343 through 344 or (resid 345 through 346 and \ (name N or name CA or name C or name O or name CB )) or resid 347 through 350 or \ (resid 351 and (name N or name CA or name C or name O or name CB )) or resid 35 \ 2 through 358 or (resid 359 and (name N or name CA or name C or name O or name C \ B or name CG )) or resid 360 or (resid 361 and (name N or name CA or name C or n \ ame O or name CB )) or resid 401)) selection = (chain 'D' and ((resid 33 and (name N or name CA or name C or name O or name CB \ )) or resid 34 through 63 or (resid 64 and (name N or name CA or name C or name \ O or name CB )) or resid 65 through 68 or resid 70 through 93 or (resid 94 throu \ gh 97 and (name N or name CA or name C or name O or name CB )) or resid 98 throu \ gh 156 or (resid 157 and (name N or name CA or name C or name O or name CB or na \ me CG )) or resid 158 through 160 or (resid 161 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 162 through 163 or (resid 164 and ( \ name N or name CA or name C or name O or name CB )) or resid 165 through 216 or \ (resid 217 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2)) or resid 218 through 223 or (resid 224 and (name N or name CA or name \ C or name O or name CB )) or resid 225 through 229 or (resid 230 and (name N or \ name CA or name C or name O or name CB )) or resid 231 through 233 or (resid 23 \ 4 and (name N or name CA or name C or name O or name CB or name CG )) or resid 2 \ 35 through 249 or resid 251 through 258 or (resid 259 and (name N or name CA or \ name C or name O or name CB )) or resid 260 through 288 or (resid 289 and (name \ N or name CA or name C or name O or name CB )) or resid 290 or (resid 291 and (n \ ame N or name CA or name C or name O or name CB )) or resid 292 through 306 or ( \ resid 307 and (name N or name CA or name C or name O or name CB )) or resid 308 \ through 327 or resid 329 through 353 or (resid 354 and (name N or name CA or nam \ e C or name O or name CB )) or resid 355 through 361 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 49 5.16 5 C 6287 2.51 5 N 1779 2.21 5 O 1914 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.720 Check model and map are aligned: 0.130 Process input model: 34.860 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 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 : 0.017 0.294 10222 Z= 1.130 Angle : 1.193 12.940 13947 Z= 0.656 Chirality : 0.059 0.369 1641 Planarity : 0.005 0.097 1809 Dihedral : 14.386 87.135 3546 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.59 % Favored : 87.26 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % 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: -5.89 (0.17), residues: 1317 helix: -4.30 (0.13), residues: 474 sheet: -4.68 (0.29), residues: 159 loop : -3.41 (0.20), residues: 684 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 1.296 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 68 average time/residue: 0.3378 time to fit residues: 30.8122 Evaluate side-chains 48 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0963 time to fit residues: 1.7543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 ASN ** D 250 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 163 GLN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN B 149 ASN B 244 ASN B 355 ASN ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 83 HIS A 149 ASN A 242 HIS A 328 GLN B A 355 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 10222 Z= 0.243 Angle : 0.611 10.084 13947 Z= 0.316 Chirality : 0.045 0.186 1641 Planarity : 0.004 0.082 1809 Dihedral : 6.147 40.396 1456 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.48 % Favored : 92.37 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -4.94 (0.19), residues: 1317 helix: -3.36 (0.18), residues: 470 sheet: -4.01 (0.29), residues: 196 loop : -2.90 (0.22), residues: 651 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 1.296 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 73 average time/residue: 0.2254 time to fit residues: 24.6098 Evaluate side-chains 57 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0998 time to fit residues: 2.9132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 106 optimal weight: 0.0000 chunk 118 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 HIS D 149 ASN ** D 250 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10222 Z= 0.199 Angle : 0.563 9.261 13947 Z= 0.287 Chirality : 0.044 0.215 1641 Planarity : 0.004 0.078 1809 Dihedral : 5.592 38.719 1456 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.86 % Favored : 91.99 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % 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: -4.23 (0.20), residues: 1317 helix: -2.63 (0.20), residues: 465 sheet: -3.72 (0.32), residues: 170 loop : -2.66 (0.22), residues: 682 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 1.111 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 62 average time/residue: 0.2079 time to fit residues: 20.1081 Evaluate side-chains 52 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 overall best weight: 2.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 ASN ** D 250 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 10222 Z= 0.310 Angle : 0.597 9.037 13947 Z= 0.304 Chirality : 0.045 0.188 1641 Planarity : 0.004 0.075 1809 Dihedral : 5.679 40.098 1456 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.54 % Favored : 91.30 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -3.89 (0.21), residues: 1317 helix: -2.36 (0.21), residues: 471 sheet: -3.49 (0.33), residues: 164 loop : -2.48 (0.22), residues: 682 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 51 time to evaluate : 1.197 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 63 average time/residue: 0.2103 time to fit residues: 20.5794 Evaluate side-chains 58 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0989 time to fit residues: 3.2229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 0.0270 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 ASN ** D 250 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 10222 Z= 0.237 Angle : 0.572 12.255 13947 Z= 0.287 Chirality : 0.044 0.183 1641 Planarity : 0.003 0.069 1809 Dihedral : 5.452 40.327 1456 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.40 % Favored : 92.45 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -3.57 (0.21), residues: 1317 helix: -1.99 (0.22), residues: 467 sheet: -3.44 (0.33), residues: 170 loop : -2.32 (0.23), residues: 680 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 1.305 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 0.2068 time to fit residues: 20.1110 Evaluate side-chains 52 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0996 time to fit residues: 1.9769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 ASN ** D 250 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 10222 Z= 0.189 Angle : 0.556 11.698 13947 Z= 0.275 Chirality : 0.043 0.163 1641 Planarity : 0.003 0.058 1809 Dihedral : 5.210 40.849 1456 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.32 % Favored : 92.52 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -3.23 (0.22), residues: 1317 helix: -1.63 (0.23), residues: 467 sheet: -3.20 (0.34), residues: 170 loop : -2.20 (0.23), residues: 680 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 1.201 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 0.2001 time to fit residues: 19.2544 Evaluate side-chains 54 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1062 time to fit residues: 1.8833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 71 optimal weight: 0.3980 chunk 106 optimal weight: 6.9990 chunk 70 optimal weight: 0.0670 chunk 126 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 overall best weight: 1.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 ASN ** D 250 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 10222 Z= 0.267 Angle : 0.588 12.019 13947 Z= 0.291 Chirality : 0.044 0.182 1641 Planarity : 0.003 0.053 1809 Dihedral : 5.319 40.954 1456 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.70 % Favored : 92.14 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -3.02 (0.22), residues: 1317 helix: -1.47 (0.23), residues: 474 sheet: -3.34 (0.34), residues: 155 loop : -2.03 (0.23), residues: 688 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 1.040 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 55 average time/residue: 0.2024 time to fit residues: 17.5511 Evaluate side-chains 51 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0948 time to fit residues: 1.5840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 ASN D 250 HIS A D 250 HIS B ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 10222 Z= 0.145 Angle : 0.554 13.509 13947 Z= 0.270 Chirality : 0.043 0.169 1641 Planarity : 0.003 0.045 1809 Dihedral : 4.986 40.691 1456 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.25 % Favored : 93.59 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -2.79 (0.22), residues: 1317 helix: -1.10 (0.24), residues: 471 sheet: -2.90 (0.35), residues: 170 loop : -2.09 (0.23), residues: 676 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 1.239 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 62 average time/residue: 0.2147 time to fit residues: 20.4516 Evaluate side-chains 56 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1023 time to fit residues: 1.6958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 ASN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 HIS ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 10222 Z= 0.151 Angle : 0.538 12.790 13947 Z= 0.265 Chirality : 0.043 0.178 1641 Planarity : 0.003 0.040 1809 Dihedral : 4.869 41.844 1456 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.64 % Favored : 93.21 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -2.70 (0.22), residues: 1317 helix: -0.95 (0.24), residues: 489 sheet: -2.73 (0.35), residues: 170 loop : -2.17 (0.23), residues: 658 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 1.187 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 61 average time/residue: 0.2036 time to fit residues: 19.6251 Evaluate side-chains 53 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 86 optimal weight: 0.0170 chunk 130 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 10222 Z= 0.136 Angle : 0.536 15.149 13947 Z= 0.263 Chirality : 0.042 0.162 1641 Planarity : 0.003 0.040 1809 Dihedral : 4.802 42.556 1456 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.33 % Favored : 93.59 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -2.37 (0.23), residues: 1317 helix: -0.59 (0.25), residues: 480 sheet: -2.55 (0.37), residues: 169 loop : -2.04 (0.23), residues: 668 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.186 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2060 time to fit residues: 19.7977 Evaluate side-chains 57 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 104 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 ASN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.083786 restraints weight = 59151.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.087333 restraints weight = 43806.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.090659 restraints weight = 15385.998| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 10222 Z= 0.241 Angle : 0.571 14.275 13947 Z= 0.283 Chirality : 0.044 0.185 1641 Planarity : 0.003 0.040 1809 Dihedral : 5.009 42.986 1456 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.55 % Favored : 92.30 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -2.35 (0.23), residues: 1317 helix: -0.60 (0.25), residues: 480 sheet: -2.48 (0.34), residues: 199 loop : -1.97 (0.24), residues: 638 =============================================================================== Job complete usr+sys time: 1768.45 seconds wall clock time: 33 minutes 19.88 seconds (1999.88 seconds total)