Starting phenix.real_space_refine on Sun Aug 4 08:17:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/08_2024/6wkw_21811.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/08_2024/6wkw_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_21811/08_2024/6wkw_21811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/08_2024/6wkw_21811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/08_2024/6wkw_21811.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/08_2024/6wkw_21811.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 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. 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-5409/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: 10.34, per 1000 atoms: 1.03 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: 4.48 Conformation dependent library (CDL) restraints added in 4.1 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... Secondary structure from input PDB file: 56 helices and 15 sheets defined 36.7% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'D' and resid 46 through 51 removed outlier: 4.222A pdb=" N ILE D 50 " --> pdb=" O VAL D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 88 through 93 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 133 through 147 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 158 Processing helix chain 'D' and resid 164 through 172 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 189 through 200 removed outlier: 3.744A pdb=" N GLN D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) 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 217 through 222 removed outlier: 3.598A pdb=" N LEU D 221 " --> pdb=" O ILE D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 257 through 261 removed outlier: 3.501A pdb=" N MET D 261 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 286 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) Processing helix chain 'D' and resid 328 through 345 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 64 through 68 removed outlier: 3.906A pdb=" N ILE C 68 " --> pdb=" O THR C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 75 Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 133 through 147 removed outlier: 3.744A pdb=" N LEU C 143 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.535A pdb=" N ARG C 169 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 removed outlier: 3.718A pdb=" N GLN C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL C 195 " --> pdb=" O THR C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 235 removed outlier: 3.509A pdb=" N LEU C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.639A pdb=" N LYS C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.606A pdb=" N LEU C 275 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 276 " --> pdb=" O GLY C 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 276' Processing helix chain 'C' and resid 278 through 288 Processing helix chain 'C' and resid 329 through 347 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 47 through 52 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 112 through 120 removed outlier: 4.209A pdb=" N GLU B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 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 142 through 147 Processing helix chain 'B' and resid 150 through 158 Processing helix chain 'B' and resid 164 through 172 removed outlier: 4.013A pdb=" N GLU B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.760A pdb=" N ALA B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 277 through 287 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 328 through 347 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 47 through 52 removed outlier: 3.892A pdb=" N LEU A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.615A pdb=" N GLU A 67 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 68 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N HIS A 69 " --> pdb=" O GLN A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 70 through 75 removed outlier: 4.218A pdb=" N ASN A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 75 " --> pdb=" O LYS A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.940A pdb=" N GLU A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 130 through 148 removed outlier: 3.603A pdb=" N ALA A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 157 removed outlier: 3.598A pdb=" N GLN A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.583A pdb=" N ARG A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 199 removed outlier: 3.536A pdb=" N GLN A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) 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 216 through 221 removed outlier: 4.115A pdb=" N LEU A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.716A pdb=" N LEU A 275 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 276 " --> pdb=" O GLY A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 276' Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 328 through 344 removed outlier: 3.836A pdb=" N GLU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 56 through 57 removed outlier: 3.623A pdb=" N VAL D 36 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU D 35 " --> pdb=" O VAL D 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 100 through 103 Processing sheet with id=AA3, first strand: chain 'D' and resid 224 through 226 removed outlier: 6.671A pdb=" N VAL D 206 " --> pdb=" O GLN D 224 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL D 226 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N PHE D 208 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR D 182 " --> pdb=" O CYS D 238 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER D 240 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY D 184 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 293 through 295 Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 38 removed outlier: 6.106A pdb=" N VAL C 36 " --> pdb=" O ALA C 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 103 Processing sheet with id=AA7, first strand: chain 'C' and resid 182 through 185 removed outlier: 6.688A pdb=" N VAL C 206 " --> pdb=" O GLN C 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241 removed outlier: 6.385A pdb=" N VAL C 239 " --> pdb=" O VAL C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 293 through 295 removed outlier: 6.462A pdb=" N ALA C 293 " --> pdb=" O ILE C 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 226 removed outlier: 6.027A pdb=" N PHE B 208 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 183 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR B 209 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU B 185 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 239 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 293 through 295 Processing sheet with id=AB4, first strand: chain 'A' and resid 56 through 58 removed outlier: 5.691A pdb=" N VAL A 36 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 78 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA A 79 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 224 through 225 removed outlier: 6.806A pdb=" N LEU A 185 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 293 through 295 249 hydrogen bonds defined for protein. 723 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: 2.64 Time building geometry restraints manager: 4.33 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: 5484 17.43 - 34.85: 543 34.85 - 52.28: 139 52.28 - 69.71: 27 69.71 - 87.14: 15 Dihedral angle restraints: 6208 sinusoidal: 2389 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 6205 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: 205 2.63 - 3.20: 9556 3.20 - 3.77: 15028 3.77 - 4.33: 21909 4.33 - 4.90: 36407 Nonbonded interactions: 83105 Sorted by model distance: nonbonded pdb=" OD2 ASP B 40 " pdb=" OG1 THR B 84 " model vdw 2.066 3.040 nonbonded pdb=" OD1 ASN B 246 " pdb=" ND2 ASN B 249 " model vdw 2.103 3.120 nonbonded pdb=" ND1 HIS A 251 " pdb=" OD1 ASP A 277 " model vdw 2.107 3.120 nonbonded pdb=" OE1 GLU B 132 " pdb=" NH2 ARG B 198 " model vdw 2.119 3.120 nonbonded pdb=" OD1 ASP A 296 " pdb=" OG1 THR A 319 " model vdw 2.143 3.040 ... (remaining 83100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '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 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: 0.790 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 37.480 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 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= 1.150 Angle : 1.193 12.940 13947 Z= 0.656 Chirality : 0.059 0.369 1641 Planarity : 0.005 0.097 1809 Dihedral : 15.787 87.135 3746 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 % Allowed : 7.34 % Favored : 92.14 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 324 HIS 0.010 0.002 HIS A 69 PHE 0.055 0.003 PHE C 188 TYR 0.024 0.002 TYR D 108 ARG 0.007 0.001 ARG B 272 *********************** 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 : 1.213 Fit side-chains REVERT: C 48 MET cc_start: 0.8450 (tpp) cc_final: 0.8231 (tpt) REVERT: C 351 GLU cc_start: 0.7740 (pt0) cc_final: 0.7469 (pt0) REVERT: A 81 MET cc_start: 0.8800 (ptm) cc_final: 0.8573 (ptm) REVERT: A 351 GLU cc_start: 0.8096 (pm20) cc_final: 0.7818 (pm20) outliers start: 1 outliers final: 1 residues processed: 68 average time/residue: 0.3162 time to fit residues: 28.5769 Evaluate side-chains 47 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 63 GLN C 149 ASN C 163 GLN C 250 HIS C 260 GLN ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10222 Z= 0.247 Angle : 0.639 10.084 13947 Z= 0.335 Chirality : 0.045 0.217 1641 Planarity : 0.005 0.079 1809 Dihedral : 9.091 51.723 1658 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.09 % Favored : 92.75 % Rotamer: Outliers : 1.55 % Allowed : 10.13 % Favored : 88.31 % 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: -4.83 (0.19), residues: 1317 helix: -3.20 (0.18), residues: 472 sheet: -3.81 (0.31), residues: 180 loop : -2.98 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.005 0.001 HIS A 251 PHE 0.023 0.001 PHE C 188 TYR 0.019 0.001 TYR D 108 ARG 0.007 0.000 ARG A 103 *********************** 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 77 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.127 Fit side-chains REVERT: C 351 GLU cc_start: 0.7689 (pt0) cc_final: 0.7411 (pt0) REVERT: A 81 MET cc_start: 0.8628 (ptm) cc_final: 0.8336 (ptm) outliers start: 12 outliers final: 8 residues processed: 73 average time/residue: 0.2148 time to fit residues: 23.2546 Evaluate side-chains 57 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 53 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 chunk 32 optimal weight: 6.9990 chunk 119 optimal weight: 0.0270 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10222 Z= 0.182 Angle : 0.582 10.632 13947 Z= 0.301 Chirality : 0.044 0.196 1641 Planarity : 0.004 0.054 1809 Dihedral : 8.285 58.166 1658 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.02 % Favored : 92.83 % Rotamer: Outliers : 1.45 % Allowed : 12.51 % Favored : 86.04 % 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: -3.99 (0.21), residues: 1317 helix: -2.37 (0.21), residues: 472 sheet: -3.43 (0.30), residues: 217 loop : -2.48 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 324 HIS 0.003 0.001 HIS A 251 PHE 0.019 0.001 PHE C 188 TYR 0.017 0.001 TYR D 108 ARG 0.004 0.000 ARG B 190 *********************** 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 72 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 1.073 Fit side-chains REVERT: C 218 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8008 (pt0) REVERT: C 261 MET cc_start: 0.8963 (mtp) cc_final: 0.8751 (mtp) REVERT: C 351 GLU cc_start: 0.7686 (pt0) cc_final: 0.7440 (pt0) REVERT: A 351 GLU cc_start: 0.7748 (pm20) cc_final: 0.7484 (pm20) outliers start: 11 outliers final: 6 residues processed: 69 average time/residue: 0.1966 time to fit residues: 21.1644 Evaluate side-chains 58 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 53 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 0.3980 chunk 126 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 34 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10222 Z= 0.204 Angle : 0.569 10.501 13947 Z= 0.293 Chirality : 0.044 0.185 1641 Planarity : 0.004 0.049 1809 Dihedral : 8.057 53.204 1658 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.02 % Favored : 92.83 % Rotamer: Outliers : 1.76 % Allowed : 13.86 % Favored : 84.38 % 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: -3.46 (0.21), residues: 1317 helix: -1.82 (0.23), residues: 463 sheet: -3.16 (0.31), residues: 217 loop : -2.25 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 324 HIS 0.003 0.001 HIS A 251 PHE 0.012 0.001 PHE C 188 TYR 0.019 0.001 TYR D 108 ARG 0.004 0.000 ARG A 103 *********************** 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 71 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 1.189 Fit side-chains REVERT: C 218 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: C 261 MET cc_start: 0.8959 (mtp) cc_final: 0.8746 (mtp) REVERT: C 351 GLU cc_start: 0.7694 (pt0) cc_final: 0.7452 (pt0) REVERT: A 351 GLU cc_start: 0.7731 (pm20) cc_final: 0.7527 (pm20) outliers start: 14 outliers final: 9 residues processed: 69 average time/residue: 0.1897 time to fit residues: 20.8798 Evaluate side-chains 59 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 53 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10222 Z= 0.207 Angle : 0.569 10.448 13947 Z= 0.290 Chirality : 0.044 0.192 1641 Planarity : 0.003 0.043 1809 Dihedral : 7.946 52.955 1658 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.71 % Favored : 93.14 % Rotamer: Outliers : 1.76 % Allowed : 14.48 % Favored : 83.76 % 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: -2.98 (0.22), residues: 1317 helix: -1.42 (0.23), residues: 466 sheet: -2.80 (0.35), residues: 181 loop : -2.10 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 324 HIS 0.003 0.001 HIS A 251 PHE 0.013 0.001 PHE C 188 TYR 0.021 0.001 TYR D 325 ARG 0.003 0.000 ARG A 103 *********************** 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 68 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 1.074 Fit side-chains REVERT: C 218 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8076 (pt0) REVERT: C 261 MET cc_start: 0.8958 (mtp) cc_final: 0.8738 (mtp) REVERT: C 351 GLU cc_start: 0.7692 (pt0) cc_final: 0.7455 (pt0) REVERT: A 152 LEU cc_start: 0.8900 (mt) cc_final: 0.8678 (mp) REVERT: A 348 ARG cc_start: 0.7247 (ptt-90) cc_final: 0.6855 (ptt180) REVERT: A 351 GLU cc_start: 0.7702 (pm20) cc_final: 0.7158 (pm20) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.1982 time to fit residues: 19.9397 Evaluate side-chains 61 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 53 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10222 Z= 0.194 Angle : 0.562 11.355 13947 Z= 0.284 Chirality : 0.044 0.170 1641 Planarity : 0.003 0.038 1809 Dihedral : 7.817 52.388 1658 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.71 % Favored : 93.14 % Rotamer: Outliers : 2.17 % Allowed : 14.27 % Favored : 83.56 % 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: -2.71 (0.22), residues: 1317 helix: -1.06 (0.24), residues: 463 sheet: -2.70 (0.35), residues: 181 loop : -2.04 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 324 HIS 0.005 0.001 HIS A 83 PHE 0.013 0.001 PHE C 188 TYR 0.020 0.001 TYR D 325 ARG 0.003 0.000 ARG B 190 *********************** 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 71 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 1.208 Fit side-chains REVERT: C 218 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8039 (pt0) REVERT: C 261 MET cc_start: 0.8940 (mtp) cc_final: 0.8717 (mtp) REVERT: C 351 GLU cc_start: 0.7694 (pt0) cc_final: 0.7458 (pt0) REVERT: A 152 LEU cc_start: 0.8899 (mt) cc_final: 0.8682 (mp) REVERT: A 348 ARG cc_start: 0.7152 (ptt-90) cc_final: 0.6778 (ptt180) REVERT: A 351 GLU cc_start: 0.7667 (pm20) cc_final: 0.7398 (pt0) outliers start: 16 outliers final: 10 residues processed: 66 average time/residue: 0.2195 time to fit residues: 22.0594 Evaluate side-chains 62 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 77 VAL 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: 4.9990 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10222 Z= 0.248 Angle : 0.582 11.360 13947 Z= 0.295 Chirality : 0.045 0.188 1641 Planarity : 0.003 0.037 1809 Dihedral : 7.951 51.874 1658 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.64 % Favored : 93.21 % Rotamer: Outliers : 1.96 % Allowed : 14.58 % Favored : 83.45 % 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: -2.55 (0.22), residues: 1317 helix: -0.88 (0.24), residues: 469 sheet: -2.70 (0.35), residues: 184 loop : -1.96 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 324 HIS 0.003 0.001 HIS B 83 PHE 0.014 0.001 PHE C 188 TYR 0.024 0.002 TYR A 325 ARG 0.003 0.000 ARG B 190 *********************** 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 63 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 1.105 Fit side-chains REVERT: C 218 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8112 (pt0) REVERT: C 261 MET cc_start: 0.8966 (mtp) cc_final: 0.8738 (mtp) REVERT: C 351 GLU cc_start: 0.7709 (pt0) cc_final: 0.7488 (pt0) REVERT: A 152 LEU cc_start: 0.8979 (mt) cc_final: 0.8740 (mp) REVERT: A 348 ARG cc_start: 0.7136 (ptt-90) cc_final: 0.6679 (ptt180) REVERT: A 351 GLU cc_start: 0.7732 (pm20) cc_final: 0.7492 (pt0) outliers start: 14 outliers final: 9 residues processed: 59 average time/residue: 0.1873 time to fit residues: 17.5833 Evaluate side-chains 58 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 77 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10222 Z= 0.244 Angle : 0.582 12.107 13947 Z= 0.295 Chirality : 0.045 0.226 1641 Planarity : 0.003 0.036 1809 Dihedral : 7.949 51.210 1658 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.17 % Favored : 92.68 % Rotamer: Outliers : 2.17 % Allowed : 14.58 % Favored : 83.25 % 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: -0.63 (0.24), residues: 466 sheet: -2.63 (0.35), residues: 181 loop : -1.89 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 324 HIS 0.003 0.001 HIS A 298 PHE 0.015 0.001 PHE C 188 TYR 0.023 0.001 TYR A 325 ARG 0.003 0.000 ARG B 190 *********************** 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 66 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 1.077 Fit side-chains REVERT: C 218 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8084 (pt0) REVERT: C 261 MET cc_start: 0.8977 (mtp) cc_final: 0.8747 (mtp) REVERT: C 351 GLU cc_start: 0.7706 (pt0) cc_final: 0.7490 (pt0) REVERT: A 152 LEU cc_start: 0.8999 (mt) cc_final: 0.8760 (mp) REVERT: A 348 ARG cc_start: 0.7086 (ptt-90) cc_final: 0.6682 (ptt180) REVERT: A 351 GLU cc_start: 0.7736 (pm20) cc_final: 0.7464 (pt0) outliers start: 16 outliers final: 10 residues processed: 62 average time/residue: 0.1824 time to fit residues: 17.9136 Evaluate side-chains 61 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 77 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 70 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10222 Z= 0.229 Angle : 0.584 12.872 13947 Z= 0.294 Chirality : 0.044 0.185 1641 Planarity : 0.003 0.035 1809 Dihedral : 7.907 51.190 1658 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.86 % Favored : 92.98 % Rotamer: Outliers : 1.65 % Allowed : 15.20 % Favored : 83.14 % 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: -2.24 (0.23), residues: 1317 helix: -0.50 (0.24), residues: 472 sheet: -2.64 (0.35), residues: 181 loop : -1.84 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 324 HIS 0.003 0.001 HIS A 298 PHE 0.014 0.001 PHE C 188 TYR 0.022 0.001 TYR A 325 ARG 0.004 0.000 ARG B 190 *********************** 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 63 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 1.081 Fit side-chains REVERT: C 218 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8087 (pt0) REVERT: C 351 GLU cc_start: 0.7706 (pt0) cc_final: 0.7489 (pt0) REVERT: A 152 LEU cc_start: 0.8994 (mt) cc_final: 0.8744 (mp) REVERT: A 348 ARG cc_start: 0.7000 (ptt-90) cc_final: 0.6658 (ptt180) REVERT: A 351 GLU cc_start: 0.7755 (pm20) cc_final: 0.7478 (pt0) outliers start: 11 outliers final: 10 residues processed: 59 average time/residue: 0.1852 time to fit residues: 17.0999 Evaluate side-chains 62 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 77 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.0770 chunk 86 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 103 optimal weight: 0.0870 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10222 Z= 0.147 Angle : 0.562 13.757 13947 Z= 0.278 Chirality : 0.043 0.169 1641 Planarity : 0.003 0.038 1809 Dihedral : 7.571 52.771 1658 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.10 % Favored : 93.75 % Rotamer: Outliers : 1.55 % Allowed : 15.51 % Favored : 82.94 % 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: -1.96 (0.23), residues: 1317 helix: -0.19 (0.25), residues: 472 sheet: -2.46 (0.36), residues: 181 loop : -1.76 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 324 HIS 0.003 0.001 HIS D 83 PHE 0.013 0.001 PHE C 188 TYR 0.018 0.001 TYR D 108 ARG 0.004 0.000 ARG B 190 ********************** 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 70 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 1.168 Fit side-chains REVERT: C 218 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: C 351 GLU cc_start: 0.7695 (pt0) cc_final: 0.7467 (pt0) REVERT: A 152 LEU cc_start: 0.8847 (mt) cc_final: 0.8626 (mp) REVERT: A 351 GLU cc_start: 0.7622 (pm20) cc_final: 0.7279 (pm20) outliers start: 10 outliers final: 6 residues processed: 66 average time/residue: 0.1881 time to fit residues: 19.5568 Evaluate side-chains 59 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 77 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.1947 > 50: distance: 56 - 139: 29.352 distance: 63 - 142: 27.712 distance: 103 - 106: 14.785 distance: 106 - 107: 15.840 distance: 107 - 108: 26.193 distance: 107 - 110: 36.684 distance: 108 - 109: 24.717 distance: 108 - 111: 8.647 distance: 111 - 112: 13.188 distance: 112 - 113: 10.122 distance: 112 - 115: 3.946 distance: 113 - 114: 8.617 distance: 113 - 116: 21.245 distance: 116 - 117: 20.450 distance: 116 - 122: 28.727 distance: 117 - 118: 15.631 distance: 117 - 120: 20.506 distance: 118 - 119: 17.289 distance: 118 - 123: 6.097 distance: 120 - 121: 10.303 distance: 121 - 122: 10.686 distance: 123 - 124: 20.120 distance: 124 - 125: 10.371 distance: 124 - 127: 11.664 distance: 125 - 126: 32.715 distance: 125 - 131: 13.418 distance: 127 - 128: 5.433 distance: 128 - 129: 8.834 distance: 128 - 130: 24.284 distance: 131 - 132: 9.894 distance: 132 - 133: 23.212 distance: 132 - 135: 12.189 distance: 133 - 134: 10.885 distance: 133 - 139: 32.693 distance: 135 - 136: 35.965 distance: 136 - 137: 13.507 distance: 136 - 138: 6.877 distance: 139 - 140: 11.515 distance: 140 - 141: 17.243 distance: 140 - 143: 30.527 distance: 141 - 142: 18.010 distance: 141 - 147: 30.687 distance: 143 - 144: 13.271 distance: 143 - 145: 11.653 distance: 144 - 146: 12.354 distance: 147 - 148: 14.264 distance: 148 - 149: 15.485 distance: 148 - 151: 14.976 distance: 149 - 150: 17.244 distance: 149 - 153: 23.754 distance: 151 - 152: 35.066 distance: 153 - 154: 15.740 distance: 154 - 155: 15.948 distance: 154 - 157: 22.953 distance: 155 - 156: 19.517 distance: 155 - 160: 13.049 distance: 157 - 158: 22.167 distance: 157 - 159: 7.096 distance: 160 - 161: 16.016 distance: 160 - 166: 25.566 distance: 161 - 162: 3.495 distance: 161 - 164: 11.824 distance: 162 - 163: 15.391 distance: 162 - 167: 10.703 distance: 164 - 165: 7.469 distance: 165 - 166: 9.012 distance: 167 - 168: 7.293 distance: 168 - 169: 3.183 distance: 168 - 171: 5.289 distance: 169 - 170: 21.055 distance: 169 - 177: 13.505 distance: 171 - 172: 3.858 distance: 172 - 173: 7.849 distance: 172 - 174: 9.935 distance: 173 - 175: 7.011 distance: 174 - 176: 7.750 distance: 175 - 176: 5.211