Starting phenix.real_space_refine on Wed Feb 14 18:51:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/02_2024/6wkw_21811_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/02_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_21811/02_2024/6wkw_21811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/02_2024/6wkw_21811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/02_2024/6wkw_21811_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkw_21811/02_2024/6wkw_21811_updated.pdb" } 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-5238/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: 10.42, per 1000 atoms: 1.04 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: 3.96 Conformation dependent library (CDL) restraints added in 3.7 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: 1.92 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: 2.60 Time building geometry restraints manager: 4.15 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: 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 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: 1.490 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: 4.120 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 37.500 Find NCS groups from input model: 0.770 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.100 ------------------------------------------------------------------------------- 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= 1.130 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 : 1.119 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: 0.3177 time to fit residues: 28.8201 Evaluate side-chains 47 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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: 1.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10222 Z= 0.206 Angle : 0.592 10.083 13947 Z= 0.307 Chirality : 0.044 0.182 1641 Planarity : 0.004 0.085 1809 Dihedral : 8.848 46.477 1658 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.71 % Favored : 93.14 % Rotamer: Outliers : 1.65 % Allowed : 10.03 % Favored : 88.31 % 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: -4.81 (0.19), residues: 1317 helix: -3.28 (0.18), residues: 467 sheet: -3.85 (0.32), residues: 166 loop : -2.94 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.004 0.001 HIS A 298 PHE 0.019 0.001 PHE C 188 TYR 0.018 0.001 TYR D 108 ARG 0.005 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: 13 poor density : 64 time to evaluate : 1.129 Fit side-chains REVERT: C 351 GLU cc_start: 0.7677 (pt0) cc_final: 0.7402 (pt0) REVERT: A 351 GLU cc_start: 0.7970 (pm20) cc_final: 0.7735 (pm20) outliers start: 13 outliers final: 8 residues processed: 72 average time/residue: 0.2128 time to fit residues: 22.7898 Evaluate side-chains 56 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 44 CYS Chi-restraints excluded: chain B residue 85 ILE 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: 3.9990 chunk 36 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 106 optimal weight: 0.0980 chunk 118 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10222 Z= 0.187 Angle : 0.551 9.139 13947 Z= 0.283 Chirality : 0.043 0.191 1641 Planarity : 0.004 0.073 1809 Dihedral : 8.112 48.169 1658 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.55 % Favored : 92.30 % Rotamer: Outliers : 1.34 % Allowed : 12.51 % Favored : 86.14 % 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: -4.15 (0.21), residues: 1317 helix: -2.58 (0.21), residues: 465 sheet: -3.62 (0.33), residues: 170 loop : -2.62 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 324 HIS 0.003 0.001 HIS A 298 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 71 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 1.203 Fit side-chains REVERT: C 351 GLU cc_start: 0.7702 (pt0) cc_final: 0.7446 (pt0) outliers start: 10 outliers final: 6 residues processed: 68 average time/residue: 0.2122 time to fit residues: 21.9665 Evaluate side-chains 58 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain B residue 85 ILE 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: 4.9990 chunk 89 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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: 0.8786 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10222 Z= 0.421 Angle : 0.648 8.844 13947 Z= 0.332 Chirality : 0.047 0.188 1641 Planarity : 0.004 0.069 1809 Dihedral : 8.592 47.347 1658 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.46 % Favored : 90.39 % Rotamer: Outliers : 2.17 % Allowed : 13.44 % 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: -3.96 (0.21), residues: 1317 helix: -2.45 (0.21), residues: 474 sheet: -3.33 (0.32), residues: 192 loop : -2.46 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 324 HIS 0.004 0.001 HIS B 83 PHE 0.019 0.002 PHE C 188 TYR 0.021 0.002 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 67 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 49 time to evaluate : 1.065 Fit side-chains REVERT: D 82 TYR cc_start: 0.8657 (m-80) cc_final: 0.8418 (m-80) REVERT: C 218 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: C 351 GLU cc_start: 0.7738 (pt0) cc_final: 0.7511 (pt0) REVERT: B 38 LEU cc_start: 0.8789 (tt) cc_final: 0.8560 (tt) REVERT: A 351 GLU cc_start: 0.7755 (pm20) cc_final: 0.7266 (pm20) outliers start: 18 outliers final: 12 residues processed: 63 average time/residue: 0.2014 time to fit residues: 19.9406 Evaluate side-chains 58 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 150 THR 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 317 ILE Chi-restraints excluded: chain B residue 322 THR 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: 4.9990 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 0.0060 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 87 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.8078 ------------------------------------------------------------------------------- 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** ** 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: 0.8691 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10222 Z= 0.160 Angle : 0.537 10.336 13947 Z= 0.272 Chirality : 0.042 0.177 1641 Planarity : 0.003 0.058 1809 Dihedral : 7.819 44.052 1658 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.86 % Favored : 92.98 % Rotamer: Outliers : 2.07 % Allowed : 14.68 % Favored : 83.25 % 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: -3.43 (0.22), residues: 1317 helix: -1.93 (0.22), residues: 467 sheet: -3.22 (0.34), residues: 164 loop : -2.25 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 324 HIS 0.003 0.001 HIS A 298 PHE 0.013 0.001 PHE C 188 TYR 0.017 0.001 TYR D 108 ARG 0.004 0.000 ARG B 190 *********************** 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 69 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 1.140 Fit side-chains REVERT: C 218 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7969 (pt0) REVERT: C 351 GLU cc_start: 0.7698 (pt0) cc_final: 0.7467 (pt0) REVERT: A 351 GLU cc_start: 0.7676 (pm20) cc_final: 0.7270 (pm20) outliers start: 17 outliers final: 9 residues processed: 65 average time/residue: 0.1848 time to fit residues: 19.0425 Evaluate side-chains 62 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 218 GLU Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 257 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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: 0.8743 moved from start: 0.2025 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= 0.286 Angle : 0.581 10.776 13947 Z= 0.292 Chirality : 0.044 0.186 1641 Planarity : 0.003 0.053 1809 Dihedral : 8.029 47.151 1658 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.09 % Favored : 91.76 % Rotamer: Outliers : 2.17 % Allowed : 15.10 % Favored : 82.73 % 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: -3.29 (0.22), residues: 1317 helix: -1.79 (0.23), residues: 474 sheet: -3.08 (0.35), residues: 164 loop : -2.20 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 324 HIS 0.002 0.001 HIS B 83 PHE 0.015 0.001 PHE B 208 TYR 0.020 0.001 TYR D 108 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 72 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 1.217 Fit side-chains REVERT: D 82 TYR cc_start: 0.8521 (m-80) cc_final: 0.8031 (m-80) REVERT: C 218 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8025 (pt0) REVERT: C 351 GLU cc_start: 0.7720 (pt0) cc_final: 0.7514 (pt0) REVERT: A 351 GLU cc_start: 0.7742 (pm20) cc_final: 0.7303 (pt0) outliers start: 18 outliers final: 14 residues processed: 68 average time/residue: 0.1896 time to fit residues: 20.3479 Evaluate side-chains 66 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 150 THR 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 317 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 257 THR 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: 1.9990 chunk 92 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 70 optimal weight: 0.0070 chunk 126 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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: 0.8667 moved from start: 0.2503 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= 0.146 Angle : 0.538 12.815 13947 Z= 0.264 Chirality : 0.042 0.174 1641 Planarity : 0.003 0.045 1809 Dihedral : 7.532 46.254 1658 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.56 % Favored : 93.29 % Rotamer: Outliers : 2.07 % Allowed : 15.93 % Favored : 82.01 % 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: -2.88 (0.22), residues: 1317 helix: -1.34 (0.24), residues: 469 sheet: -2.86 (0.36), residues: 164 loop : -2.05 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.003 0.000 HIS A 298 PHE 0.025 0.001 PHE C 361 TYR 0.017 0.001 TYR D 108 ARG 0.005 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 74 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 57 time to evaluate : 1.213 Fit side-chains REVERT: C 218 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7979 (pt0) REVERT: C 351 GLU cc_start: 0.7688 (pt0) cc_final: 0.7479 (pt0) REVERT: A 351 GLU cc_start: 0.7646 (pm20) cc_final: 0.7305 (pt0) outliers start: 17 outliers final: 9 residues processed: 70 average time/residue: 0.2092 time to fit residues: 22.9068 Evaluate side-chains 63 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 150 THR 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 77 VAL Chi-restraints excluded: chain A residue 257 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10222 Z= 0.211 Angle : 0.557 11.380 13947 Z= 0.277 Chirality : 0.044 0.196 1641 Planarity : 0.003 0.043 1809 Dihedral : 7.670 47.699 1658 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.48 % Favored : 92.37 % Rotamer: Outliers : 1.86 % Allowed : 16.65 % Favored : 81.49 % 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: -1.11 (0.24), residues: 462 sheet: -2.76 (0.37), residues: 163 loop : -2.01 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 324 HIS 0.004 0.001 HIS A 83 PHE 0.029 0.001 PHE C 361 TYR 0.019 0.001 TYR D 108 ARG 0.004 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 70 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 1.091 Fit side-chains REVERT: D 82 TYR cc_start: 0.8451 (m-80) cc_final: 0.7799 (m-80) REVERT: C 218 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8021 (pt0) REVERT: C 351 GLU cc_start: 0.7697 (pt0) cc_final: 0.7473 (pt0) REVERT: A 351 GLU cc_start: 0.7641 (pm20) cc_final: 0.7391 (pt0) outliers start: 15 outliers final: 11 residues processed: 68 average time/residue: 0.1815 time to fit residues: 19.4119 Evaluate side-chains 65 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 150 THR 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 317 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 70 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 0.0070 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.8655 moved from start: 0.2713 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= 0.140 Angle : 0.541 14.034 13947 Z= 0.264 Chirality : 0.043 0.182 1641 Planarity : 0.003 0.039 1809 Dihedral : 7.383 47.503 1658 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.33 % Favored : 93.52 % Rotamer: Outliers : 1.65 % Allowed : 16.75 % Favored : 81.59 % 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: -2.44 (0.23), residues: 1317 helix: -0.76 (0.25), residues: 459 sheet: -2.64 (0.37), residues: 163 loop : -1.95 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 324 HIS 0.003 0.001 HIS A 83 PHE 0.029 0.001 PHE C 361 TYR 0.017 0.001 TYR D 108 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 74 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 1.286 Fit side-chains REVERT: C 218 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8023 (pt0) REVERT: C 351 GLU cc_start: 0.7675 (pt0) cc_final: 0.7447 (pt0) REVERT: A 351 GLU cc_start: 0.7568 (pm20) cc_final: 0.7351 (pm20) outliers start: 13 outliers final: 9 residues processed: 72 average time/residue: 0.1920 time to fit residues: 21.3919 Evaluate side-chains 64 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 357 VAL 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 317 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 285 LEU 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: 0.6980 chunk 86 optimal weight: 0.0370 chunk 130 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10222 Z= 0.231 Angle : 0.563 11.992 13947 Z= 0.281 Chirality : 0.044 0.190 1641 Planarity : 0.003 0.037 1809 Dihedral : 7.632 49.052 1658 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.17 % Favored : 92.68 % Rotamer: Outliers : 1.86 % Allowed : 16.86 % Favored : 81.28 % 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: -2.33 (0.23), residues: 1317 helix: -0.69 (0.25), residues: 462 sheet: -2.42 (0.35), residues: 193 loop : -1.85 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 324 HIS 0.002 0.001 HIS B 69 PHE 0.030 0.001 PHE C 361 TYR 0.027 0.001 TYR A 325 ARG 0.005 0.000 ARG A 348 ********************** 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 72 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 1.132 Fit side-chains REVERT: C 218 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: C 351 GLU cc_start: 0.7700 (pt0) cc_final: 0.7487 (pt0) REVERT: A 348 ARG cc_start: 0.7056 (ptt90) cc_final: 0.6846 (ptt180) REVERT: A 351 GLU cc_start: 0.7676 (pm20) cc_final: 0.7425 (pm20) outliers start: 15 outliers final: 11 residues processed: 70 average time/residue: 0.1865 time to fit residues: 20.4760 Evaluate side-chains 68 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 357 VAL 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 317 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.0870 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 0.0470 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 167 GLN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.077822 restraints weight = 61157.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.081804 restraints weight = 36631.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.084469 restraints weight = 14394.136| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10222 Z= 0.144 Angle : 0.546 14.481 13947 Z= 0.267 Chirality : 0.043 0.184 1641 Planarity : 0.003 0.035 1809 Dihedral : 7.382 48.127 1658 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.25 % Favored : 93.59 % Rotamer: Outliers : 1.45 % Allowed : 17.27 % Favored : 81.28 % 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: -2.16 (0.23), residues: 1317 helix: -0.44 (0.25), residues: 462 sheet: -2.48 (0.38), residues: 163 loop : -1.85 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 324 HIS 0.003 0.001 HIS A 298 PHE 0.031 0.001 PHE C 361 TYR 0.021 0.001 TYR A 325 ARG 0.004 0.000 ARG B 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1827.77 seconds wall clock time: 34 minutes 22.96 seconds (2062.96 seconds total)