Starting phenix.real_space_refine (version: dev) on Fri Feb 24 15:49:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plz_13507/02_2023/7plz_13507_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plz_13507/02_2023/7plz_13507.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plz_13507/02_2023/7plz_13507_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plz_13507/02_2023/7plz_13507_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plz_13507/02_2023/7plz_13507_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plz_13507/02_2023/7plz_13507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plz_13507/02_2023/7plz_13507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plz_13507/02_2023/7plz_13507_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plz_13507/02_2023/7plz_13507_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A ASP 30": "OD1" <-> "OD2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ASP 344": "OD1" <-> "OD2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D ASP 30": "OD1" <-> "OD2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D ARG 343": "NH1" <-> "NH2" Residue "D ASP 344": "OD1" <-> "OD2" Residue "D PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 442": "OE1" <-> "OE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 512": "OE1" <-> "OE2" Residue "D GLU 539": "OE1" <-> "OE2" Residue "D PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 674": "OD1" <-> "OD2" Residue "D ARG 712": "NH1" <-> "NH2" Residue "D ASP 723": "OD1" <-> "OD2" Residue "D ARG 724": "NH1" <-> "NH2" Residue "D PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 789": "NH1" <-> "NH2" Residue "D ARG 792": "NH1" <-> "NH2" Residue "F PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 206": "NH1" <-> "NH2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 311": "OD1" <-> "OD2" Residue "F GLU 361": "OE1" <-> "OE2" Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 123": "OE1" <-> "OE2" Residue "G PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 195": "OE1" <-> "OE2" Residue "G PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 206": "NH1" <-> "NH2" Residue "G ARG 254": "NH1" <-> "NH2" Residue "G PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 311": "OD1" <-> "OD2" Residue "G GLU 361": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23278 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6110 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 6110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6110 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 4 Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 127 Unusual residues: {' MG': 1, '9UE': 2, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 13.76, per 1000 atoms: 0.59 Number of scatterers: 23278 At special positions: 0 Unit cell: (170.5, 207.9, 178.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 3 34.99 S 145 16.00 P 9 15.00 Mg 3 11.99 O 4355 8.00 N 3938 7.00 C 14825 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: 9.95 Conformation dependent library (CDL) restraints added in 3.6 seconds 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5422 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 142 helices and 32 sheets defined 48.5% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.711A pdb=" N ASN A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 169 through 184 Processing helix chain 'A' and resid 193 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 247 through 250 No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.534A pdb=" N SER A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 4.136A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 289 No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.730A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 376 removed outlier: 4.073A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 Processing helix chain 'A' and resid 449 through 479 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.532A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 574 through 581 Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 704 through 713 removed outlier: 4.792A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 755 through 791 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.379A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.661A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 removed outlier: 4.005A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 333 through 348 removed outlier: 4.618A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.762A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.237A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.943A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.683A pdb=" N ASN D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 152 Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 169 through 184 Processing helix chain 'D' and resid 193 through 207 Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 247 through 250 No H-bonds generated for 'chain 'D' and resid 247 through 250' Processing helix chain 'D' and resid 260 through 268 Processing helix chain 'D' and resid 273 through 277 removed outlier: 4.112A pdb=" N THR D 276 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 289 No H-bonds generated for 'chain 'D' and resid 286 through 289' Processing helix chain 'D' and resid 301 through 315 Processing helix chain 'D' and resid 319 through 337 removed outlier: 3.766A pdb=" N ASN D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 Processing helix chain 'D' and resid 368 through 376 removed outlier: 4.134A pdb=" N CYS D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 423 Processing helix chain 'D' and resid 449 through 479 Processing helix chain 'D' and resid 484 through 486 No H-bonds generated for 'chain 'D' and resid 484 through 486' Processing helix chain 'D' and resid 493 through 500 Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.557A pdb=" N LYS D 514 " --> pdb=" O ASP D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 531 Processing helix chain 'D' and resid 564 through 568 Processing helix chain 'D' and resid 574 through 582 Processing helix chain 'D' and resid 587 through 592 Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 636 through 652 Processing helix chain 'D' and resid 675 through 684 Processing helix chain 'D' and resid 687 through 695 Processing helix chain 'D' and resid 704 through 713 removed outlier: 4.848A pdb=" N VAL D 713 " --> pdb=" O SER D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 735 Processing helix chain 'D' and resid 739 through 741 No H-bonds generated for 'chain 'D' and resid 739 through 741' Processing helix chain 'D' and resid 755 through 791 Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 126 Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 196 removed outlier: 4.417A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 removed outlier: 3.691A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 252 through 261 removed outlier: 4.000A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 289 through 295 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 333 through 348 removed outlier: 4.587A pdb=" N LYS F 336 " --> pdb=" O PRO F 333 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY F 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 354 Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 367 through 373 removed outlier: 3.734A pdb=" N VAL F 370 " --> pdb=" O PRO F 367 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS F 373 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 19 Processing helix chain 'E' and resid 29 through 38 removed outlier: 4.269A pdb=" N GLY E 33 " --> pdb=" O TYR E 29 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 52 Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 67 through 78 Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 87 through 96 removed outlier: 4.006A pdb=" N PHE E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 115 Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 141 through 149 Processing helix chain 'G' and resid 56 through 60 Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 125 Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 182 through 196 removed outlier: 4.374A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 216 removed outlier: 3.673A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 252 through 261 removed outlier: 4.004A pdb=" N CYS G 257 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'G' and resid 274 through 283 Processing helix chain 'G' and resid 289 through 295 Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 309 through 320 Processing helix chain 'G' and resid 333 through 348 removed outlier: 4.634A pdb=" N LYS G 336 " --> pdb=" O PRO G 333 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL G 339 " --> pdb=" O LYS G 336 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY G 342 " --> pdb=" O VAL G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 354 Processing helix chain 'G' and resid 359 through 365 Processing helix chain 'G' and resid 367 through 373 removed outlier: 3.710A pdb=" N VAL G 370 " --> pdb=" O PRO G 367 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS G 373 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 11 through 16 removed outlier: 4.246A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 37 through 41 Processing sheet with id= C, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.527A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 377 through 382 Processing sheet with id= E, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= F, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.641A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.851A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 8 through 11 Processing sheet with id= I, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= J, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 7.391A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= N, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.197A pdb=" N ALA D 11 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 37 through 41 removed outlier: 3.583A pdb=" N LEU D 38 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR D 50 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 100 through 103 removed outlier: 3.764A pdb=" N GLY D 236 " --> pdb=" O GLY D 227 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 377 through 382 Processing sheet with id= R, first strand: chain 'D' and resid 547 through 551 Processing sheet with id= S, first strand: chain 'D' and resid 700 through 703 Processing sheet with id= T, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.852A pdb=" N SER D 347 " --> pdb=" O ARG D 343 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 8 through 11 Processing sheet with id= V, first strand: chain 'F' and resid 35 through 38 Processing sheet with id= W, first strand: chain 'F' and resid 103 through 107 Processing sheet with id= X, first strand: chain 'F' and resid 297 through 300 removed outlier: 7.357A pdb=" N VAL F 298 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= Z, first strand: chain 'E' and resid 26 through 28 Processing sheet with id= AA, first strand: chain 'E' and resid 103 through 105 Processing sheet with id= AB, first strand: chain 'G' and resid 8 through 11 Processing sheet with id= AC, first strand: chain 'G' and resid 35 through 38 Processing sheet with id= AD, first strand: chain 'G' and resid 103 through 107 Processing sheet with id= AE, first strand: chain 'G' and resid 297 through 300 removed outlier: 6.828A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 238 through 241 1028 hydrogen bonds defined for protein. 2811 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: 8.01 Time building geometry restraints manager: 10.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5511 1.33 - 1.46: 7497 1.46 - 1.60: 10517 1.60 - 1.73: 9 1.73 - 1.86: 242 Bond restraints: 23776 Sorted by residual: bond pdb=" C4 9UE C 405 " pdb=" C5 9UE C 405 " ideal model delta sigma weight residual 0.880 1.498 -0.618 2.00e-02 2.50e+03 9.54e+02 bond pdb=" C4 9UE C 404 " pdb=" C5 9UE C 404 " ideal model delta sigma weight residual 0.880 1.497 -0.617 2.00e-02 2.50e+03 9.52e+02 bond pdb=" C4 9UE G 401 " pdb=" C5 9UE G 401 " ideal model delta sigma weight residual 0.880 1.496 -0.616 2.00e-02 2.50e+03 9.49e+02 bond pdb=" C11 9UE G 401 " pdb=" C12 9UE G 401 " ideal model delta sigma weight residual 2.064 1.516 0.548 2.00e-02 2.50e+03 7.50e+02 bond pdb=" C11 9UE C 404 " pdb=" C12 9UE C 404 " ideal model delta sigma weight residual 2.064 1.517 0.547 2.00e-02 2.50e+03 7.48e+02 ... (remaining 23771 not shown) Histogram of bond angle deviations from ideal: 96.97 - 104.98: 493 104.98 - 112.99: 12564 112.99 - 121.01: 12599 121.01 - 129.02: 6318 129.02 - 137.03: 160 Bond angle restraints: 32134 Sorted by residual: angle pdb=" C20 9UE G 401 " pdb=" C21 9UE G 401 " pdb=" C28 9UE G 401 " ideal model delta sigma weight residual 73.46 131.86 -58.40 3.00e+00 1.11e-01 3.79e+02 angle pdb=" C20 9UE C 405 " pdb=" C21 9UE C 405 " pdb=" C28 9UE C 405 " ideal model delta sigma weight residual 73.46 130.97 -57.51 3.00e+00 1.11e-01 3.67e+02 angle pdb=" C20 9UE C 404 " pdb=" C21 9UE C 404 " pdb=" C28 9UE C 404 " ideal model delta sigma weight residual 73.46 130.87 -57.41 3.00e+00 1.11e-01 3.66e+02 angle pdb=" C20 9UE G 401 " pdb=" C21 9UE G 401 " pdb=" C22 9UE G 401 " ideal model delta sigma weight residual 176.54 122.58 53.96 3.00e+00 1.11e-01 3.23e+02 angle pdb=" C20 9UE C 404 " pdb=" C21 9UE C 404 " pdb=" C22 9UE C 404 " ideal model delta sigma weight residual 176.54 123.47 53.07 3.00e+00 1.11e-01 3.13e+02 ... (remaining 32129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.11: 13894 32.11 - 64.22: 284 64.22 - 96.33: 67 96.33 - 128.44: 9 128.44 - 160.55: 9 Dihedral angle restraints: 14263 sinusoidal: 5843 harmonic: 8420 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 151.73 148.27 1 2.00e+01 2.50e-03 4.44e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 151.88 148.12 1 2.00e+01 2.50e-03 4.44e+01 dihedral pdb=" O1B ADP G 402 " pdb=" O3A ADP G 402 " pdb=" PB ADP G 402 " pdb=" PA ADP G 402 " ideal model delta sinusoidal sigma weight residual 300.00 152.16 147.84 1 2.00e+01 2.50e-03 4.43e+01 ... (remaining 14260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 3466 0.143 - 0.287: 32 0.287 - 0.430: 3 0.430 - 0.574: 2 0.574 - 0.717: 4 Chirality restraints: 3507 Sorted by residual: chirality pdb=" C6 9UE C 404 " pdb=" N 9UE C 404 " pdb=" C29 9UE C 404 " pdb=" C5 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.65 -1.93 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C6 9UE G 401 " pdb=" N 9UE G 401 " pdb=" C29 9UE G 401 " pdb=" C5 9UE G 401 " both_signs ideal model delta sigma weight residual False -2.65 -1.95 -0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" C6 9UE C 405 " pdb=" N 9UE C 405 " pdb=" C29 9UE C 405 " pdb=" C5 9UE C 405 " both_signs ideal model delta sigma weight residual False -2.65 -1.96 -0.68 2.00e-01 2.50e+01 1.17e+01 ... (remaining 3504 not shown) Planarity restraints: 4110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 147 " 0.114 9.50e-02 1.11e+02 6.57e-02 2.29e+01 pdb=" NE ARG F 147 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG F 147 " 0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG F 147 " -0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG F 147 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 147 " -0.116 9.50e-02 1.11e+02 6.62e-02 2.29e+01 pdb=" NE ARG G 147 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG G 147 " -0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG G 147 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG G 147 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 147 " -0.115 9.50e-02 1.11e+02 6.61e-02 2.28e+01 pdb=" NE ARG C 147 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG C 147 " -0.078 2.00e-02 2.50e+03 pdb=" NH1 ARG C 147 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG C 147 " 0.022 2.00e-02 2.50e+03 ... (remaining 4107 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 179 2.62 - 3.19: 21164 3.19 - 3.76: 34677 3.76 - 4.33: 49911 4.33 - 4.90: 82067 Nonbonded interactions: 187998 Sorted by model distance: nonbonded pdb=" OG1 THR C 202 " pdb=" OE2 GLU F 270 " model vdw 2.054 2.440 nonbonded pdb=" OE2 GLU C 270 " pdb=" OG1 THR G 202 " model vdw 2.076 2.440 nonbonded pdb=" NH2 ARG A 791 " pdb=" O GLU B 11 " model vdw 2.160 2.520 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.185 2.440 nonbonded pdb=" OD1 ASN F 111 " pdb=" NH1 ARG F 177 " model vdw 2.194 2.520 ... (remaining 187993 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' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and resid 5 through 375) selection = (chain 'F' and resid 5 through 375) selection = (chain 'G' and resid 5 through 375) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Br 3 7.06 5 P 9 5.49 5 Mg 3 5.21 5 S 145 5.16 5 C 14825 2.51 5 N 3938 2.21 5 O 4355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.030 Check model and map are aligned: 0.360 Process input model: 61.870 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.190 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.016 0.618 23776 Z= 1.064 Angle : 1.529 58.405 32134 Z= 0.627 Chirality : 0.057 0.717 3507 Planarity : 0.007 0.087 4110 Dihedral : 15.388 160.554 8841 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 2840 helix: -1.03 (0.11), residues: 1386 sheet: -0.16 (0.24), residues: 403 loop : -0.27 (0.17), residues: 1051 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.4121 time to fit residues: 281.8074 Evaluate side-chains 217 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 2.834 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 9.9990 chunk 216 optimal weight: 0.6980 chunk 119 optimal weight: 30.0000 chunk 73 optimal weight: 20.0000 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 135 optimal weight: 8.9990 chunk 166 optimal weight: 0.7980 chunk 258 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 264 GLN A 398 ASN A 406 HIS A 410 ASN A 455 ASN A 497 ASN A 632 HIS A 638 HIS C 128 ASN C 161 HIS C 246 GLN C 353 GLN B 75 GLN D 191 ASN D 264 GLN D 398 ASN D 410 ASN D 455 ASN D 497 ASN D 638 HIS D 639 GLN D 657 HIS F 353 GLN E 75 GLN G 161 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 23776 Z= 0.204 Angle : 0.913 46.343 32134 Z= 0.384 Chirality : 0.044 0.296 3507 Planarity : 0.004 0.050 4110 Dihedral : 10.833 178.388 3189 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.15), residues: 2840 helix: 0.96 (0.14), residues: 1376 sheet: 0.44 (0.25), residues: 398 loop : 0.61 (0.19), residues: 1066 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 243 time to evaluate : 2.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 261 average time/residue: 0.3726 time to fit residues: 153.0966 Evaluate side-chains 212 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 200 time to evaluate : 3.508 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2447 time to fit residues: 10.1026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 259 optimal weight: 1.9990 chunk 280 optimal weight: 0.9980 chunk 230 optimal weight: 0.4980 chunk 257 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN A 726 GLN A 730 ASN D 216 ASN D 455 ASN F 162 ASN G 246 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 23776 Z= 0.264 Angle : 0.900 47.336 32134 Z= 0.372 Chirality : 0.044 0.280 3507 Planarity : 0.004 0.047 4110 Dihedral : 10.564 178.833 3189 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.16), residues: 2840 helix: 1.35 (0.14), residues: 1364 sheet: 0.43 (0.25), residues: 407 loop : 0.72 (0.19), residues: 1069 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 213 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 230 average time/residue: 0.3527 time to fit residues: 130.0581 Evaluate side-chains 198 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 185 time to evaluate : 2.918 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2553 time to fit residues: 9.6459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 123 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 chunk 275 optimal weight: 0.6980 chunk 135 optimal weight: 9.9990 chunk 246 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN G 40 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 23776 Z= 0.225 Angle : 0.874 47.448 32134 Z= 0.355 Chirality : 0.042 0.276 3507 Planarity : 0.004 0.048 4110 Dihedral : 10.307 178.803 3189 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.16), residues: 2840 helix: 1.42 (0.14), residues: 1366 sheet: 0.46 (0.24), residues: 407 loop : 0.76 (0.19), residues: 1067 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 203 average time/residue: 0.3393 time to fit residues: 111.7788 Evaluate side-chains 187 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 2.956 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2377 time to fit residues: 9.1100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 0.4980 chunk 156 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 205 optimal weight: 0.8980 chunk 113 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 247 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS C 87 HIS D 88 ASN ** D 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 657 HIS F 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.086 23776 Z= 0.728 Angle : 1.042 47.763 32134 Z= 0.458 Chirality : 0.053 0.434 3507 Planarity : 0.005 0.060 4110 Dihedral : 11.036 179.364 3189 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2840 helix: 0.84 (0.14), residues: 1369 sheet: 0.09 (0.25), residues: 381 loop : 0.28 (0.19), residues: 1090 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 186 time to evaluate : 2.955 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 22 residues processed: 216 average time/residue: 0.3317 time to fit residues: 117.0545 Evaluate side-chains 184 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 2.718 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2200 time to fit residues: 12.6231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 161 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 275 optimal weight: 0.9980 chunk 228 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 418 HIS C 246 GLN D 726 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 23776 Z= 0.182 Angle : 0.873 47.511 32134 Z= 0.354 Chirality : 0.042 0.262 3507 Planarity : 0.004 0.045 4110 Dihedral : 10.261 176.863 3189 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.16), residues: 2840 helix: 1.23 (0.14), residues: 1362 sheet: 0.30 (0.25), residues: 407 loop : 0.46 (0.19), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 192 time to evaluate : 3.131 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 202 average time/residue: 0.3495 time to fit residues: 114.6162 Evaluate side-chains 176 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 171 time to evaluate : 2.860 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2192 time to fit residues: 5.9235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 201 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS D 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 23776 Z= 0.221 Angle : 0.874 47.448 32134 Z= 0.353 Chirality : 0.042 0.281 3507 Planarity : 0.004 0.042 4110 Dihedral : 10.147 176.594 3189 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.16), residues: 2840 helix: 1.33 (0.15), residues: 1362 sheet: 0.24 (0.25), residues: 411 loop : 0.47 (0.19), residues: 1067 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 181 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 189 average time/residue: 0.3564 time to fit residues: 108.9123 Evaluate side-chains 174 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 171 time to evaluate : 2.923 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2094 time to fit residues: 5.1217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 2.9990 chunk 109 optimal weight: 0.0570 chunk 164 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 135 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS D 726 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 23776 Z= 0.235 Angle : 0.875 47.508 32134 Z= 0.354 Chirality : 0.042 0.280 3507 Planarity : 0.003 0.041 4110 Dihedral : 10.095 177.089 3189 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.16), residues: 2840 helix: 1.30 (0.14), residues: 1377 sheet: 0.29 (0.25), residues: 405 loop : 0.47 (0.19), residues: 1058 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 177 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 182 average time/residue: 0.3736 time to fit residues: 111.6132 Evaluate side-chains 173 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 2.679 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2149 time to fit residues: 5.6353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 1.9990 chunk 240 optimal weight: 0.7980 chunk 255 optimal weight: 0.4980 chunk 154 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 23776 Z= 0.311 Angle : 0.895 47.535 32134 Z= 0.368 Chirality : 0.044 0.306 3507 Planarity : 0.004 0.041 4110 Dihedral : 10.235 177.943 3189 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 2840 helix: 1.26 (0.14), residues: 1376 sheet: 0.23 (0.25), residues: 411 loop : 0.42 (0.19), residues: 1053 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 172 time to evaluate : 2.960 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 175 average time/residue: 0.3409 time to fit residues: 97.9537 Evaluate side-chains 169 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 2.962 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1902 time to fit residues: 4.6774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 283 optimal weight: 0.7980 chunk 261 optimal weight: 0.5980 chunk 226 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 240 optimal weight: 50.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 23776 Z= 0.196 Angle : 0.868 47.435 32134 Z= 0.349 Chirality : 0.042 0.279 3507 Planarity : 0.003 0.052 4110 Dihedral : 9.970 178.240 3189 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.16), residues: 2840 helix: 1.34 (0.14), residues: 1383 sheet: 0.09 (0.26), residues: 391 loop : 0.45 (0.19), residues: 1066 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3490 time to fit residues: 102.8627 Evaluate side-chains 167 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 3.038 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 10.0000 chunk 208 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 28 optimal weight: 0.0020 chunk 41 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.116545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.074824 restraints weight = 47926.801| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.38 r_work: 0.2915 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 23776 Z= 0.239 Angle : 0.882 47.471 32134 Z= 0.357 Chirality : 0.043 0.308 3507 Planarity : 0.003 0.046 4110 Dihedral : 10.030 178.078 3189 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.16), residues: 2840 helix: 1.35 (0.14), residues: 1385 sheet: 0.06 (0.26), residues: 391 loop : 0.45 (0.19), residues: 1064 =============================================================================== Job complete usr+sys time: 4772.00 seconds wall clock time: 87 minutes 21.82 seconds (5241.82 seconds total)