Starting phenix.real_space_refine on Thu Aug 8 01:07:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/08_2024/7s60_24845.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/08_2024/7s60_24845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/08_2024/7s60_24845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/08_2024/7s60_24845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/08_2024/7s60_24845.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/08_2024/7s60_24845.cif" } resolution = 3.7 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= -0.005 sd= 0.083 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 122 5.16 5 C 13635 2.51 5 N 3585 2.21 5 O 3737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 32": "NH1" <-> "NH2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ASP 237": "OD1" <-> "OD2" Residue "B ASP 262": "OD1" <-> "OD2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ASP 274": "OD1" <-> "OD2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "C TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 329": "OD1" <-> "OD2" Residue "C GLU 351": "OE1" <-> "OE2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D ASP 274": "OD1" <-> "OD2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D ASP 323": "OD1" <-> "OD2" Residue "D TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 351": "OE1" <-> "OE2" Residue "E PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E ASP 30": "OD1" <-> "OD2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 247": "OD1" <-> "OD2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E ASP 311": "OD1" <-> "OD2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 495": "OE1" <-> "OE2" Residue "E TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 571": "OD1" <-> "OD2" Residue "E PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 613": "OE1" <-> "OE2" Residue "E TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 703": "NH1" <-> "NH2" Residue "E ARG 842": "NH1" <-> "NH2" Residue "E ASP 855": "OD1" <-> "OD2" Residue "E GLU 875": "OE1" <-> "OE2" Residue "E ASP 916": "OD1" <-> "OD2" Residue "E ASP 1039": "OD1" <-> "OD2" Residue "E ARG 1124": "NH1" <-> "NH2" Residue "E ASP 1133": "OD1" <-> "OD2" Residue "E ASP 1193": "OD1" <-> "OD2" Residue "E PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1222": "NH1" <-> "NH2" Residue "E ASP 1232": "OD1" <-> "OD2" Residue "E PHE 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1253": "OE1" <-> "OE2" Residue "E TYR 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1304": "OD1" <-> "OD2" Residue "E GLU 1306": "OE1" <-> "OE2" Residue "E ARG 1314": "NH1" <-> "NH2" Residue "E TYR 1326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1400": "OE1" <-> "OE2" Residue "E ARG 1419": "NH1" <-> "NH2" Residue "E ARG 1437": "NH1" <-> "NH2" Residue "E GLU 1443": "OE1" <-> "OE2" Residue "E GLU 1453": "OE1" <-> "OE2" Residue "E ARG 1487": "NH1" <-> "NH2" Residue "E ARG 1494": "NH1" <-> "NH2" Residue "E ARG 1498": "NH1" <-> "NH2" Residue "E ASP 1530": "OD1" <-> "OD2" Residue "E GLU 1559": "OE1" <-> "OE2" Residue "E PHE 1560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1561": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 21086 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "B" Number of atoms: 2527 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Conformer: "B" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} bond proxies already assigned to first conformer: 2567 Chain: "C" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "D" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "E" Number of atoms: 10942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1395, 10942 Classifications: {'peptide': 1395} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 1352} Chain breaks: 7 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AMET B 88 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 88 " occ=0.50 Time building chain proxies: 14.09, per 1000 atoms: 0.67 Number of scatterers: 21086 At special positions: 0 Unit cell: (140.4, 148.2, 139.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 122 16.00 P 5 15.00 Mg 2 11.99 O 3737 8.00 N 3585 7.00 C 13635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.04 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 27 " distance=2.03 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: 8.48 Conformation dependent library (CDL) restraints added in 4.6 seconds 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5056 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 27 sheets defined 48.9% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 58 through 65 removed outlier: 4.086A pdb=" N THR A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 97 Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.887A pdb=" N ALA A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.701A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 removed outlier: 4.151A pdb=" N ARG A 176 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 178 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 179 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 333 removed outlier: 3.763A pdb=" N PHE A 333 " --> pdb=" O TYR A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 333' Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 67 through 97 removed outlier: 3.925A pdb=" N LEU B 73 " --> pdb=" O PRO B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 142 through 172 removed outlier: 3.895A pdb=" N ILE B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 4.314A pdb=" N ARG B 176 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 178 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 179 " --> pdb=" O ARG B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 removed outlier: 3.723A pdb=" N PHE B 333 " --> pdb=" O TYR B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 67 through 97 Processing helix chain 'C' and resid 117 through 129 removed outlier: 3.534A pdb=" N VAL C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 172 Processing helix chain 'C' and resid 176 through 179 removed outlier: 3.516A pdb=" N GLU C 179 " --> pdb=" O ARG C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 179' Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.539A pdb=" N LEU C 275 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 333 removed outlier: 3.660A pdb=" N PHE C 333 " --> pdb=" O TYR C 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 330 through 333' Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'D' and resid 51 through 56 removed outlier: 3.974A pdb=" N ARG D 54 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D 55 " --> pdb=" O GLN D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.971A pdb=" N THR D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 97 Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.612A pdb=" N ALA D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 172 removed outlier: 3.524A pdb=" N ILE D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 179 removed outlier: 3.616A pdb=" N GLU D 179 " --> pdb=" O ARG D 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 176 through 179' Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.765A pdb=" N LEU D 275 " --> pdb=" O PRO D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 333 removed outlier: 3.839A pdb=" N PHE D 333 " --> pdb=" O TYR D 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 330 through 333' Processing helix chain 'E' and resid 25 through 52 removed outlier: 3.965A pdb=" N VAL E 35 " --> pdb=" O ALA E 31 " (cutoff:3.500A) Proline residue: E 36 - end of helix Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 71 through 98 Processing helix chain 'E' and resid 104 through 107 removed outlier: 3.838A pdb=" N LEU E 107 " --> pdb=" O HIS E 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 104 through 107' Processing helix chain 'E' and resid 108 through 130 Processing helix chain 'E' and resid 137 through 161 removed outlier: 4.111A pdb=" N HIS E 161 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 183 removed outlier: 3.907A pdb=" N CYS E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 191 removed outlier: 3.835A pdb=" N ASN E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 233 through 240 removed outlier: 3.952A pdb=" N PHE E 237 " --> pdb=" O TRP E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 259 removed outlier: 3.673A pdb=" N ARG E 259 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 270 Processing helix chain 'E' and resid 285 through 296 Processing helix chain 'E' and resid 296 through 310 removed outlier: 3.662A pdb=" N LEU E 302 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 329 removed outlier: 3.908A pdb=" N ASP E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 353 Processing helix chain 'E' and resid 355 through 401 removed outlier: 3.540A pdb=" N LEU E 368 " --> pdb=" O PHE E 364 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU E 369 " --> pdb=" O LEU E 365 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN E 375 " --> pdb=" O ARG E 371 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 435 removed outlier: 3.659A pdb=" N VAL E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR E 426 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASN E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 435 " --> pdb=" O TRP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 440 removed outlier: 3.839A pdb=" N LEU E 439 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TRP E 440 " --> pdb=" O CYS E 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 435 through 440' Processing helix chain 'E' and resid 441 through 457 removed outlier: 4.156A pdb=" N ILE E 446 " --> pdb=" O MET E 442 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL E 448 " --> pdb=" O VAL E 444 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 461 Processing helix chain 'E' and resid 464 through 469 removed outlier: 4.257A pdb=" N ILE E 468 " --> pdb=" O GLY E 464 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE E 469 " --> pdb=" O ALA E 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 464 through 469' Processing helix chain 'E' and resid 471 through 506 removed outlier: 4.402A pdb=" N SER E 488 " --> pdb=" O GLN E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 513 Processing helix chain 'E' and resid 515 through 565 removed outlier: 3.939A pdb=" N SER E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) Proline residue: E 552 - end of helix removed outlier: 4.011A pdb=" N VAL E 564 " --> pdb=" O PHE E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 589 Processing helix chain 'E' and resid 590 through 592 No H-bonds generated for 'chain 'E' and resid 590 through 592' Processing helix chain 'E' and resid 593 through 616 removed outlier: 3.887A pdb=" N SER E 616 " --> pdb=" O SER E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 728 Processing helix chain 'E' and resid 783 through 790 Processing helix chain 'E' and resid 795 through 807 removed outlier: 3.594A pdb=" N CYS E 806 " --> pdb=" O VAL E 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 813 Processing helix chain 'E' and resid 817 through 821 removed outlier: 3.968A pdb=" N THR E 821 " --> pdb=" O GLY E 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 832 through 841 removed outlier: 3.512A pdb=" N ARG E 837 " --> pdb=" O GLY E 833 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 871 removed outlier: 3.529A pdb=" N ALA E 871 " --> pdb=" O HIS E 867 " (cutoff:3.500A) Processing helix chain 'E' and resid 890 through 894 removed outlier: 3.552A pdb=" N TYR E 893 " --> pdb=" O LYS E 890 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 920 Processing helix chain 'E' and resid 922 through 932 Processing helix chain 'E' and resid 999 through 1009 Processing helix chain 'E' and resid 1009 through 1039 removed outlier: 4.160A pdb=" N LEU E1015 " --> pdb=" O LEU E1011 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER E1019 " --> pdb=" O LEU E1015 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN E1020 " --> pdb=" O LEU E1016 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU E1022 " --> pdb=" O PHE E1018 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR E1038 " --> pdb=" O LEU E1034 " (cutoff:3.500A) Processing helix chain 'E' and resid 1062 through 1097 removed outlier: 4.092A pdb=" N VAL E1067 " --> pdb=" O VAL E1063 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE E1068 " --> pdb=" O TYR E1064 " (cutoff:3.500A) Processing helix chain 'E' and resid 1100 through 1106 Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.578A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1117 through 1124 removed outlier: 3.755A pdb=" N ILE E1121 " --> pdb=" O PRO E1117 " (cutoff:3.500A) Processing helix chain 'E' and resid 1126 through 1134 Processing helix chain 'E' and resid 1134 through 1160 removed outlier: 4.410A pdb=" N SER E1138 " --> pdb=" O GLN E1134 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR E1139 " --> pdb=" O HIS E1135 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER E1158 " --> pdb=" O LEU E1154 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR E1159 " --> pdb=" O ALA E1155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E1160 " --> pdb=" O VAL E1156 " (cutoff:3.500A) Processing helix chain 'E' and resid 1164 through 1210 removed outlier: 4.026A pdb=" N LEU E1169 " --> pdb=" O LEU E1165 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 4.634A pdb=" N ALA E1185 " --> pdb=" O TYR E1181 " (cutoff:3.500A) Proline residue: E1199 - end of helix removed outlier: 4.196A pdb=" N GLU E1209 " --> pdb=" O ALA E1205 " (cutoff:3.500A) Processing helix chain 'E' and resid 1210 through 1215 Processing helix chain 'E' and resid 1219 through 1270 Processing helix chain 'E' and resid 1278 through 1295 Processing helix chain 'E' and resid 1295 through 1320 removed outlier: 4.298A pdb=" N ALA E1311 " --> pdb=" O LEU E1307 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS E1320 " --> pdb=" O HIS E1316 " (cutoff:3.500A) Processing helix chain 'E' and resid 1384 through 1391 Processing helix chain 'E' and resid 1392 through 1394 No H-bonds generated for 'chain 'E' and resid 1392 through 1394' Processing helix chain 'E' and resid 1414 through 1422 removed outlier: 3.934A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E1422 " --> pdb=" O LEU E1418 " (cutoff:3.500A) Processing helix chain 'E' and resid 1436 through 1441 Processing helix chain 'E' and resid 1447 through 1457 Processing helix chain 'E' and resid 1460 through 1466 removed outlier: 3.598A pdb=" N ALA E1466 " --> pdb=" O LEU E1462 " (cutoff:3.500A) Processing helix chain 'E' and resid 1483 through 1496 Processing helix chain 'E' and resid 1513 through 1528 removed outlier: 3.642A pdb=" N LYS E1522 " --> pdb=" O ASN E1518 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR E1526 " --> pdb=" O LYS E1522 " (cutoff:3.500A) Processing helix chain 'E' and resid 1539 through 1544 removed outlier: 3.512A pdb=" N ILE E1543 " --> pdb=" O ARG E1539 " (cutoff:3.500A) Processing helix chain 'E' and resid 1562 through 1569 Processing helix chain 'E' and resid 1572 through 1582 Processing sheet with id=AA1, first strand: chain 'A' and resid 256 through 260 removed outlier: 6.756A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 230 through 238 removed outlier: 5.054A pdb=" N THR A 223 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A 221 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA A 213 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU A 288 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE A 215 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 286 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET A 217 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A 284 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL A 219 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU A 282 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 322 Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.299A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 236 through 238 removed outlier: 4.614A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB1, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AB2, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.499A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 234 through 237 removed outlier: 3.577A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA C 213 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 234 through 237 removed outlier: 3.577A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER C 212 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL C 290 " --> pdb=" O SER C 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 319 through 322 Processing sheet with id=AB7, first strand: chain 'D' and resid 181 through 182 Processing sheet with id=AB8, first strand: chain 'D' and resid 256 through 260 removed outlier: 6.366A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 230 through 238 removed outlier: 5.202A pdb=" N THR D 223 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG D 221 " --> pdb=" O HIS D 234 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N SER D 212 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N VAL D 290 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 313 through 315 Processing sheet with id=AC2, first strand: chain 'D' and resid 319 through 322 Processing sheet with id=AC3, first strand: chain 'E' and resid 678 through 680 removed outlier: 3.520A pdb=" N CYS E 679 " --> pdb=" O ILE E 704 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE E 704 " --> pdb=" O CYS E 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 697 through 701 removed outlier: 7.192A pdb=" N SER E 698 " --> pdb=" O TYR E 686 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR E 686 " --> pdb=" O SER E 698 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE E 700 " --> pdb=" O GLY E 684 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 771 through 773 removed outlier: 6.483A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU E 709 " --> pdb=" O TRP E 899 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE E 901 " --> pdb=" O LEU E 709 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N MET E 711 " --> pdb=" O ILE E 901 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N MET E 903 " --> pdb=" O MET E 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL E 713 " --> pdb=" O MET E 903 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 1345 through 1350 removed outlier: 5.330A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 1352 through 1353 Processing sheet with id=AC8, first strand: chain 'E' and resid 1502 through 1505 removed outlier: 6.689A pdb=" N PHE E1503 " --> pdb=" O VAL E1534 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ILE E1536 " --> pdb=" O PHE E1503 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N MET E1505 " --> pdb=" O ILE E1536 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLY E1376 " --> pdb=" O ILE E1550 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU E1552 " --> pdb=" O GLY E1376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS E1378 " --> pdb=" O LEU E1552 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP E1561 " --> pdb=" O VAL E1549 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU E1559 " --> pdb=" O VAL E1551 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 1434 through 1435 1045 hydrogen bonds defined for protein. 3040 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: 8.77 Time building geometry restraints manager: 9.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6321 1.34 - 1.46: 5281 1.46 - 1.59: 9741 1.59 - 1.71: 11 1.71 - 1.83: 196 Bond restraints: 21550 Sorted by residual: bond pdb=" C VAL E 35 " pdb=" N PRO E 36 " ideal model delta sigma weight residual 1.336 1.451 -0.116 1.25e-02 6.40e+03 8.55e+01 bond pdb=" C4 ATP E1604 " pdb=" C5 ATP E1604 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.65e+01 bond pdb=" C5 ATP E1604 " pdb=" N7 ATP E1604 " ideal model delta sigma weight residual 1.387 1.330 0.057 1.00e-02 1.00e+04 3.21e+01 bond pdb=" C5 ATP E1604 " pdb=" C6 ATP E1604 " ideal model delta sigma weight residual 1.409 1.461 -0.052 1.00e-02 1.00e+04 2.72e+01 bond pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 1.374 1.326 0.048 1.00e-02 1.00e+04 2.33e+01 ... (remaining 21545 not shown) Histogram of bond angle deviations from ideal: 97.16 - 106.06: 540 106.06 - 114.97: 13144 114.97 - 123.87: 14868 123.87 - 132.77: 665 132.77 - 141.67: 68 Bond angle restraints: 29285 Sorted by residual: angle pdb=" PA ATP E1604 " pdb=" O3A ATP E1604 " pdb=" PB ATP E1604 " ideal model delta sigma weight residual 136.83 118.92 17.91 1.00e+00 1.00e+00 3.21e+02 angle pdb=" PB ATP E1604 " pdb=" O3B ATP E1604 " pdb=" PG ATP E1604 " ideal model delta sigma weight residual 139.87 122.87 17.00 1.00e+00 1.00e+00 2.89e+02 angle pdb=" N SER E1158 " pdb=" CA SER E1158 " pdb=" C SER E1158 " ideal model delta sigma weight residual 114.62 104.51 10.11 1.14e+00 7.69e-01 7.86e+01 angle pdb=" C ASN E 263 " pdb=" N TYR E 264 " pdb=" CA TYR E 264 " ideal model delta sigma weight residual 121.54 137.59 -16.05 1.91e+00 2.74e-01 7.06e+01 angle pdb=" C5 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N3 ATP E1604 " ideal model delta sigma weight residual 126.80 119.23 7.57 1.00e+00 1.00e+00 5.73e+01 ... (remaining 29280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 11075 17.51 - 35.02: 1399 35.02 - 52.53: 264 52.53 - 70.04: 52 70.04 - 87.55: 15 Dihedral angle restraints: 12805 sinusoidal: 5022 harmonic: 7783 Sorted by residual: dihedral pdb=" CA HIS E 12 " pdb=" C HIS E 12 " pdb=" N SER E 13 " pdb=" CA SER E 13 " ideal model delta harmonic sigma weight residual -180.00 -111.89 -68.11 0 5.00e+00 4.00e-02 1.86e+02 dihedral pdb=" CA LYS E1499 " pdb=" C LYS E1499 " pdb=" N THR E1500 " pdb=" CA THR E1500 " ideal model delta harmonic sigma weight residual 180.00 123.82 56.18 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA ARG E1498 " pdb=" C ARG E1498 " pdb=" N LYS E1499 " pdb=" CA LYS E1499 " ideal model delta harmonic sigma weight residual 180.00 -135.19 -44.81 0 5.00e+00 4.00e-02 8.03e+01 ... (remaining 12802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2900 0.095 - 0.190: 464 0.190 - 0.285: 78 0.285 - 0.380: 15 0.380 - 0.475: 6 Chirality restraints: 3463 Sorted by residual: chirality pdb=" CG LEU E 40 " pdb=" CB LEU E 40 " pdb=" CD1 LEU E 40 " pdb=" CD2 LEU E 40 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CB VAL B 36 " pdb=" CA VAL B 36 " pdb=" CG1 VAL B 36 " pdb=" CG2 VAL B 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CB ILE E1403 " pdb=" CA ILE E1403 " pdb=" CG1 ILE E1403 " pdb=" CG2 ILE E1403 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 3460 not shown) Planarity restraints: 3641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E1502 " -0.024 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" C ILE E1502 " 0.085 2.00e-02 2.50e+03 pdb=" O ILE E1502 " -0.032 2.00e-02 2.50e+03 pdb=" N PHE E1503 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 110 " 0.021 2.00e-02 2.50e+03 4.34e-02 1.89e+01 pdb=" C CYS B 110 " -0.075 2.00e-02 2.50e+03 pdb=" O CYS B 110 " 0.029 2.00e-02 2.50e+03 pdb=" N VAL B 111 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 136 " 0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C LEU E 136 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU E 136 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU E 137 " 0.025 2.00e-02 2.50e+03 ... (remaining 3638 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 916 2.71 - 3.25: 18591 3.25 - 3.80: 34997 3.80 - 4.35: 42961 4.35 - 4.90: 72235 Nonbonded interactions: 169700 Sorted by model distance: nonbonded pdb="MG MG E1602 " pdb=" O3B ATP E1604 " model vdw 2.157 2.170 nonbonded pdb=" O3A ADP E1601 " pdb="MG MG E1603 " model vdw 2.159 2.170 nonbonded pdb=" OE1 GLN E 775 " pdb="MG MG E1602 " model vdw 2.160 2.170 nonbonded pdb="MG MG E1602 " pdb=" O2B ATP E1604 " model vdw 2.163 2.170 nonbonded pdb=" OG SER E1386 " pdb="MG MG E1603 " model vdw 2.175 2.170 ... (remaining 169695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 87 or resid 89 through 352)) selection = (chain 'B' and (resid 32 through 87 or resid 89 through 352)) selection = (chain 'C' and (resid 32 through 87 or resid 89 through 352)) selection = (chain 'D' and (resid 32 through 87 or resid 89 through 352)) } 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=0.50 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: 11.650 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: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 62.290 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: