Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 9 04:16:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/05_2023/7s60_24845_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/05_2023/7s60_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_24845/05_2023/7s60_24845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/05_2023/7s60_24845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/05_2023/7s60_24845_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/05_2023/7s60_24845_updated.pdb" } resolution = 3.7 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= -0.005 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 21086 Number of models: 1 Model: "" Number of chains: 5 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: 11002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1399, 11002 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'peptide': 1395, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 1352, None: 4} Not linked: pdbres="LYS E1582 " pdbres="ADP E1601 " Not linked: pdbres="ADP E1601 " pdbres=" MG E1602 " Not linked: pdbres=" MG E1602 " pdbres=" MG E1603 " Not linked: pdbres=" MG E1603 " pdbres="ATP E1604 " 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 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: 12.61, per 1000 atoms: 0.60 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: 10.26 Conformation dependent library (CDL) restraints added in 4.0 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... running ksdssp... Secondary structure from input PDB file: 88 helices and 21 sheets defined 43.8% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 68 through 96 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 171 Processing helix chain 'A' and resid 174 through 179 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 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'B' and resid 54 through 57 No H-bonds generated for 'chain 'B' and resid 54 through 57' Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 68 through 96 removed outlier: 3.925A pdb=" N LEU B 73 " --> pdb=" O PRO B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 143 through 171 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.545A pdb=" N ASP B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 346 through 350' Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 68 through 96 Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 143 through 171 Processing helix chain 'C' and resid 177 through 180 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 68 through 96 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 143 through 171 Processing helix chain 'D' and resid 177 through 180 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'E' and resid 26 through 51 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 72 through 99 removed outlier: 4.191A pdb=" N VAL E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 107 No H-bonds generated for 'chain 'E' and resid 105 through 107' Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 138 through 159 Processing helix chain 'E' and resid 168 through 182 Processing helix chain 'E' and resid 185 through 190 removed outlier: 3.660A pdb=" N VAL E 190 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 229 Processing helix chain 'E' and resid 234 through 239 Processing helix chain 'E' and resid 256 through 258 No H-bonds generated for 'chain 'E' and resid 256 through 258' Processing helix chain 'E' and resid 265 through 269 Processing helix chain 'E' and resid 285 through 295 Processing helix chain 'E' and resid 297 through 309 removed outlier: 3.662A pdb=" N LEU E 302 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 328 removed outlier: 3.908A pdb=" N ASP E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 352 No H-bonds generated for 'chain 'E' and resid 349 through 352' Processing helix chain 'E' and resid 356 through 400 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 415 through 434 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) Processing helix chain 'E' and resid 436 through 456 removed outlier: 3.925A pdb=" N TRP E 440 " --> pdb=" O CYS E 436 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET E 442 " --> pdb=" O ASN E 438 " (cutoff:3.500A) Proline residue: E 443 - end of helix 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 460 No H-bonds generated for 'chain 'E' and resid 458 through 460' Processing helix chain 'E' and resid 465 through 468 No H-bonds generated for 'chain 'E' and resid 465 through 468' Processing helix chain 'E' and resid 472 through 505 removed outlier: 4.402A pdb=" N SER E 488 " --> pdb=" O GLN E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 512 Processing helix chain 'E' and resid 516 through 564 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 574 through 589 Processing helix chain 'E' and resid 591 through 615 removed outlier: 4.651A pdb=" N SER E 595 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG E 599 " --> pdb=" O SER E 596 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR E 601 " --> pdb=" O VAL E 598 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 602 " --> pdb=" O ARG E 599 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL E 606 " --> pdb=" O LYS E 603 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL E 608 " --> pdb=" O LEU E 605 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER E 612 " --> pdb=" O GLN E 609 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU E 613 " --> pdb=" O LYS E 610 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU E 615 " --> pdb=" O SER E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 722 through 728 Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 796 through 806 removed outlier: 3.594A pdb=" N CYS E 806 " --> pdb=" O VAL E 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 812 No H-bonds generated for 'chain 'E' and resid 809 through 812' Processing helix chain 'E' and resid 818 through 820 No H-bonds generated for 'chain 'E' and resid 818 through 820' Processing helix chain 'E' and resid 833 through 840 removed outlier: 3.512A pdb=" N ARG E 837 " --> pdb=" O GLY E 833 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'E' and resid 891 through 895 Proline residue: E 895 - end of helix Processing helix chain 'E' and resid 914 through 919 Processing helix chain 'E' and resid 923 through 931 Processing helix chain 'E' and resid 999 through 1008 Processing helix chain 'E' and resid 1010 through 1038 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 1063 through 1096 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 1101 through 1105 Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1118 through 1123 Processing helix chain 'E' and resid 1127 through 1159 removed outlier: 4.774A pdb=" N ILE E1136 " --> pdb=" O ILE E1132 " (cutoff:3.500A) Proline residue: E1137 - end of helix 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) Processing helix chain 'E' and resid 1163 through 1209 removed outlier: 3.625A pdb=" N VAL E1166 " --> pdb=" O VAL E1163 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU E1168 " --> pdb=" O LEU E1165 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU E1169 " --> pdb=" O VAL E1166 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 3.501A pdb=" N CYS E1175 " --> pdb=" O ALA E1172 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE E1177 " --> pdb=" O VAL E1174 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS E1180 " --> pdb=" O PHE E1177 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR E1181 " --> pdb=" O ILE E1178 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE E1182 " --> pdb=" O GLN E1179 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL E1184 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E1186 " --> pdb=" O ARG E1183 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG E1187 " --> pdb=" O VAL E1184 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP E1188 " --> pdb=" O ALA E1185 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU E1189 " --> pdb=" O SER E1186 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E1191 " --> pdb=" O ASP E1188 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E1195 " --> pdb=" O LEU E1192 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR E1196 " --> pdb=" O ASP E1193 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU E1198 " --> pdb=" O THR E1195 " (cutoff:3.500A) Proline residue: E1199 - end of helix removed outlier: 3.629A pdb=" N SER E1202 " --> pdb=" O PRO E1199 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL E1208 " --> pdb=" O ALA E1205 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU E1209 " --> pdb=" O GLU E1206 " (cutoff:3.500A) Processing helix chain 'E' and resid 1211 through 1214 No H-bonds generated for 'chain 'E' and resid 1211 through 1214' Processing helix chain 'E' and resid 1220 through 1269 Processing helix chain 'E' and resid 1279 through 1294 Processing helix chain 'E' and resid 1296 through 1319 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) Processing helix chain 'E' and resid 1385 through 1393 removed outlier: 4.252A pdb=" N PHE E1392 " --> pdb=" O PHE E1388 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE E1393 " --> pdb=" O SER E1389 " (cutoff:3.500A) Processing helix chain 'E' and resid 1415 through 1421 removed outlier: 3.934A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) Processing helix chain 'E' and resid 1436 through 1440 Processing helix chain 'E' and resid 1448 through 1456 Processing helix chain 'E' and resid 1461 through 1465 Processing helix chain 'E' and resid 1484 through 1495 Processing helix chain 'E' and resid 1514 through 1527 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 1540 through 1545 removed outlier: 4.887A pdb=" N SER E1545 " --> pdb=" O HIS E1541 " (cutoff:3.500A) Processing helix chain 'E' and resid 1563 through 1569 Processing helix chain 'E' and resid 1573 through 1581 Processing sheet with id= A, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.756A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 234 through 238 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) Processing sheet with id= C, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= D, first strand: chain 'A' and resid 319 through 322 Processing sheet with id= E, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'B' and resid 309 through 311 removed outlier: 6.299A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id= G, 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) Processing sheet with id= H, first strand: chain 'B' and resid 313 through 315 Processing sheet with id= I, first strand: chain 'B' and resid 319 through 322 Processing sheet with id= J, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= K, first strand: chain 'C' and resid 309 through 311 removed outlier: 6.499A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id= L, 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) Processing sheet with id= M, first strand: chain 'C' and resid 319 through 322 Processing sheet with id= N, first strand: chain 'D' and resid 309 through 311 removed outlier: 6.366A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 234 through 238 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) Processing sheet with id= P, first strand: chain 'D' and resid 313 through 315 Processing sheet with id= Q, first strand: chain 'D' and resid 319 through 322 Processing sheet with id= R, first strand: chain 'E' and resid 710 through 714 removed outlier: 6.501A pdb=" N TRP E 899 " --> pdb=" O MET E 711 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL E 713 " --> pdb=" O TRP E 899 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE E 901 " --> pdb=" O VAL E 713 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 771 through 773 removed outlier: 3.578A pdb=" N ALA E 773 " --> pdb=" O PHE E 852 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 1376 through 1379 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= U, first strand: chain 'E' and resid 1345 through 1350 removed outlier: 5.330A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) 906 hydrogen bonds defined for protein. 2539 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: 7.57 Time building geometry restraints manager: 10.86 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: 11060 17.51 - 35.02: 1386 35.02 - 52.53: 261 52.53 - 70.04: 52 70.04 - 87.55: 15 Dihedral angle restraints: 12774 sinusoidal: 4991 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 12771 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: 919 2.71 - 3.25: 18729 3.25 - 3.80: 35109 3.80 - 4.35: 43223 4.35 - 4.90: 72248 Nonbonded interactions: 170228 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 170223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.100 Check model and map are aligned: 0.290 Set scattering table: 0.150 Process input model: 58.440 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 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 : 0.009 0.116 21550 Z= 0.592 Angle : 1.419 25.370 29285 Z= 0.800 Chirality : 0.075 0.475 3463 Planarity : 0.012 0.100 3641 Dihedral : 16.053 87.545 7706 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.27 % Favored : 94.61 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.66 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.53 (0.11), residues: 2658 helix: -4.50 (0.06), residues: 1312 sheet: -1.77 (0.27), residues: 290 loop : -2.81 (0.15), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 489 time to evaluate : 2.817 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 outliers start: 30 outliers final: 10 residues processed: 512 average time/residue: 0.3423 time to fit residues: 268.5037 Evaluate side-chains 354 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 344 time to evaluate : 2.722 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1857 time to fit residues: 7.0448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 242 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 128 GLN B 218 GLN C 175 HIS C 234 HIS D 43 ASN D 264 ASN E 60 HIS E 189 ASN E 375 GLN E 445 GLN E 677 ASN E 708 GLN E 715 GLN E 797 GLN E 909 GLN ** E1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1459 GLN E1488 GLN E1518 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 21550 Z= 0.192 Angle : 0.689 18.285 29285 Z= 0.350 Chirality : 0.043 0.208 3463 Planarity : 0.006 0.079 3641 Dihedral : 6.489 70.912 2873 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.01 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.14), residues: 2658 helix: -1.98 (0.12), residues: 1278 sheet: -1.27 (0.29), residues: 290 loop : -2.28 (0.16), residues: 1090 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 353 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 374 average time/residue: 0.3289 time to fit residues: 193.1461 Evaluate side-chains 321 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 306 time to evaluate : 2.623 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1994 time to fit residues: 9.2957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 201 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 242 optimal weight: 0.0270 chunk 262 optimal weight: 0.2980 chunk 216 optimal weight: 5.9990 chunk 240 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 264 ASN B 128 GLN B 160 ASN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN D 41 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 ASN E 189 ASN ** E1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1427 GLN E1488 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 21550 Z= 0.205 Angle : 0.654 17.575 29285 Z= 0.326 Chirality : 0.043 0.181 3463 Planarity : 0.004 0.071 3641 Dihedral : 5.890 80.043 2873 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.37 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.75 (0.15), residues: 2658 helix: -0.57 (0.14), residues: 1316 sheet: -1.10 (0.29), residues: 303 loop : -1.82 (0.18), residues: 1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 332 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 362 average time/residue: 0.3319 time to fit residues: 190.0086 Evaluate side-chains 319 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 300 time to evaluate : 2.806 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2127 time to fit residues: 11.3919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 258 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 153 ASN B 160 ASN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 923 GLN ** E1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1191 GLN ** E1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1488 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 21550 Z= 0.435 Angle : 0.767 14.958 29285 Z= 0.389 Chirality : 0.047 0.202 3463 Planarity : 0.005 0.069 3641 Dihedral : 6.060 89.442 2873 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.57 % Favored : 94.35 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.95 (0.16), residues: 2658 helix: 0.22 (0.14), residues: 1289 sheet: -1.14 (0.29), residues: 302 loop : -1.45 (0.19), residues: 1067 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 280 time to evaluate : 2.817 Fit side-chains revert: symmetry clash outliers start: 65 outliers final: 35 residues processed: 330 average time/residue: 0.3330 time to fit residues: 173.9538 Evaluate side-chains 291 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 256 time to evaluate : 2.791 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1936 time to fit residues: 16.3139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 3 optimal weight: 0.0010 chunk 192 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN D 41 ASN D 242 ASN E1024 HIS ** E1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1488 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 21550 Z= 0.215 Angle : 0.662 18.749 29285 Z= 0.325 Chirality : 0.044 0.260 3463 Planarity : 0.004 0.065 3641 Dihedral : 5.757 82.509 2873 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.48 % Favored : 95.44 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.50 (0.17), residues: 2658 helix: 0.60 (0.15), residues: 1290 sheet: -1.03 (0.29), residues: 302 loop : -1.20 (0.19), residues: 1066 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 303 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 16 residues processed: 335 average time/residue: 0.3347 time to fit residues: 177.6415 Evaluate side-chains 296 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 280 time to evaluate : 2.682 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2030 time to fit residues: 9.6401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 0.0270 chunk 232 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 258 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 119 optimal weight: 0.0470 chunk 21 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN B 160 ASN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 HIS D 173 GLN ** E1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1402 HIS E1488 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3195 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: