Starting phenix.real_space_refine on Mon Mar 18 13:54:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/03_2024/7s60_24845_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/03_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_24845/03_2024/7s60_24845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/03_2024/7s60_24845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/03_2024/7s60_24845_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s60_24845/03_2024/7s60_24845_updated.pdb" } 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-5265/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: 12.09, per 1000 atoms: 0.57 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: 7.82 Conformation dependent library (CDL) restraints added in 4.4 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: 5.08 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: 7.37 Time building geometry restraints manager: 8.50 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: 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.140 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 58.260 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.170 ------------------------------------------------------------------------------- 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 : 16.091 87.545 7737 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 % Allowed : 12.07 % Favored : 86.58 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E1037 HIS 0.008 0.002 HIS D 278 PHE 0.046 0.003 PHE E 222 TYR 0.030 0.003 TYR E 379 ARG 0.018 0.001 ARG B 314 *********************** 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 : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9467 (tp) cc_final: 0.9159 (tp) REVERT: A 152 GLN cc_start: 0.8120 (tt0) cc_final: 0.7795 (tm-30) REVERT: A 179 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7901 (mp0) REVERT: B 83 TRP cc_start: 0.9386 (m-10) cc_final: 0.9115 (m-10) REVERT: B 128 GLN cc_start: 0.8576 (tt0) cc_final: 0.8183 (tt0) REVERT: B 147 LEU cc_start: 0.8913 (tp) cc_final: 0.8531 (tp) REVERT: B 170 LYS cc_start: 0.9219 (tptt) cc_final: 0.8854 (tptm) REVERT: B 185 LYS cc_start: 0.9240 (ttpp) cc_final: 0.8933 (ttpp) REVERT: B 258 TYR cc_start: 0.9036 (p90) cc_final: 0.8715 (p90) REVERT: B 283 ILE cc_start: 0.9045 (mp) cc_final: 0.8831 (tp) REVERT: C 39 LYS cc_start: 0.9225 (mmtm) cc_final: 0.8964 (mmmm) REVERT: C 47 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8866 (mttm) REVERT: C 52 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8501 (tp-100) REVERT: C 65 ASP cc_start: 0.8277 (t70) cc_final: 0.7874 (t0) REVERT: C 144 LEU cc_start: 0.8871 (tp) cc_final: 0.8617 (tp) REVERT: C 160 ASN cc_start: 0.8845 (m-40) cc_final: 0.8594 (t0) REVERT: C 170 LYS cc_start: 0.9024 (tptt) cc_final: 0.8777 (tppt) REVERT: C 209 MET cc_start: 0.8768 (tpp) cc_final: 0.8552 (tpp) REVERT: C 240 MET cc_start: 0.8354 (tmm) cc_final: 0.8126 (ttt) REVERT: D 47 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8829 (mtmm) REVERT: D 57 GLN cc_start: 0.8784 (mt0) cc_final: 0.8353 (mp10) REVERT: D 209 MET cc_start: 0.8753 (mmm) cc_final: 0.8543 (tpp) REVERT: D 251 LEU cc_start: 0.9089 (tp) cc_final: 0.8805 (tp) REVERT: D 290 VAL cc_start: 0.9398 (t) cc_final: 0.9145 (p) REVERT: D 332 LYS cc_start: 0.9228 (mttt) cc_final: 0.8952 (mtpt) REVERT: E 84 PHE cc_start: 0.8984 (t80) cc_final: 0.8709 (t80) REVERT: E 109 MET cc_start: 0.8408 (tpt) cc_final: 0.8169 (tpp) REVERT: E 153 ILE cc_start: 0.9366 (tp) cc_final: 0.9023 (tp) REVERT: E 189 ASN cc_start: 0.9023 (m-40) cc_final: 0.8500 (t0) REVERT: E 369 LEU cc_start: 0.9009 (tp) cc_final: 0.8798 (tt) REVERT: E 410 MET cc_start: 0.7613 (tpt) cc_final: 0.6947 (tmm) REVERT: E 546 PHE cc_start: 0.8882 (t80) cc_final: 0.8280 (t80) REVERT: E 919 ARG cc_start: 0.8387 (ttp-110) cc_final: 0.7990 (ptm-80) REVERT: E 1080 LEU cc_start: 0.9132 (tp) cc_final: 0.8764 (tp) REVERT: E 1141 GLU cc_start: 0.8816 (pp20) cc_final: 0.8501 (pp20) REVERT: E 1180 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8352 (mtmt) REVERT: E 1248 LEU cc_start: 0.8966 (tp) cc_final: 0.8644 (tp) REVERT: E 1505 MET cc_start: 0.8588 (mtt) cc_final: 0.7767 (mmt) REVERT: E 1551 VAL cc_start: 0.9256 (t) cc_final: 0.9003 (p) outliers start: 30 outliers final: 10 residues processed: 512 average time/residue: 0.3312 time to fit residues: 258.6416 Evaluate side-chains 354 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 344 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1082 THR Chi-restraints excluded: chain E residue 1535 THR 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: 4.9990 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 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: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 218 GLN C 175 HIS C 234 HIS D 43 ASN D 264 ASN E 60 HIS 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** E1427 GLN E1459 GLN E1488 GLN E1518 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21550 Z= 0.180 Angle : 0.663 17.806 29285 Z= 0.337 Chirality : 0.043 0.184 3463 Planarity : 0.006 0.077 3641 Dihedral : 6.979 72.184 2916 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.88 % Favored : 96.01 % Rotamer: Outliers : 1.92 % Allowed : 19.35 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.06 (0.14), residues: 2658 helix: -1.90 (0.12), residues: 1282 sheet: -1.26 (0.29), residues: 290 loop : -2.25 (0.16), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E1037 HIS 0.003 0.001 HIS E 37 PHE 0.017 0.001 PHE E1503 TYR 0.023 0.001 TYR D 268 ARG 0.009 0.000 ARG E1222 *********************** 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 415 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 372 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9485 (tp) cc_final: 0.9260 (tp) REVERT: B 77 MET cc_start: 0.7802 (tpp) cc_final: 0.7579 (tpt) REVERT: B 83 TRP cc_start: 0.9330 (m-10) cc_final: 0.9061 (m-10) REVERT: B 170 LYS cc_start: 0.9195 (tptt) cc_final: 0.8747 (tptm) REVERT: B 218 GLN cc_start: 0.8305 (mt0) cc_final: 0.8009 (mm110) REVERT: B 240 MET cc_start: 0.8792 (ttp) cc_final: 0.8414 (ttp) REVERT: C 47 LYS cc_start: 0.9077 (mtmt) cc_final: 0.8850 (mttp) REVERT: C 65 ASP cc_start: 0.8345 (t70) cc_final: 0.7838 (t0) REVERT: C 325 ARG cc_start: 0.8026 (ptp-110) cc_final: 0.7478 (ptm-80) REVERT: C 330 TYR cc_start: 0.8262 (m-80) cc_final: 0.7808 (m-80) REVERT: D 57 GLN cc_start: 0.8767 (mt0) cc_final: 0.8333 (mp10) REVERT: D 92 LEU cc_start: 0.9326 (mt) cc_final: 0.9015 (mt) REVERT: D 128 GLN cc_start: 0.8259 (tt0) cc_final: 0.7908 (tm-30) REVERT: D 197 CYS cc_start: 0.8590 (m) cc_final: 0.7959 (m) REVERT: D 251 LEU cc_start: 0.8886 (tp) cc_final: 0.8516 (tp) REVERT: E 153 ILE cc_start: 0.9305 (tp) cc_final: 0.9048 (tp) REVERT: E 170 PHE cc_start: 0.8012 (t80) cc_final: 0.7653 (t80) REVERT: E 189 ASN cc_start: 0.8993 (m-40) cc_final: 0.8530 (t0) REVERT: E 410 MET cc_start: 0.7754 (tpt) cc_final: 0.6989 (tmm) REVERT: E 546 PHE cc_start: 0.8915 (t80) cc_final: 0.8306 (t80) REVERT: E 1080 LEU cc_start: 0.9196 (tp) cc_final: 0.8867 (tp) REVERT: E 1151 VAL cc_start: 0.9396 (m) cc_final: 0.9178 (p) REVERT: E 1191 GLN cc_start: 0.8805 (tp40) cc_final: 0.8483 (pp30) REVERT: E 1229 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7701 (tm-30) REVERT: E 1287 TYR cc_start: 0.8698 (m-80) cc_final: 0.8229 (m-10) REVERT: E 1305 MET cc_start: 0.9042 (mmm) cc_final: 0.8744 (mmm) REVERT: E 1505 MET cc_start: 0.8613 (mtt) cc_final: 0.7865 (mmt) outliers start: 43 outliers final: 23 residues processed: 401 average time/residue: 0.3125 time to fit residues: 195.6648 Evaluate side-chains 335 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 312 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1500 THR Chi-restraints excluded: chain E residue 1535 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 201 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 242 optimal weight: 0.0980 chunk 262 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 160 ASN C 153 ASN D 41 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 ASN ** 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: 0.8421 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21550 Z= 0.226 Angle : 0.653 17.370 29285 Z= 0.327 Chirality : 0.043 0.176 3463 Planarity : 0.004 0.070 3641 Dihedral : 6.659 79.781 2915 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.86 % Favored : 95.07 % Rotamer: Outliers : 3.09 % Allowed : 21.13 % Favored : 75.77 % 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: -1.57 (0.15), residues: 2658 helix: -0.39 (0.14), residues: 1312 sheet: -1.02 (0.29), residues: 303 loop : -1.79 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E1037 HIS 0.005 0.001 HIS E1203 PHE 0.029 0.002 PHE E1503 TYR 0.016 0.001 TYR D 268 ARG 0.005 0.000 ARG E 194 *********************** 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 394 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 324 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9288 (mmmt) cc_final: 0.8882 (mtmm) REVERT: A 74 ILE cc_start: 0.9515 (tp) cc_final: 0.9243 (tp) REVERT: A 197 CYS cc_start: 0.8532 (m) cc_final: 0.8302 (m) REVERT: A 288 GLU cc_start: 0.7912 (pp20) cc_final: 0.7677 (pp20) REVERT: B 170 LYS cc_start: 0.9234 (tptt) cc_final: 0.9017 (tptp) REVERT: B 338 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8590 (ttmm) REVERT: C 47 LYS cc_start: 0.9097 (mtmt) cc_final: 0.8878 (mttp) REVERT: C 56 LEU cc_start: 0.9188 (mt) cc_final: 0.8832 (pp) REVERT: C 65 ASP cc_start: 0.8595 (t70) cc_final: 0.7958 (t0) REVERT: C 321 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8304 (mt-10) REVERT: C 325 ARG cc_start: 0.8080 (ptp-110) cc_final: 0.7565 (ptm-80) REVERT: C 330 TYR cc_start: 0.8501 (m-80) cc_final: 0.8157 (m-80) REVERT: D 47 LYS cc_start: 0.9183 (mtmt) cc_final: 0.8705 (mtmm) REVERT: D 49 ILE cc_start: 0.9184 (mt) cc_final: 0.8771 (tt) REVERT: D 57 GLN cc_start: 0.8836 (mt0) cc_final: 0.8424 (mp10) REVERT: D 77 MET cc_start: 0.8137 (mmm) cc_final: 0.7643 (mmm) REVERT: D 128 GLN cc_start: 0.8246 (tt0) cc_final: 0.7853 (tm-30) REVERT: D 197 CYS cc_start: 0.8415 (m) cc_final: 0.7794 (m) REVERT: D 332 LYS cc_start: 0.9300 (mtpt) cc_final: 0.8717 (mtpt) REVERT: E 153 ILE cc_start: 0.9334 (tp) cc_final: 0.9075 (tp) REVERT: E 170 PHE cc_start: 0.8116 (t80) cc_final: 0.7597 (t80) REVERT: E 189 ASN cc_start: 0.9042 (m-40) cc_final: 0.8590 (t0) REVERT: E 234 MET cc_start: 0.8844 (mmm) cc_final: 0.8176 (mmm) REVERT: E 309 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9200 (tt) REVERT: E 410 MET cc_start: 0.7827 (tpt) cc_final: 0.7091 (tmm) REVERT: E 546 PHE cc_start: 0.8970 (t80) cc_final: 0.8478 (t80) REVERT: E 599 ARG cc_start: 0.8161 (ptp90) cc_final: 0.7943 (ptt-90) REVERT: E 1080 LEU cc_start: 0.9297 (tp) cc_final: 0.9029 (tp) REVERT: E 1151 VAL cc_start: 0.9428 (m) cc_final: 0.9221 (p) REVERT: E 1191 GLN cc_start: 0.8942 (tp40) cc_final: 0.8529 (pp30) REVERT: E 1229 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7751 (tm-30) REVERT: E 1246 ARG cc_start: 0.8607 (mmp80) cc_final: 0.8317 (mmp80) REVERT: E 1287 TYR cc_start: 0.8673 (m-80) cc_final: 0.8060 (m-10) REVERT: E 1305 MET cc_start: 0.9040 (mmm) cc_final: 0.8820 (mmm) REVERT: E 1425 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7940 (tt) REVERT: E 1492 LEU cc_start: 0.9368 (mt) cc_final: 0.9111 (mm) REVERT: E 1505 MET cc_start: 0.8322 (mtt) cc_final: 0.7673 (mmp) outliers start: 70 outliers final: 40 residues processed: 373 average time/residue: 0.3223 time to fit residues: 187.1619 Evaluate side-chains 340 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 297 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 547 MET Chi-restraints excluded: chain E residue 580 SER Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1249 GLU Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1500 THR Chi-restraints excluded: chain E residue 1535 THR Chi-restraints excluded: chain E residue 1542 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 243 optimal weight: 0.1980 chunk 258 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 153 ASN C 153 ASN D 41 ASN D 242 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2662 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= 0.173 Angle : 0.618 16.131 29285 Z= 0.303 Chirality : 0.043 0.213 3463 Planarity : 0.004 0.066 3641 Dihedral : 6.414 88.643 2915 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 2.88 % Allowed : 22.27 % Favored : 74.86 % 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: -0.81 (0.16), residues: 2658 helix: 0.35 (0.15), residues: 1286 sheet: -0.90 (0.29), residues: 306 loop : -1.47 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.008 0.001 HIS E 60 PHE 0.021 0.001 PHE E1503 TYR 0.012 0.001 TYR D 268 ARG 0.003 0.000 ARG E 371 *********************** 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 392 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 327 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9293 (mmmt) cc_final: 0.8887 (mtmm) REVERT: A 74 ILE cc_start: 0.9505 (tp) cc_final: 0.9251 (tp) REVERT: A 197 CYS cc_start: 0.8495 (m) cc_final: 0.8267 (m) REVERT: A 240 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7319 (ptm) REVERT: A 288 GLU cc_start: 0.7926 (pp20) cc_final: 0.7585 (pp20) REVERT: A 330 TYR cc_start: 0.8628 (m-10) cc_final: 0.8308 (m-80) REVERT: B 170 LYS cc_start: 0.9187 (tptt) cc_final: 0.8981 (tptp) REVERT: B 338 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8561 (ttmm) REVERT: C 47 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8872 (mttp) REVERT: C 56 LEU cc_start: 0.9141 (mt) cc_final: 0.8825 (pp) REVERT: C 65 ASP cc_start: 0.8579 (t70) cc_final: 0.7931 (t0) REVERT: C 321 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8299 (mt-10) REVERT: C 325 ARG cc_start: 0.8208 (ptp-110) cc_final: 0.7781 (ptm-80) REVERT: C 330 TYR cc_start: 0.8600 (m-80) cc_final: 0.8333 (m-80) REVERT: D 47 LYS cc_start: 0.9181 (mtmt) cc_final: 0.8622 (mtmm) REVERT: D 57 GLN cc_start: 0.8822 (mt0) cc_final: 0.8458 (mp10) REVERT: D 128 GLN cc_start: 0.8250 (tt0) cc_final: 0.7887 (tm-30) REVERT: D 197 CYS cc_start: 0.8531 (m) cc_final: 0.7825 (m) REVERT: E 80 PHE cc_start: 0.8763 (m-80) cc_final: 0.8358 (m-80) REVERT: E 170 PHE cc_start: 0.8096 (t80) cc_final: 0.7703 (t80) REVERT: E 189 ASN cc_start: 0.9036 (m-40) cc_final: 0.8557 (t0) REVERT: E 234 MET cc_start: 0.8839 (mmm) cc_final: 0.8268 (mmm) REVERT: E 309 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9223 (tt) REVERT: E 401 MET cc_start: 0.8995 (tpp) cc_final: 0.8715 (mpp) REVERT: E 410 MET cc_start: 0.7787 (tpt) cc_final: 0.7033 (tmm) REVERT: E 413 MET cc_start: 0.7639 (ptp) cc_final: 0.7338 (ptt) REVERT: E 503 MET cc_start: 0.8904 (tpt) cc_final: 0.8702 (tpt) REVERT: E 546 PHE cc_start: 0.8917 (t80) cc_final: 0.8525 (t80) REVERT: E 594 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8407 (mm) REVERT: E 599 ARG cc_start: 0.8129 (ptp90) cc_final: 0.7924 (ptt-90) REVERT: E 1080 LEU cc_start: 0.9318 (tp) cc_final: 0.9062 (tp) REVERT: E 1122 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9256 (mm) REVERT: E 1124 ARG cc_start: 0.8593 (mmt-90) cc_final: 0.8097 (mmt-90) REVERT: E 1151 VAL cc_start: 0.9402 (m) cc_final: 0.9198 (p) REVERT: E 1191 GLN cc_start: 0.8896 (tp40) cc_final: 0.8507 (pp30) REVERT: E 1246 ARG cc_start: 0.8559 (mmp80) cc_final: 0.8212 (mmp80) REVERT: E 1287 TYR cc_start: 0.8592 (m-80) cc_final: 0.7995 (m-10) REVERT: E 1305 MET cc_start: 0.8946 (mmm) cc_final: 0.8726 (mmm) REVERT: E 1492 LEU cc_start: 0.9347 (mt) cc_final: 0.9104 (mm) outliers start: 65 outliers final: 35 residues processed: 375 average time/residue: 0.3221 time to fit residues: 188.9955 Evaluate side-chains 340 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 300 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1249 GLU Chi-restraints excluded: chain E residue 1500 THR Chi-restraints excluded: chain E residue 1535 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 192 optimal weight: 0.0870 chunk 106 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 0.3980 chunk 231 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- 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 153 ASN B 160 ASN D 41 ASN E 923 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2877 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= 0.215 Angle : 0.626 14.247 29285 Z= 0.310 Chirality : 0.043 0.279 3463 Planarity : 0.004 0.062 3641 Dihedral : 6.183 69.202 2915 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.86 % Favored : 95.07 % Rotamer: Outliers : 2.88 % Allowed : 23.27 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.40 (0.17), residues: 2658 helix: 0.69 (0.15), residues: 1289 sheet: -0.80 (0.30), residues: 304 loop : -1.23 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 83 HIS 0.004 0.001 HIS E1203 PHE 0.019 0.001 PHE E1503 TYR 0.013 0.001 TYR C 268 ARG 0.009 0.000 ARG E 371 *********************** 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 378 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 313 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9292 (mmmt) cc_final: 0.8891 (mtmm) REVERT: A 74 ILE cc_start: 0.9509 (tp) cc_final: 0.9162 (tp) REVERT: A 197 CYS cc_start: 0.8548 (m) cc_final: 0.8339 (m) REVERT: A 288 GLU cc_start: 0.7951 (pp20) cc_final: 0.7558 (pp20) REVERT: B 77 MET cc_start: 0.7676 (tpt) cc_final: 0.7417 (tpp) REVERT: B 170 LYS cc_start: 0.9211 (tptt) cc_final: 0.8946 (tttp) REVERT: B 338 LYS cc_start: 0.8924 (ttmm) cc_final: 0.8572 (ttmm) REVERT: C 56 LEU cc_start: 0.9161 (mt) cc_final: 0.8830 (pp) REVERT: C 65 ASP cc_start: 0.8634 (t70) cc_final: 0.8086 (t0) REVERT: C 321 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8278 (mt-10) REVERT: C 325 ARG cc_start: 0.8182 (ptp-110) cc_final: 0.7778 (ptm-80) REVERT: D 47 LYS cc_start: 0.9296 (mtmt) cc_final: 0.8798 (mtmm) REVERT: D 57 GLN cc_start: 0.8853 (mt0) cc_final: 0.8451 (mp10) REVERT: D 128 GLN cc_start: 0.8270 (tt0) cc_final: 0.7950 (tm-30) REVERT: D 251 LEU cc_start: 0.8854 (tp) cc_final: 0.8648 (tp) REVERT: E 153 ILE cc_start: 0.9361 (tp) cc_final: 0.9136 (tp) REVERT: E 170 PHE cc_start: 0.8194 (t80) cc_final: 0.7852 (t80) REVERT: E 189 ASN cc_start: 0.9055 (m-40) cc_final: 0.8571 (t0) REVERT: E 234 MET cc_start: 0.8867 (mmm) cc_final: 0.8453 (mmm) REVERT: E 410 MET cc_start: 0.7824 (tpt) cc_final: 0.7072 (tmm) REVERT: E 413 MET cc_start: 0.7660 (ptp) cc_final: 0.7373 (ptt) REVERT: E 503 MET cc_start: 0.8998 (tpt) cc_final: 0.8685 (tpt) REVERT: E 546 PHE cc_start: 0.8882 (t80) cc_final: 0.8540 (t80) REVERT: E 594 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8403 (mm) REVERT: E 599 ARG cc_start: 0.8171 (ptp90) cc_final: 0.7964 (ptt-90) REVERT: E 869 MET cc_start: 0.8734 (mmm) cc_final: 0.8490 (mmm) REVERT: E 1122 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9266 (mm) REVERT: E 1124 ARG cc_start: 0.8603 (mmt-90) cc_final: 0.8200 (mmt-90) REVERT: E 1191 GLN cc_start: 0.8937 (tp40) cc_final: 0.8674 (pp30) REVERT: E 1246 ARG cc_start: 0.8580 (mmp80) cc_final: 0.8240 (mmp80) REVERT: E 1305 MET cc_start: 0.8963 (mmm) cc_final: 0.8724 (mmm) outliers start: 65 outliers final: 51 residues processed: 364 average time/residue: 0.3163 time to fit residues: 180.0831 Evaluate side-chains 354 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 300 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 580 SER Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1249 GLU Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1500 THR Chi-restraints excluded: chain E residue 1535 THR Chi-restraints excluded: chain E residue 1542 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 5.9990 chunk 232 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 258 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 119 optimal weight: 0.0370 chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 0.0470 chunk 135 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN C 277 HIS D 41 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 21550 Z= 0.153 Angle : 0.609 10.699 29285 Z= 0.295 Chirality : 0.043 0.241 3463 Planarity : 0.003 0.058 3641 Dihedral : 6.045 54.967 2915 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.48 % Favored : 95.44 % Rotamer: Outliers : 3.01 % Allowed : 23.53 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.27 (0.17), residues: 2658 helix: 0.79 (0.15), residues: 1309 sheet: -0.75 (0.30), residues: 304 loop : -1.19 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1037 HIS 0.002 0.000 HIS E1024 PHE 0.018 0.001 PHE C 250 TYR 0.011 0.001 TYR D 304 ARG 0.003 0.000 ARG E1246 *********************** REFINEMENT MACRO_CYCLE 6 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 400 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 332 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9283 (mmmt) cc_final: 0.8888 (mtmm) REVERT: A 74 ILE cc_start: 0.9504 (tp) cc_final: 0.9140 (tp) REVERT: A 197 CYS cc_start: 0.8480 (m) cc_final: 0.8231 (m) REVERT: A 288 GLU cc_start: 0.7880 (pp20) cc_final: 0.7451 (pp20) REVERT: A 330 TYR cc_start: 0.8556 (m-10) cc_final: 0.8315 (m-10) REVERT: B 77 MET cc_start: 0.7630 (tpt) cc_final: 0.7429 (tpp) REVERT: B 170 LYS cc_start: 0.9189 (tptt) cc_final: 0.8975 (tttp) REVERT: B 338 LYS cc_start: 0.8895 (ttmm) cc_final: 0.8542 (ttmm) REVERT: C 56 LEU cc_start: 0.9108 (mt) cc_final: 0.8796 (pp) REVERT: C 65 ASP cc_start: 0.8608 (t70) cc_final: 0.8061 (t0) REVERT: C 277 HIS cc_start: 0.8807 (OUTLIER) cc_final: 0.8531 (t70) REVERT: C 325 ARG cc_start: 0.8145 (ptp-110) cc_final: 0.7735 (ptm-80) REVERT: D 44 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8795 (t) REVERT: D 47 LYS cc_start: 0.9270 (mtmt) cc_final: 0.9017 (mtmt) REVERT: D 57 GLN cc_start: 0.8793 (mt0) cc_final: 0.8421 (mp10) REVERT: E 80 PHE cc_start: 0.8687 (m-80) cc_final: 0.8232 (m-80) REVERT: E 170 PHE cc_start: 0.8128 (t80) cc_final: 0.7815 (t80) REVERT: E 189 ASN cc_start: 0.9024 (m-40) cc_final: 0.8539 (t0) REVERT: E 234 MET cc_start: 0.8851 (mmm) cc_final: 0.8365 (mmm) REVERT: E 410 MET cc_start: 0.7742 (tpt) cc_final: 0.6974 (tmm) REVERT: E 413 MET cc_start: 0.7483 (ptp) cc_final: 0.7216 (ptt) REVERT: E 503 MET cc_start: 0.8989 (tpt) cc_final: 0.8654 (tpt) REVERT: E 546 PHE cc_start: 0.8952 (t80) cc_final: 0.8632 (t80) REVERT: E 594 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8374 (mm) REVERT: E 1122 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9266 (mm) REVERT: E 1124 ARG cc_start: 0.8595 (mmt-90) cc_final: 0.8184 (mmt-90) REVERT: E 1191 GLN cc_start: 0.8867 (tp40) cc_final: 0.8515 (pp30) REVERT: E 1305 MET cc_start: 0.8881 (mmm) cc_final: 0.8626 (mmm) outliers start: 68 outliers final: 40 residues processed: 388 average time/residue: 0.3150 time to fit residues: 191.1463 Evaluate side-chains 346 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 302 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 580 SER Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1163 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1249 GLU Chi-restraints excluded: chain E residue 1535 THR Chi-restraints excluded: chain E residue 1542 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 257 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 160 ASN C 277 HIS D 41 ASN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21550 Z= 0.305 Angle : 0.676 11.284 29285 Z= 0.334 Chirality : 0.045 0.244 3463 Planarity : 0.004 0.058 3641 Dihedral : 6.108 51.238 2914 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.42 % Favored : 94.46 % Rotamer: Outliers : 3.31 % Allowed : 24.27 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.16 (0.17), residues: 2658 helix: 0.85 (0.15), residues: 1316 sheet: -0.71 (0.30), residues: 304 loop : -1.09 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 83 HIS 0.008 0.001 HIS C 277 PHE 0.030 0.002 PHE C 250 TYR 0.016 0.002 TYR A 304 ARG 0.006 0.000 ARG E1246 *********************** REFINEMENT MACRO_CYCLE 7 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 373 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 298 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9290 (mmmt) cc_final: 0.8907 (mtmm) REVERT: A 74 ILE cc_start: 0.9514 (tp) cc_final: 0.9166 (tp) REVERT: A 197 CYS cc_start: 0.8575 (m) cc_final: 0.8369 (m) REVERT: A 288 GLU cc_start: 0.7984 (pp20) cc_final: 0.7550 (pp20) REVERT: B 77 MET cc_start: 0.7726 (tpt) cc_final: 0.7496 (tpp) REVERT: B 170 LYS cc_start: 0.9254 (tptt) cc_final: 0.9012 (tttp) REVERT: B 338 LYS cc_start: 0.8966 (ttmm) cc_final: 0.8589 (ttmm) REVERT: C 56 LEU cc_start: 0.9169 (mt) cc_final: 0.8865 (pp) REVERT: C 65 ASP cc_start: 0.8683 (t70) cc_final: 0.8101 (t0) REVERT: C 220 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.9073 (m) REVERT: C 325 ARG cc_start: 0.8128 (ptp-110) cc_final: 0.7695 (ptm-80) REVERT: D 44 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8835 (t) REVERT: D 47 LYS cc_start: 0.9250 (mtmt) cc_final: 0.8909 (mtmm) REVERT: D 332 LYS cc_start: 0.9196 (mtpt) cc_final: 0.8745 (mtmt) REVERT: E 153 ILE cc_start: 0.9382 (tp) cc_final: 0.9175 (tp) REVERT: E 170 PHE cc_start: 0.8322 (t80) cc_final: 0.8048 (t80) REVERT: E 189 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8560 (t0) REVERT: E 234 MET cc_start: 0.8932 (mmm) cc_final: 0.8491 (mmm) REVERT: E 410 MET cc_start: 0.7846 (tpt) cc_final: 0.7080 (tmm) REVERT: E 503 MET cc_start: 0.9034 (tpt) cc_final: 0.8774 (tpt) REVERT: E 546 PHE cc_start: 0.9056 (t80) cc_final: 0.8763 (t80) REVERT: E 594 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8322 (mm) REVERT: E 1191 GLN cc_start: 0.8953 (tp40) cc_final: 0.8684 (pp30) REVERT: E 1305 MET cc_start: 0.8927 (mmm) cc_final: 0.8662 (mmm) outliers start: 75 outliers final: 56 residues processed: 356 average time/residue: 0.3434 time to fit residues: 193.3410 Evaluate side-chains 349 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 289 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 580 SER Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 936 ASP Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1163 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1249 GLU Chi-restraints excluded: chain E residue 1339 TRP Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1535 THR Chi-restraints excluded: chain E residue 1542 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 163 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 127 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 202 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN D 41 ASN ** E1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 21550 Z= 0.159 Angle : 0.639 14.691 29285 Z= 0.306 Chirality : 0.044 0.289 3463 Planarity : 0.003 0.054 3641 Dihedral : 6.047 50.216 2914 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.63 % Rotamer: Outliers : 2.61 % Allowed : 25.32 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.08 (0.17), residues: 2658 helix: 1.03 (0.15), residues: 1290 sheet: -0.63 (0.30), residues: 300 loop : -0.88 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 83 HIS 0.003 0.000 HIS B 216 PHE 0.026 0.001 PHE C 250 TYR 0.015 0.001 TYR A 304 ARG 0.006 0.000 ARG E1246 *********************** REFINEMENT MACRO_CYCLE 8 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 379 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 320 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9279 (mmmt) cc_final: 0.8884 (mtmm) REVERT: A 74 ILE cc_start: 0.9487 (tp) cc_final: 0.9141 (tp) REVERT: A 197 CYS cc_start: 0.8428 (m) cc_final: 0.8207 (m) REVERT: A 288 GLU cc_start: 0.7874 (pp20) cc_final: 0.7428 (pp20) REVERT: B 77 MET cc_start: 0.7667 (tpt) cc_final: 0.7448 (tpp) REVERT: B 170 LYS cc_start: 0.9223 (tptt) cc_final: 0.9010 (tttp) REVERT: B 338 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8592 (ttmm) REVERT: C 56 LEU cc_start: 0.9071 (mt) cc_final: 0.8777 (pp) REVERT: C 65 ASP cc_start: 0.8614 (t70) cc_final: 0.8028 (t0) REVERT: C 277 HIS cc_start: 0.8788 (OUTLIER) cc_final: 0.8488 (t70) REVERT: C 325 ARG cc_start: 0.8113 (ptp-110) cc_final: 0.7765 (ptm-80) REVERT: C 330 TYR cc_start: 0.8688 (m-80) cc_final: 0.8453 (m-80) REVERT: D 47 LYS cc_start: 0.9241 (mtmt) cc_final: 0.8920 (mtmt) REVERT: D 197 CYS cc_start: 0.8760 (m) cc_final: 0.8353 (t) REVERT: E 80 PHE cc_start: 0.8668 (m-80) cc_final: 0.8181 (m-80) REVERT: E 81 MET cc_start: 0.8519 (mtp) cc_final: 0.8235 (mtm) REVERT: E 170 PHE cc_start: 0.8156 (t80) cc_final: 0.7895 (t80) REVERT: E 189 ASN cc_start: 0.8934 (m-40) cc_final: 0.8632 (t0) REVERT: E 234 MET cc_start: 0.8840 (mmm) cc_final: 0.8440 (mmm) REVERT: E 410 MET cc_start: 0.7708 (tpt) cc_final: 0.6893 (tmm) REVERT: E 413 MET cc_start: 0.7499 (ptp) cc_final: 0.7204 (ptt) REVERT: E 442 MET cc_start: 0.7566 (ttt) cc_final: 0.7300 (tmm) REVERT: E 503 MET cc_start: 0.8997 (tpt) cc_final: 0.8763 (tpt) REVERT: E 546 PHE cc_start: 0.9027 (t80) cc_final: 0.8735 (t80) REVERT: E 1305 MET cc_start: 0.8884 (mmm) cc_final: 0.8606 (mmm) outliers start: 59 outliers final: 51 residues processed: 364 average time/residue: 0.3199 time to fit residues: 182.4506 Evaluate side-chains 354 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 302 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 580 SER Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 936 ASP Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1163 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1249 GLU Chi-restraints excluded: chain E residue 1339 TRP Chi-restraints excluded: chain E residue 1535 THR Chi-restraints excluded: chain E residue 1542 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 0.5980 chunk 246 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 239 optimal weight: 0.8980 chunk 144 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 chunk 216 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN D 41 ASN ** E1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21550 Z= 0.187 Angle : 0.660 13.235 29285 Z= 0.316 Chirality : 0.044 0.354 3463 Planarity : 0.003 0.054 3641 Dihedral : 5.983 47.625 2913 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.16 % Favored : 94.80 % Rotamer: Outliers : 2.92 % Allowed : 24.92 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.14 (0.17), residues: 2658 helix: 1.06 (0.15), residues: 1291 sheet: -0.61 (0.30), residues: 300 loop : -0.83 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 83 HIS 0.003 0.000 HIS E1203 PHE 0.025 0.001 PHE E1164 TYR 0.025 0.001 TYR E 231 ARG 0.006 0.000 ARG E1246 *********************** REFINEMENT MACRO_CYCLE 9 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: 66 poor density : 312 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9492 (tp) cc_final: 0.9141 (tp) REVERT: A 197 CYS cc_start: 0.8486 (m) cc_final: 0.8242 (m) REVERT: A 288 GLU cc_start: 0.7875 (pp20) cc_final: 0.7440 (pp20) REVERT: B 77 MET cc_start: 0.7707 (tpt) cc_final: 0.7474 (tpp) REVERT: B 170 LYS cc_start: 0.9229 (tptt) cc_final: 0.9020 (tttp) REVERT: B 338 LYS cc_start: 0.8979 (ttmm) cc_final: 0.8615 (ttmm) REVERT: C 56 LEU cc_start: 0.9072 (mt) cc_final: 0.8789 (pp) REVERT: C 65 ASP cc_start: 0.8650 (t70) cc_final: 0.8052 (t0) REVERT: C 277 HIS cc_start: 0.8792 (OUTLIER) cc_final: 0.8490 (t70) REVERT: C 325 ARG cc_start: 0.8108 (ptp-110) cc_final: 0.7710 (ptm-80) REVERT: C 330 TYR cc_start: 0.8693 (m-80) cc_final: 0.8302 (m-80) REVERT: D 44 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8757 (t) REVERT: D 47 LYS cc_start: 0.9226 (mtmt) cc_final: 0.8911 (mtmt) REVERT: D 197 CYS cc_start: 0.8737 (m) cc_final: 0.8371 (t) REVERT: E 80 PHE cc_start: 0.8727 (m-80) cc_final: 0.8213 (m-80) REVERT: E 153 ILE cc_start: 0.9315 (tp) cc_final: 0.9113 (tp) REVERT: E 170 PHE cc_start: 0.8204 (t80) cc_final: 0.7938 (t80) REVERT: E 189 ASN cc_start: 0.9018 (m-40) cc_final: 0.8644 (t0) REVERT: E 234 MET cc_start: 0.8869 (mmm) cc_final: 0.8494 (mmm) REVERT: E 410 MET cc_start: 0.7720 (tpt) cc_final: 0.6895 (tmm) REVERT: E 413 MET cc_start: 0.7531 (ptp) cc_final: 0.7249 (ptt) REVERT: E 442 MET cc_start: 0.7553 (ttt) cc_final: 0.7295 (tmm) REVERT: E 503 MET cc_start: 0.8997 (tpt) cc_final: 0.8745 (tpt) REVERT: E 546 PHE cc_start: 0.9029 (t80) cc_final: 0.8738 (t80) REVERT: E 1305 MET cc_start: 0.8890 (mmm) cc_final: 0.8609 (mmm) outliers start: 66 outliers final: 56 residues processed: 359 average time/residue: 0.3213 time to fit residues: 181.2590 Evaluate side-chains 357 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 299 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 580 SER Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 936 ASP Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1163 VAL Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1249 GLU Chi-restraints excluded: chain E residue 1339 TRP Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1535 THR Chi-restraints excluded: chain E residue 1542 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 160 ASN B 242 ASN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21550 Z= 0.219 Angle : 0.667 13.372 29285 Z= 0.320 Chirality : 0.044 0.249 3463 Planarity : 0.004 0.053 3641 Dihedral : 6.014 46.908 2913 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.16 % Favored : 94.80 % Rotamer: Outliers : 2.79 % Allowed : 25.23 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.15 (0.17), residues: 2658 helix: 1.07 (0.15), residues: 1291 sheet: -0.65 (0.30), residues: 300 loop : -0.81 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 83 HIS 0.004 0.001 HIS E1203 PHE 0.018 0.001 PHE C 250 TYR 0.029 0.001 TYR E1159 ARG 0.006 0.000 ARG E1246 ********************** REFINEMENT MACRO_CYCLE 10 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 359 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 296 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9492 (tp) cc_final: 0.9153 (tp) REVERT: A 197 CYS cc_start: 0.8529 (m) cc_final: 0.8256 (m) REVERT: A 240 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7252 (ptm) REVERT: A 288 GLU cc_start: 0.7915 (pp20) cc_final: 0.7483 (pp20) REVERT: B 77 MET cc_start: 0.7711 (tpt) cc_final: 0.7486 (tpp) REVERT: B 170 LYS cc_start: 0.9245 (tptt) cc_final: 0.9026 (tttp) REVERT: B 338 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8656 (ttmm) REVERT: C 56 LEU cc_start: 0.9087 (mt) cc_final: 0.8807 (pp) REVERT: C 65 ASP cc_start: 0.8674 (t70) cc_final: 0.8070 (t0) REVERT: C 277 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.8460 (t70) REVERT: C 325 ARG cc_start: 0.8134 (ptp-110) cc_final: 0.7735 (ptm-80) REVERT: D 44 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8778 (t) REVERT: D 47 LYS cc_start: 0.9206 (mtmt) cc_final: 0.8901 (mtmt) REVERT: E 43 ILE cc_start: 0.9327 (tt) cc_final: 0.9030 (pt) REVERT: E 153 ILE cc_start: 0.9321 (tp) cc_final: 0.9104 (tp) REVERT: E 170 PHE cc_start: 0.8252 (t80) cc_final: 0.7991 (t80) REVERT: E 189 ASN cc_start: 0.9034 (m-40) cc_final: 0.8557 (t0) REVERT: E 410 MET cc_start: 0.7759 (tpt) cc_final: 0.6919 (tmm) REVERT: E 442 MET cc_start: 0.7580 (ttt) cc_final: 0.7308 (tmm) REVERT: E 503 MET cc_start: 0.9007 (tpt) cc_final: 0.8747 (tpt) REVERT: E 546 PHE cc_start: 0.9026 (t80) cc_final: 0.8820 (t80) REVERT: E 869 MET cc_start: 0.8777 (mmm) cc_final: 0.8417 (mmm) REVERT: E 1305 MET cc_start: 0.8900 (mmm) cc_final: 0.8621 (mmm) outliers start: 63 outliers final: 56 residues processed: 344 average time/residue: 0.3214 time to fit residues: 174.1881 Evaluate side-chains 351 residues out of total 2315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 292 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 580 SER Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 936 ASP Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1163 VAL Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1249 GLU Chi-restraints excluded: chain E residue 1262 ILE Chi-restraints excluded: chain E residue 1339 TRP Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1535 THR Chi-restraints excluded: chain E residue 1542 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 0.2980 chunk 225 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 195 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN D 41 ASN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.075329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.060420 restraints weight = 118596.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.062782 restraints weight = 48170.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.064377 restraints weight = 26921.731| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21550 Z= 0.188 Angle : 0.660 13.484 29285 Z= 0.314 Chirality : 0.044 0.245 3463 Planarity : 0.003 0.053 3641 Dihedral : 5.980 46.434 2913 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.20 % Favored : 94.76 % Rotamer: Outliers : 2.66 % Allowed : 25.45 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.20 (0.17), residues: 2658 helix: 1.12 (0.15), residues: 1288 sheet: -0.65 (0.30), residues: 300 loop : -0.79 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 83 HIS 0.003 0.000 HIS E1203 PHE 0.025 0.001 PHE E1164 TYR 0.028 0.001 TYR E1159 ARG 0.005 0.000 ARG E1246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4464.62 seconds wall clock time: 83 minutes 11.53 seconds (4991.53 seconds total)