Starting phenix.real_space_refine on Thu Apr 11 02:24:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5x_24842/04_2024/7s5x_24842_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5x_24842/04_2024/7s5x_24842.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/7s5x_24842/04_2024/7s5x_24842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5x_24842/04_2024/7s5x_24842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5x_24842/04_2024/7s5x_24842_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5x_24842/04_2024/7s5x_24842_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= 0.085 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 13714 2.51 5 N 3607 2.21 5 O 3763 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 PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A ASP 352": "OD1" <-> "OD2" 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 65": "OD1" <-> "OD2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ASP 237": "OD1" <-> "OD2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 350": "OD1" <-> "OD2" Residue "B ASP 352": "OD1" <-> "OD2" 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 108": "OE1" <-> "OE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ASP 237": "OD1" <-> "OD2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "C TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D ASP 237": "OD1" <-> "OD2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D GLU 288": "OE1" <-> "OE2" Residue "D ASP 323": "OD1" <-> "OD2" Residue "D TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 350": "OD1" <-> "OD2" Residue "D ASP 352": "OD1" <-> "OD2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 210": "OD1" <-> "OD2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 326": "OD1" <-> "OD2" Residue "E TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 425": "OD1" <-> "OD2" Residue "E PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 560": "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 PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 842": "NH1" <-> "NH2" Residue "E ASP 866": "OD1" <-> "OD2" Residue "E GLU 911": "OE1" <-> "OE2" Residue "E ASP 916": "OD1" <-> "OD2" Residue "E PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 942": "OE1" <-> "OE2" Residue "E ASP 1031": "OD1" <-> "OD2" Residue "E ARG 1124": "NH1" <-> "NH2" Residue "E ASP 1133": "OD1" <-> "OD2" Residue "E TYR 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1188": "OD1" <-> "OD2" Residue "E ASP 1193": "OD1" <-> "OD2" Residue "E GLU 1220": "OE1" <-> "OE2" Residue "E ARG 1222": "NH1" <-> "NH2" Residue "E ASP 1232": "OD1" <-> "OD2" Residue "E PHE 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1249": "OE1" <-> "OE2" Residue "E GLU 1275": "OE1" <-> "OE2" Residue "E GLU 1306": "OE1" <-> "OE2" Residue "E ARG 1314": "NH1" <-> "NH2" Residue "E TYR 1326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1419": "NH1" <-> "NH2" Residue "E ARG 1437": "NH1" <-> "NH2" Residue "E ARG 1487": "NH1" <-> "NH2" Residue "E ARG 1494": "NH1" <-> "NH2" Residue "E ARG 1498": "NH1" <-> "NH2" Residue "E PHE 1503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1530": "OD1" <-> "OD2" Residue "E GLU 1559": "OE1" <-> "OE2" Residue "E PHE 1560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1581": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 21213 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: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} 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: 11137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1416, 11137 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'peptide': 1412, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 46, 'TRANS': 1365, 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: 6 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 Time building chain proxies: 11.46, per 1000 atoms: 0.54 Number of scatterers: 21213 At special positions: 0 Unit cell: (135.2, 154.7, 137.8, 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 3763 8.00 N 3607 7.00 C 13714 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=2.02 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.02 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.02 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.23 Conformation dependent library (CDL) restraints added in 4.1 seconds 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 17 sheets defined 43.4% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.91 Creating SS restraints... Processing helix chain 'A' and resid 60 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: 3.728A pdb=" N ALA A 178 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 179 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 68 through 96 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 143 through 171 Processing helix chain 'B' and resid 174 through 179 removed outlier: 3.728A pdb=" N ALA B 178 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 179 " --> pdb=" O ARG B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 68 through 96 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 171 Processing helix chain 'C' and resid 174 through 179 removed outlier: 3.728A pdb=" N ALA C 178 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU C 179 " --> pdb=" O ARG C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'D' and resid 60 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 174 through 179 removed outlier: 3.728A pdb=" N ALA D 178 " --> pdb=" O HIS D 175 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU D 179 " --> pdb=" O ARG D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'E' and resid 28 through 33 Processing helix chain 'E' and resid 35 through 51 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 72 through 97 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 131 Processing helix chain 'E' and resid 138 through 160 Processing helix chain 'E' and resid 168 through 182 Processing helix chain 'E' and resid 186 through 190 Processing helix chain 'E' and resid 225 through 229 removed outlier: 3.584A pdb=" N GLY E 229 " --> pdb=" O LEU E 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 225 through 229' Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 265 through 271 Processing helix chain 'E' and resid 285 through 295 Processing helix chain 'E' and resid 298 through 312 removed outlier: 5.061A pdb=" N ASP E 311 " --> pdb=" O ARG E 307 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU E 312 " --> pdb=" O ILE E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 329 Proline residue: E 318 - end of helix removed outlier: 4.989A pdb=" N VAL E 325 " --> pdb=" O PHE E 322 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP E 326 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU E 328 " --> pdb=" O VAL E 325 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY E 329 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 354 removed outlier: 3.592A pdb=" N ALA E 354 " --> pdb=" O GLN E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 402 removed outlier: 3.974A pdb=" N HIS E 402 " --> pdb=" O ASN E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 409 removed outlier: 4.295A pdb=" N SER E 409 " --> pdb=" O SER E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 424 removed outlier: 3.807A pdb=" N VAL E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 456 Proline residue: E 437 - end of helix Proline residue: E 443 - end of helix Processing helix chain 'E' and resid 458 through 504 removed outlier: 3.512A pdb=" N ALA E 461 " --> pdb=" O GLY E 458 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 463 " --> pdb=" O SER E 460 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA E 465 " --> pdb=" O LEU E 462 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU E 470 " --> pdb=" O VAL E 467 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA E 472 " --> pdb=" O ILE E 469 " (cutoff:3.500A) Proline residue: E 473 - end of helix removed outlier: 5.595A pdb=" N PHE E 477 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL E 478 " --> pdb=" O GLN E 475 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA E 479 " --> pdb=" O TYR E 476 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN E 484 " --> pdb=" O LYS E 481 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA E 485 " --> pdb=" O LEU E 482 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG E 487 " --> pdb=" O GLN E 484 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 488 " --> pdb=" O ALA E 485 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 497 " --> pdb=" O ASN E 494 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS E 498 " --> pdb=" O GLU E 495 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR E 500 " --> pdb=" O LEU E 497 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN E 501 " --> pdb=" O LYS E 498 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU E 502 " --> pdb=" O GLN E 499 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 504 " --> pdb=" O ASN E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 512 Processing helix chain 'E' and resid 516 through 564 Proline residue: E 552 - end of helix removed outlier: 3.842A pdb=" N LEU E 557 " --> pdb=" O ILE E 553 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL E 564 " --> pdb=" O PHE E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 588 Processing helix chain 'E' and resid 591 through 615 removed outlier: 3.636A pdb=" N LEU E 594 " --> pdb=" O LEU E 591 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER E 595 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 598 " --> pdb=" O SER E 595 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER E 600 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR E 601 " --> pdb=" O VAL E 598 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS E 603 " --> pdb=" O SER E 600 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL E 606 " --> pdb=" O LYS E 603 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL E 608 " --> pdb=" O LEU E 605 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN E 609 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS E 610 " --> pdb=" O SER E 607 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER E 612 " --> pdb=" O GLN E 609 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E 615 " --> pdb=" O SER E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 720 through 728 removed outlier: 3.756A pdb=" N LEU E 724 " --> pdb=" O LYS E 720 " (cutoff:3.500A) Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 796 through 806 removed outlier: 3.742A pdb=" N CYS E 806 " --> pdb=" O VAL E 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 813 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 844 removed outlier: 3.850A pdb=" N ARG E 837 " --> pdb=" O GLY E 833 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 843 " --> pdb=" O SER E 839 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU E 844 " --> pdb=" O VAL E 840 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'E' and resid 876 through 879 No H-bonds generated for 'chain 'E' and resid 876 through 879' Processing helix chain 'E' and resid 893 through 895 No H-bonds generated for 'chain 'E' and resid 893 through 895' Processing helix chain 'E' and resid 914 through 919 Processing helix chain 'E' and resid 922 through 932 Processing helix chain 'E' and resid 999 through 1008 Processing helix chain 'E' and resid 1011 through 1038 removed outlier: 3.956A pdb=" N LEU E1015 " --> pdb=" O LEU E1011 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN E1020 " --> pdb=" O LEU E1016 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU E1027 " --> pdb=" O LYS E1023 " (cutoff:3.500A) Processing helix chain 'E' and resid 1064 through 1096 Processing helix chain 'E' and resid 1102 through 1105 No H-bonds generated for 'chain 'E' and resid 1102 through 1105' Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1118 through 1160 removed outlier: 3.789A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE E1136 " --> pdb=" O ILE E1132 " (cutoff:3.500A) Proline residue: E1137 - end of helix removed outlier: 3.519A pdb=" N VAL E1160 " --> pdb=" O VAL E1156 " (cutoff:3.500A) Processing helix chain 'E' and resid 1168 through 1209 removed outlier: 4.376A pdb=" N ALA E1185 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) Proline residue: E1199 - end of helix removed outlier: 3.556A pdb=" N GLU E1209 " --> pdb=" O ALA E1205 " (cutoff:3.500A) Processing helix chain 'E' and resid 1220 through 1272 removed outlier: 4.042A pdb=" N GLU E1249 " --> pdb=" O ASN E1245 " (cutoff:3.500A) Processing helix chain 'E' and resid 1279 through 1319 removed outlier: 3.541A pdb=" N SER E1292 " --> pdb=" O ALA E1288 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TRP E1297 " --> pdb=" O ASN E1293 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA E1311 " --> pdb=" O LEU E1307 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1385 through 1391 removed outlier: 3.791A pdb=" N SER E1389 " --> pdb=" O LYS E1385 " (cutoff:3.500A) Processing helix chain 'E' and resid 1415 through 1420 Processing helix chain 'E' and resid 1436 through 1440 Processing helix chain 'E' and resid 1448 through 1457 Processing helix chain 'E' and resid 1461 through 1466 Processing helix chain 'E' and resid 1484 through 1495 Processing helix chain 'E' and resid 1514 through 1527 Processing helix chain 'E' and resid 1563 through 1567 Processing helix chain 'E' and resid 1573 through 1581 Processing sheet with id= A, first strand: chain 'A' and resid 188 through 192 removed outlier: 3.514A pdb=" N VAL A 202 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 234 through 237 removed outlier: 3.787A pdb=" N ARG A 221 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 319 through 322 Processing sheet with id= D, first strand: chain 'B' and resid 188 through 192 removed outlier: 3.515A pdb=" N VAL B 202 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 234 through 237 removed outlier: 3.787A pdb=" N ARG B 221 " --> pdb=" O HIS B 234 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 319 through 322 Processing sheet with id= G, first strand: chain 'C' and resid 188 through 192 removed outlier: 3.515A pdb=" N VAL C 202 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 234 through 237 removed outlier: 3.787A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 319 through 322 Processing sheet with id= J, first strand: chain 'D' and resid 188 through 192 removed outlier: 3.515A pdb=" N VAL D 202 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 234 through 237 removed outlier: 3.786A pdb=" N ARG D 221 " --> pdb=" O HIS D 234 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 319 through 322 Processing sheet with id= M, first strand: chain 'E' and resid 907 through 912 removed outlier: 7.075A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU E 911 " --> pdb=" O ILE E 900 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE E 900 " --> pdb=" O GLU E 911 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N MET E 711 " --> pdb=" O ILE E 901 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N MET E 903 " --> pdb=" O MET E 711 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 713 " --> pdb=" O MET E 903 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 712 " --> pdb=" O LEU E 886 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 887 " --> pdb=" O LEU E 853 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA E 773 " --> pdb=" O PHE E 852 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 1556 through 1561 removed outlier: 6.719A pdb=" N VAL E1551 " --> pdb=" O LEU E1558 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE E1560 " --> pdb=" O VAL E1549 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL E1549 " --> pdb=" O PHE E1560 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY E1376 " --> pdb=" O ILE E1550 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU E1552 " --> pdb=" O GLY E1376 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS E1378 " --> pdb=" O LEU E1552 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N SER E1423 " --> pdb=" O ILE E1504 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 686 through 688 removed outlier: 7.157A pdb=" N THR E 688 " --> pdb=" O LYS E 733 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LYS E 733 " --> pdb=" O THR E 688 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 1346 through 1350 removed outlier: 5.239A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 1351 through 1353 removed outlier: 3.613A pdb=" N GLU E1400 " --> pdb=" O SER E1351 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ARG E1353 " --> pdb=" O THR E1398 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N THR E1398 " --> pdb=" O ARG E1353 " (cutoff:3.500A) 943 hydrogen bonds defined for protein. 2595 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: 7.41 Time building geometry restraints manager: 8.94 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: 6243 1.34 - 1.46: 4868 1.46 - 1.58: 10355 1.58 - 1.70: 18 1.70 - 1.82: 196 Bond restraints: 21680 Sorted by residual: bond pdb=" C4 ATP E1604 " pdb=" C5 ATP E1604 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.50e+01 bond pdb=" C5 ATP E1604 " pdb=" C6 ATP E1604 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.64e+01 bond pdb=" C5 ATP E1604 " pdb=" N7 ATP E1604 " ideal model delta sigma weight residual 1.387 1.337 0.050 1.00e-02 1.00e+04 2.54e+01 bond pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 1.374 1.324 0.050 1.00e-02 1.00e+04 2.54e+01 bond pdb=" C8 ATP E1604 " pdb=" N7 ATP E1604 " ideal model delta sigma weight residual 1.310 1.352 -0.042 1.00e-02 1.00e+04 1.78e+01 ... (remaining 21675 not shown) Histogram of bond angle deviations from ideal: 98.69 - 106.53: 668 106.53 - 114.37: 12716 114.37 - 122.21: 12162 122.21 - 130.05: 3702 130.05 - 137.88: 215 Bond angle restraints: 29463 Sorted by residual: angle pdb=" PB ATP E1604 " pdb=" O3B ATP E1604 " pdb=" PG ATP E1604 " ideal model delta sigma weight residual 139.87 122.49 17.38 1.00e+00 1.00e+00 3.02e+02 angle pdb=" PA ATP E1604 " pdb=" O3A ATP E1604 " pdb=" PB ATP E1604 " ideal model delta sigma weight residual 136.83 119.81 17.02 1.00e+00 1.00e+00 2.90e+02 angle pdb=" C5 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N3 ATP E1604 " ideal model delta sigma weight residual 126.80 119.57 7.23 1.00e+00 1.00e+00 5.23e+01 angle pdb=" C ILE E 191 " pdb=" N ARG E 192 " pdb=" CA ARG E 192 " ideal model delta sigma weight residual 121.54 135.31 -13.77 1.91e+00 2.74e-01 5.20e+01 angle pdb=" N3 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 127.04 134.79 -7.75 1.15e+00 7.59e-01 4.56e+01 ... (remaining 29458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 12435 35.58 - 71.15: 437 71.15 - 106.73: 18 106.73 - 142.30: 1 142.30 - 177.88: 1 Dihedral angle restraints: 12892 sinusoidal: 5063 harmonic: 7829 Sorted by residual: dihedral pdb=" CA ALA E 250 " pdb=" C ALA E 250 " pdb=" N ILE E 251 " pdb=" CA ILE E 251 " ideal model delta harmonic sigma weight residual 180.00 143.62 36.38 0 5.00e+00 4.00e-02 5.29e+01 dihedral pdb=" O1B ADP E1601 " pdb=" O3A ADP E1601 " pdb=" PB ADP E1601 " pdb=" PA ADP E1601 " ideal model delta sinusoidal sigma weight residual 300.00 122.12 177.88 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA ASN E 11 " pdb=" C ASN E 11 " pdb=" N HIS E 12 " pdb=" CA HIS E 12 " ideal model delta harmonic sigma weight residual 180.00 145.55 34.45 0 5.00e+00 4.00e-02 4.75e+01 ... (remaining 12889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2707 0.081 - 0.162: 597 0.162 - 0.243: 114 0.243 - 0.324: 48 0.324 - 0.405: 16 Chirality restraints: 3482 Sorted by residual: 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 2.24 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CB VAL E 325 " pdb=" CA VAL E 325 " pdb=" CG1 VAL E 325 " pdb=" CG2 VAL E 325 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CG LEU E 453 " pdb=" CB LEU E 453 " pdb=" CD1 LEU E 453 " pdb=" CD2 LEU E 453 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 3479 not shown) Planarity restraints: 3667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 894 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO E 895 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO E 895 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO E 895 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E1250 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C VAL E1250 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL E1250 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG E1251 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E1291 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C VAL E1291 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL E1291 " 0.020 2.00e-02 2.50e+03 pdb=" N SER E1292 " 0.019 2.00e-02 2.50e+03 ... (remaining 3664 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1026 2.71 - 3.26: 19303 3.26 - 3.81: 36623 3.81 - 4.35: 43017 4.35 - 4.90: 72433 Nonbonded interactions: 172402 Sorted by model distance: nonbonded pdb=" O2A ADP E1601 " pdb="MG MG E1603 " model vdw 2.165 2.170 nonbonded pdb=" OG SER E1386 " pdb="MG MG E1603 " model vdw 2.178 2.170 nonbonded pdb=" OE1 GLN E 775 " pdb="MG MG E1602 " model vdw 2.185 2.170 nonbonded pdb=" OG SER E 721 " pdb="MG MG E1602 " model vdw 2.194 2.170 nonbonded pdb=" O1B ADP E1601 " pdb="MG MG E1603 " model vdw 2.206 2.170 ... (remaining 172397 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=1.00 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: 3.080 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: 11.470 Check model and map are aligned: 0.340 Set scattering table: 0.240 Process input model: 56.820 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.120 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.010 0.098 21680 Z= 0.627 Angle : 1.394 19.155 29463 Z= 0.770 Chirality : 0.079 0.405 3482 Planarity : 0.012 0.110 3667 Dihedral : 17.259 177.881 7794 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 6.10 % Allowed : 11.08 % Favored : 82.81 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.19 (0.11), residues: 2674 helix: -4.23 (0.06), residues: 1298 sheet: -1.33 (0.32), residues: 237 loop : -2.73 (0.15), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 144 HIS 0.012 0.002 HIS E 585 PHE 0.031 0.003 PHE E 578 TYR 0.026 0.003 TYR E 397 ARG 0.008 0.001 ARG E 522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 539 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7632 (m) REVERT: A 47 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8357 (mmmt) REVERT: A 48 ASN cc_start: 0.8097 (m-40) cc_final: 0.7784 (m-40) REVERT: A 207 LYS cc_start: 0.9046 (tptt) cc_final: 0.8816 (tppt) REVERT: A 217 MET cc_start: 0.8827 (mtm) cc_final: 0.8599 (mtm) REVERT: A 222 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8424 (ttmm) REVERT: A 283 ILE cc_start: 0.9218 (mt) cc_final: 0.8823 (tt) REVERT: A 288 GLU cc_start: 0.7951 (pm20) cc_final: 0.7544 (pm20) REVERT: A 304 TYR cc_start: 0.8718 (m-80) cc_final: 0.8449 (m-80) REVERT: B 137 MET cc_start: 0.8557 (ptt) cc_final: 0.8253 (ptt) REVERT: B 144 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8469 (tp) REVERT: B 148 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9073 (tp) REVERT: B 169 MET cc_start: 0.8759 (ttm) cc_final: 0.8539 (mtp) REVERT: B 170 LYS cc_start: 0.8844 (tptt) cc_final: 0.8617 (tptp) REVERT: B 179 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8337 (mt-10) REVERT: B 184 SER cc_start: 0.9429 (OUTLIER) cc_final: 0.9093 (t) REVERT: B 200 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8580 (pt) REVERT: B 224 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8495 (p) REVERT: B 240 MET cc_start: 0.8973 (tmm) cc_final: 0.8503 (tmm) REVERT: B 304 TYR cc_start: 0.8824 (m-80) cc_final: 0.8477 (m-80) REVERT: B 332 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8431 (ttpt) REVERT: B 343 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8258 (tt) REVERT: C 144 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8369 (tt) REVERT: C 214 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.7998 (p) REVERT: C 288 GLU cc_start: 0.8190 (pm20) cc_final: 0.7814 (pm20) REVERT: C 303 SER cc_start: 0.9302 (OUTLIER) cc_final: 0.8987 (t) REVERT: C 327 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8075 (p) REVERT: D 39 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8146 (ttpt) REVERT: D 47 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8435 (mmmt) REVERT: D 118 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8572 (p) REVERT: D 126 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8589 (mt-10) REVERT: D 137 MET cc_start: 0.8732 (ptt) cc_final: 0.8335 (ptm) REVERT: D 144 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8655 (tp) REVERT: D 167 ILE cc_start: 0.9423 (tp) cc_final: 0.9201 (tp) REVERT: D 184 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.8891 (m) REVERT: D 222 LYS cc_start: 0.8844 (ttmt) cc_final: 0.8580 (tttm) REVERT: D 268 TYR cc_start: 0.8328 (t80) cc_final: 0.8089 (t80) REVERT: D 304 TYR cc_start: 0.9030 (m-80) cc_final: 0.8826 (m-80) REVERT: D 327 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8152 (p) REVERT: E 74 LEU cc_start: 0.8963 (tp) cc_final: 0.8498 (tp) REVERT: E 89 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7539 (tm-30) REVERT: E 178 ILE cc_start: 0.8964 (mm) cc_final: 0.8562 (mm) REVERT: E 209 GLU cc_start: 0.8226 (mp0) cc_final: 0.7970 (mp0) REVERT: E 309 LEU cc_start: 0.9138 (mt) cc_final: 0.8818 (mt) REVERT: E 311 ASP cc_start: 0.7977 (p0) cc_final: 0.7659 (p0) REVERT: E 367 LEU cc_start: 0.9550 (mm) cc_final: 0.9318 (mm) REVERT: E 388 LEU cc_start: 0.9450 (tp) cc_final: 0.9186 (tp) REVERT: E 1016 LEU cc_start: 0.9184 (tp) cc_final: 0.8874 (tp) REVERT: E 1141 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7978 (tm-30) REVERT: E 1143 LEU cc_start: 0.9245 (tp) cc_final: 0.8993 (tp) REVERT: E 1190 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7745 (tm-30) REVERT: E 1191 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8163 (tm-30) REVERT: E 1192 LEU cc_start: 0.9373 (tp) cc_final: 0.9042 (tt) REVERT: E 1200 LEU cc_start: 0.9263 (tt) cc_final: 0.8965 (tt) REVERT: E 1225 GLN cc_start: 0.7893 (tm-30) cc_final: 0.6783 (tm-30) REVERT: E 1229 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7146 (mm-30) REVERT: E 1246 ARG cc_start: 0.8462 (mmp80) cc_final: 0.8195 (mmp80) REVERT: E 1262 ILE cc_start: 0.9397 (tp) cc_final: 0.9161 (tp) REVERT: E 1402 HIS cc_start: 0.8045 (m90) cc_final: 0.7306 (m90) outliers start: 141 outliers final: 31 residues processed: 627 average time/residue: 0.3313 time to fit residues: 325.9510 Evaluate side-chains 396 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 348 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 770 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 244 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 48 ASN A 277 HIS ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 HIS B 277 HIS C 276 HIS C 335 ASN D 48 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 HIS E 167 GLN E 224 ASN E 375 GLN E 398 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 699 ASN E 708 GLN E 732 GLN E 787 ASN E 795 ASN E 820 GLN E 863 HIS E 889 HIS E 935 GLN E 937 GLN ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1316 HIS E1373 GLN ** E1521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21680 Z= 0.169 Angle : 0.626 9.523 29463 Z= 0.323 Chirality : 0.042 0.164 3482 Planarity : 0.006 0.076 3667 Dihedral : 8.550 170.444 2987 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.51 % Allowed : 18.18 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.14), residues: 2674 helix: -1.60 (0.12), residues: 1304 sheet: -0.80 (0.33), residues: 244 loop : -2.36 (0.16), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 90 HIS 0.003 0.001 HIS E 63 PHE 0.020 0.001 PHE E1182 TYR 0.013 0.001 TYR E1287 ARG 0.010 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 404 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8300 (mmmt) REVERT: A 48 ASN cc_start: 0.8240 (m110) cc_final: 0.7813 (m110) REVERT: A 54 ARG cc_start: 0.8078 (mtt90) cc_final: 0.7840 (mtp85) REVERT: A 153 ASN cc_start: 0.8866 (m-40) cc_final: 0.8619 (m110) REVERT: A 160 ASN cc_start: 0.8722 (m-40) cc_final: 0.8145 (m110) REVERT: A 217 MET cc_start: 0.8656 (mtm) cc_final: 0.8401 (mtm) REVERT: A 304 TYR cc_start: 0.8637 (m-80) cc_final: 0.8397 (m-80) REVERT: B 137 MET cc_start: 0.8642 (ptt) cc_final: 0.8336 (ptm) REVERT: B 169 MET cc_start: 0.8708 (ttm) cc_final: 0.8500 (mtp) REVERT: B 179 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: B 222 LYS cc_start: 0.9044 (ttpp) cc_final: 0.8812 (ttpt) REVERT: B 304 TYR cc_start: 0.8844 (m-80) cc_final: 0.8601 (m-80) REVERT: C 39 LYS cc_start: 0.8511 (mmmm) cc_final: 0.8307 (mmmm) REVERT: C 160 ASN cc_start: 0.8807 (m-40) cc_final: 0.8585 (m-40) REVERT: C 173 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8637 (pm20) REVERT: C 303 SER cc_start: 0.9229 (t) cc_final: 0.8769 (p) REVERT: C 304 TYR cc_start: 0.8574 (m-80) cc_final: 0.8099 (m-80) REVERT: C 327 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8345 (p) REVERT: D 57 GLN cc_start: 0.7890 (mt0) cc_final: 0.6492 (tp40) REVERT: D 67 LYS cc_start: 0.7929 (mmmt) cc_final: 0.7703 (tptt) REVERT: D 122 LEU cc_start: 0.9281 (mm) cc_final: 0.8924 (mm) REVERT: D 137 MET cc_start: 0.8921 (ptt) cc_final: 0.8578 (ptm) REVERT: D 141 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: D 163 MET cc_start: 0.9056 (mmt) cc_final: 0.8534 (mmp) REVERT: D 167 ILE cc_start: 0.9290 (tp) cc_final: 0.9061 (tp) REVERT: D 197 CYS cc_start: 0.8485 (m) cc_final: 0.8052 (m) REVERT: D 222 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8494 (tttm) REVERT: D 327 SER cc_start: 0.8802 (OUTLIER) cc_final: 0.8454 (p) REVERT: E 95 LEU cc_start: 0.9145 (mt) cc_final: 0.8821 (mt) REVERT: E 178 ILE cc_start: 0.9125 (mm) cc_final: 0.8827 (mm) REVERT: E 243 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7798 (mptt) REVERT: E 367 LEU cc_start: 0.9477 (mm) cc_final: 0.9269 (mm) REVERT: E 370 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8735 (tm-30) REVERT: E 371 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8311 (mmt-90) REVERT: E 388 LEU cc_start: 0.9458 (tp) cc_final: 0.9225 (tp) REVERT: E 587 LEU cc_start: 0.9064 (mm) cc_final: 0.8612 (mt) REVERT: E 731 MET cc_start: 0.6817 (tpp) cc_final: 0.6530 (tpp) REVERT: E 1141 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8144 (tm-30) REVERT: E 1190 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7349 (tm-30) REVERT: E 1225 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7356 (tm-30) REVERT: E 1229 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7374 (mt-10) REVERT: E 1242 THR cc_start: 0.9049 (m) cc_final: 0.8681 (m) REVERT: E 1262 ILE cc_start: 0.9356 (tp) cc_final: 0.9138 (tp) REVERT: E 1392 PHE cc_start: 0.8200 (m-80) cc_final: 0.7935 (m-80) REVERT: E 1395 MET cc_start: 0.8387 (mmt) cc_final: 0.8068 (mmt) REVERT: E 1505 MET cc_start: 0.7275 (mpp) cc_final: 0.7034 (mpp) outliers start: 81 outliers final: 33 residues processed: 465 average time/residue: 0.3316 time to fit residues: 241.4312 Evaluate side-chains 367 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 328 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1337 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 135 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 244 optimal weight: 9.9990 chunk 264 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 242 optimal weight: 0.0370 chunk 83 optimal weight: 10.0000 chunk 196 optimal weight: 0.0070 overall best weight: 0.9278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN D 128 GLN D 335 ASN E 398 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 ASN E 563 HIS E 609 GLN E 836 GLN ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1521 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21680 Z= 0.182 Angle : 0.602 14.175 29463 Z= 0.301 Chirality : 0.042 0.281 3482 Planarity : 0.004 0.062 3667 Dihedral : 7.219 166.506 2943 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.81 % Allowed : 19.74 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.15), residues: 2674 helix: -0.26 (0.14), residues: 1301 sheet: -0.53 (0.33), residues: 258 loop : -1.90 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E1033 HIS 0.005 0.001 HIS D 278 PHE 0.035 0.001 PHE E 537 TYR 0.025 0.001 TYR D 268 ARG 0.005 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 358 time to evaluate : 2.595 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: A 47 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8332 (mmmt) REVERT: A 48 ASN cc_start: 0.8390 (m110) cc_final: 0.7930 (m110) REVERT: A 54 ARG cc_start: 0.8159 (mtt90) cc_final: 0.7923 (mtp85) REVERT: A 84 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9018 (mm) REVERT: A 137 MET cc_start: 0.8693 (ptp) cc_final: 0.8326 (ptm) REVERT: A 153 ASN cc_start: 0.8835 (m-40) cc_final: 0.8598 (m110) REVERT: A 217 MET cc_start: 0.8703 (mtm) cc_final: 0.8465 (mtm) REVERT: A 288 GLU cc_start: 0.8489 (pm20) cc_final: 0.8221 (pm20) REVERT: B 137 MET cc_start: 0.8552 (ptt) cc_final: 0.8259 (ptm) REVERT: B 144 LEU cc_start: 0.9300 (tp) cc_final: 0.8917 (tp) REVERT: B 179 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8334 (mt-10) REVERT: B 222 LYS cc_start: 0.8982 (ttpp) cc_final: 0.8758 (ttpt) REVERT: B 288 GLU cc_start: 0.7730 (pm20) cc_final: 0.7348 (pm20) REVERT: C 173 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8753 (pm20) REVERT: C 288 GLU cc_start: 0.7934 (pt0) cc_final: 0.7697 (pt0) REVERT: C 303 SER cc_start: 0.9141 (t) cc_final: 0.8924 (t) REVERT: C 304 TYR cc_start: 0.8690 (m-80) cc_final: 0.8183 (m-80) REVERT: D 137 MET cc_start: 0.8957 (ptt) cc_final: 0.8662 (ptm) REVERT: D 141 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: D 160 ASN cc_start: 0.8908 (m-40) cc_final: 0.8665 (m110) REVERT: D 163 MET cc_start: 0.9040 (mmt) cc_final: 0.8428 (mmp) REVERT: D 170 LYS cc_start: 0.9141 (tppt) cc_final: 0.8890 (tptt) REVERT: D 197 CYS cc_start: 0.8500 (m) cc_final: 0.7972 (m) REVERT: E 178 ILE cc_start: 0.9154 (mm) cc_final: 0.8898 (mm) REVERT: E 179 LEU cc_start: 0.9073 (tp) cc_final: 0.8817 (tp) REVERT: E 243 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7852 (mmtt) REVERT: E 304 SER cc_start: 0.9021 (t) cc_final: 0.8615 (p) REVERT: E 309 LEU cc_start: 0.9142 (mt) cc_final: 0.8866 (mt) REVERT: E 388 LEU cc_start: 0.9441 (tp) cc_final: 0.9103 (tp) REVERT: E 731 MET cc_start: 0.6797 (tpp) cc_final: 0.6436 (tpp) REVERT: E 1141 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8388 (tm-30) REVERT: E 1190 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7634 (tm-30) REVERT: E 1225 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7182 (tm-30) REVERT: E 1229 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7430 (mt-10) REVERT: E 1392 PHE cc_start: 0.8303 (m-80) cc_final: 0.8055 (m-80) REVERT: E 1395 MET cc_start: 0.8368 (mmt) cc_final: 0.8074 (mmt) outliers start: 88 outliers final: 49 residues processed: 421 average time/residue: 0.3282 time to fit residues: 214.7168 Evaluate side-chains 376 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 323 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 911 GLU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 241 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 127 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 245 optimal weight: 0.8980 chunk 260 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 216 HIS E 398 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 797 GLN E 847 HIS ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21680 Z= 0.199 Angle : 0.597 12.308 29463 Z= 0.298 Chirality : 0.042 0.303 3482 Planarity : 0.004 0.056 3667 Dihedral : 6.756 164.801 2935 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.50 % Allowed : 20.56 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2674 helix: 0.48 (0.15), residues: 1273 sheet: -0.10 (0.34), residues: 254 loop : -1.55 (0.17), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 83 HIS 0.005 0.001 HIS E 60 PHE 0.023 0.001 PHE E 537 TYR 0.038 0.001 TYR D 268 ARG 0.004 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 345 time to evaluate : 1.901 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: 0.9027 (tptt) cc_final: 0.8569 (tppt) REVERT: A 47 LYS cc_start: 0.8588 (mtpp) cc_final: 0.8242 (mmmt) REVERT: A 48 ASN cc_start: 0.8547 (m110) cc_final: 0.8137 (m110) REVERT: A 84 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9052 (mm) REVERT: A 137 MET cc_start: 0.8780 (ptp) cc_final: 0.8538 (ptm) REVERT: A 153 ASN cc_start: 0.8839 (m-40) cc_final: 0.8564 (m110) REVERT: A 160 ASN cc_start: 0.8817 (m-40) cc_final: 0.8514 (m110) REVERT: A 175 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.8604 (p-80) REVERT: A 217 MET cc_start: 0.8801 (mtm) cc_final: 0.8536 (mtm) REVERT: A 288 GLU cc_start: 0.8459 (pm20) cc_final: 0.8212 (pm20) REVERT: A 332 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8206 (mtmm) REVERT: B 39 LYS cc_start: 0.8273 (tmtt) cc_final: 0.7889 (ttpt) REVERT: B 137 MET cc_start: 0.8562 (ptt) cc_final: 0.8251 (ptm) REVERT: B 144 LEU cc_start: 0.9378 (tp) cc_final: 0.9072 (tp) REVERT: B 179 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8341 (mt-10) REVERT: B 222 LYS cc_start: 0.8946 (ttpp) cc_final: 0.8715 (ttpt) REVERT: B 288 GLU cc_start: 0.7836 (pm20) cc_final: 0.7384 (pm20) REVERT: C 173 GLN cc_start: 0.9319 (OUTLIER) cc_final: 0.8836 (pm20) REVERT: C 303 SER cc_start: 0.9086 (t) cc_final: 0.8850 (t) REVERT: C 304 TYR cc_start: 0.8770 (m-80) cc_final: 0.8141 (m-80) REVERT: D 137 MET cc_start: 0.8934 (ptt) cc_final: 0.8671 (ptm) REVERT: D 141 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: D 163 MET cc_start: 0.9008 (mmt) cc_final: 0.8630 (mmm) REVERT: D 170 LYS cc_start: 0.9110 (tppt) cc_final: 0.8887 (tptt) REVERT: D 197 CYS cc_start: 0.8546 (m) cc_final: 0.8014 (m) REVERT: D 251 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8753 (tt) REVERT: E 1 MET cc_start: 0.6824 (mmm) cc_final: 0.6491 (mmm) REVERT: E 179 LEU cc_start: 0.9045 (tp) cc_final: 0.8800 (tp) REVERT: E 243 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7786 (mmtt) REVERT: E 304 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8580 (p) REVERT: E 731 MET cc_start: 0.6837 (tpp) cc_final: 0.6623 (tpp) REVERT: E 1190 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7640 (tm-30) REVERT: E 1392 PHE cc_start: 0.8341 (m-80) cc_final: 0.8111 (m-80) REVERT: E 1395 MET cc_start: 0.8385 (mmt) cc_final: 0.8101 (mmt) outliers start: 104 outliers final: 60 residues processed: 416 average time/residue: 0.2660 time to fit residues: 175.1003 Evaluate side-chains 382 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 315 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 911 GLU Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1232 ASP Chi-restraints excluded: chain E residue 1262 ILE Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 216 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 193 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 221 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 132 optimal weight: 0.0170 chunk 233 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 overall best weight: 1.1738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 216 HIS E 398 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21680 Z= 0.193 Angle : 0.589 12.329 29463 Z= 0.292 Chirality : 0.042 0.258 3482 Planarity : 0.003 0.053 3667 Dihedral : 6.391 159.693 2932 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.50 % Allowed : 21.77 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.16), residues: 2674 helix: 0.84 (0.15), residues: 1272 sheet: 0.07 (0.34), residues: 254 loop : -1.32 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E1033 HIS 0.003 0.001 HIS D 97 PHE 0.019 0.001 PHE E 537 TYR 0.025 0.001 TYR D 268 ARG 0.007 0.000 ARG E1246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 338 time to evaluate : 2.765 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: A 47 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8275 (mmmt) REVERT: A 48 ASN cc_start: 0.8666 (m110) cc_final: 0.8176 (m110) REVERT: A 137 MET cc_start: 0.8775 (ptp) cc_final: 0.8556 (ptm) REVERT: A 153 ASN cc_start: 0.8825 (m-40) cc_final: 0.8574 (m110) REVERT: A 160 ASN cc_start: 0.8717 (m-40) cc_final: 0.8438 (m110) REVERT: A 288 GLU cc_start: 0.8437 (pm20) cc_final: 0.8173 (pm20) REVERT: A 332 LYS cc_start: 0.8457 (mtmm) cc_final: 0.8181 (mtmm) REVERT: B 39 LYS cc_start: 0.8335 (tmtt) cc_final: 0.7941 (ttpt) REVERT: B 41 ASN cc_start: 0.8715 (p0) cc_final: 0.8175 (p0) REVERT: B 56 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8785 (mm) REVERT: B 88 MET cc_start: 0.8339 (tpp) cc_final: 0.8101 (ttp) REVERT: B 137 MET cc_start: 0.8562 (ptt) cc_final: 0.8271 (ptm) REVERT: B 144 LEU cc_start: 0.9398 (tp) cc_final: 0.9144 (tp) REVERT: B 222 LYS cc_start: 0.8932 (ttpp) cc_final: 0.8692 (ttpt) REVERT: B 288 GLU cc_start: 0.7811 (pm20) cc_final: 0.7313 (pm20) REVERT: C 86 PHE cc_start: 0.8949 (m-80) cc_final: 0.8128 (m-10) REVERT: C 173 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.8882 (pm20) REVERT: C 303 SER cc_start: 0.9067 (t) cc_final: 0.8840 (t) REVERT: C 304 TYR cc_start: 0.8795 (m-80) cc_final: 0.8132 (m-80) REVERT: D 115 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7438 (p90) REVERT: D 137 MET cc_start: 0.8889 (ptt) cc_final: 0.8628 (ptm) REVERT: D 141 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: D 163 MET cc_start: 0.8954 (mmt) cc_final: 0.8607 (mmm) REVERT: D 197 CYS cc_start: 0.8472 (m) cc_final: 0.7944 (m) REVERT: D 251 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8771 (tt) REVERT: D 332 LYS cc_start: 0.9065 (mtmm) cc_final: 0.8615 (mtmm) REVERT: E 179 LEU cc_start: 0.9024 (tp) cc_final: 0.8782 (tp) REVERT: E 243 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7792 (mmtt) REVERT: E 304 SER cc_start: 0.9085 (t) cc_final: 0.8604 (p) REVERT: E 731 MET cc_start: 0.6848 (tpp) cc_final: 0.6549 (tpp) REVERT: E 932 MET cc_start: 0.7998 (tpp) cc_final: 0.7777 (tpp) REVERT: E 1190 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7704 (tm-30) REVERT: E 1392 PHE cc_start: 0.8411 (m-80) cc_final: 0.8045 (m-80) REVERT: E 1395 MET cc_start: 0.8365 (mmt) cc_final: 0.8087 (mmt) outliers start: 104 outliers final: 67 residues processed: 415 average time/residue: 0.3371 time to fit residues: 220.5942 Evaluate side-chains 382 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 310 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 911 GLU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1166 VAL Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1262 ILE Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 87 optimal weight: 0.0870 chunk 234 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 260 optimal weight: 8.9990 chunk 216 optimal weight: 0.5980 chunk 120 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 173 GLN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS D 52 GLN E 263 ASN ** E 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 GLN E 398 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 HIS ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21680 Z= 0.154 Angle : 0.588 12.416 29463 Z= 0.285 Chirality : 0.042 0.259 3482 Planarity : 0.003 0.050 3667 Dihedral : 6.012 153.854 2926 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.20 % Allowed : 22.29 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2674 helix: 0.97 (0.15), residues: 1281 sheet: -0.06 (0.32), residues: 270 loop : -1.25 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 83 HIS 0.007 0.000 HIS D 175 PHE 0.017 0.001 PHE E 537 TYR 0.022 0.001 TYR D 268 ARG 0.005 0.000 ARG E1246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 347 time to evaluate : 2.444 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 73 LEU cc_start: 0.9006 (mt) cc_final: 0.8745 (tp) REVERT: A 137 MET cc_start: 0.8740 (ptp) cc_final: 0.8538 (ptm) REVERT: A 153 ASN cc_start: 0.8822 (m-40) cc_final: 0.8573 (m110) REVERT: A 160 ASN cc_start: 0.8711 (m-40) cc_final: 0.8445 (m110) REVERT: A 173 GLN cc_start: 0.8358 (pt0) cc_final: 0.8085 (pt0) REVERT: A 217 MET cc_start: 0.8855 (mtp) cc_final: 0.8644 (mtm) REVERT: A 288 GLU cc_start: 0.8377 (pm20) cc_final: 0.8152 (pm20) REVERT: A 332 LYS cc_start: 0.8477 (mtmm) cc_final: 0.8215 (mtmm) REVERT: B 39 LYS cc_start: 0.8297 (tmtt) cc_final: 0.7915 (ttpt) REVERT: B 41 ASN cc_start: 0.8678 (p0) cc_final: 0.8155 (p0) REVERT: B 56 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8801 (mm) REVERT: B 88 MET cc_start: 0.8307 (tpp) cc_final: 0.8101 (ttp) REVERT: B 137 MET cc_start: 0.8508 (ptt) cc_final: 0.8243 (ptm) REVERT: B 144 LEU cc_start: 0.9368 (tp) cc_final: 0.9130 (tp) REVERT: B 288 GLU cc_start: 0.7797 (pm20) cc_final: 0.7372 (pm20) REVERT: C 173 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.8881 (pm20) REVERT: C 217 MET cc_start: 0.8737 (mtm) cc_final: 0.8526 (mtm) REVERT: C 303 SER cc_start: 0.8964 (t) cc_final: 0.8731 (t) REVERT: C 304 TYR cc_start: 0.8774 (m-80) cc_final: 0.8184 (m-80) REVERT: D 115 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.7246 (p90) REVERT: D 137 MET cc_start: 0.8963 (ptt) cc_final: 0.8705 (ptm) REVERT: D 141 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: D 163 MET cc_start: 0.8930 (mmt) cc_final: 0.8582 (mmm) REVERT: D 197 CYS cc_start: 0.8425 (m) cc_final: 0.7934 (m) REVERT: D 332 LYS cc_start: 0.9022 (mtmm) cc_final: 0.8537 (mtmm) REVERT: E 179 LEU cc_start: 0.8974 (tp) cc_final: 0.8739 (tp) REVERT: E 243 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7662 (mmtt) REVERT: E 304 SER cc_start: 0.9005 (OUTLIER) cc_final: 0.8549 (p) REVERT: E 731 MET cc_start: 0.6823 (tpp) cc_final: 0.6499 (tpp) REVERT: E 1295 LEU cc_start: 0.8804 (tp) cc_final: 0.8505 (tp) REVERT: E 1392 PHE cc_start: 0.8393 (m-80) cc_final: 0.8045 (m-80) REVERT: E 1395 MET cc_start: 0.8430 (mmt) cc_final: 0.8157 (mmt) outliers start: 97 outliers final: 67 residues processed: 418 average time/residue: 0.3192 time to fit residues: 212.0979 Evaluate side-chains 390 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 318 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 808 LEU Chi-restraints excluded: chain E residue 911 GLU Chi-restraints excluded: chain E residue 1022 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1166 VAL Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 250 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 148 optimal weight: 9.9990 chunk 190 optimal weight: 0.0870 chunk 147 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 259 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 HIS E 265 GLN E 398 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21680 Z= 0.195 Angle : 0.618 11.781 29463 Z= 0.300 Chirality : 0.043 0.269 3482 Planarity : 0.003 0.049 3667 Dihedral : 5.904 149.435 2926 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.46 % Allowed : 22.51 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2674 helix: 1.17 (0.15), residues: 1262 sheet: 0.05 (0.32), residues: 270 loop : -1.19 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 52 HIS 0.010 0.001 HIS D 175 PHE 0.015 0.001 PHE E 537 TYR 0.023 0.001 TYR D 268 ARG 0.005 0.000 ARG E1246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 328 time to evaluate : 2.558 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 48 ASN cc_start: 0.7963 (m110) cc_final: 0.7520 (m110) REVERT: A 73 LEU cc_start: 0.9017 (mt) cc_final: 0.8744 (tp) REVERT: A 148 ILE cc_start: 0.9611 (tp) cc_final: 0.9359 (tp) REVERT: A 153 ASN cc_start: 0.8831 (m-40) cc_final: 0.8588 (m110) REVERT: A 160 ASN cc_start: 0.8737 (m-40) cc_final: 0.8474 (m110) REVERT: A 258 TYR cc_start: 0.8615 (p90) cc_final: 0.8291 (p90) REVERT: A 288 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8130 (pm20) REVERT: B 39 LYS cc_start: 0.8311 (tmtt) cc_final: 0.7941 (ttpt) REVERT: B 41 ASN cc_start: 0.8609 (p0) cc_final: 0.8093 (p0) REVERT: B 50 ARG cc_start: 0.7697 (mmt180) cc_final: 0.7436 (mmp-170) REVERT: B 137 MET cc_start: 0.8524 (ptt) cc_final: 0.8272 (ptm) REVERT: B 144 LEU cc_start: 0.9399 (tp) cc_final: 0.8964 (tp) REVERT: B 288 GLU cc_start: 0.7833 (pm20) cc_final: 0.7378 (pm20) REVERT: C 173 GLN cc_start: 0.9398 (OUTLIER) cc_final: 0.9100 (pm20) REVERT: C 217 MET cc_start: 0.8754 (mtm) cc_final: 0.8522 (mtm) REVERT: C 303 SER cc_start: 0.9026 (t) cc_final: 0.8807 (t) REVERT: C 304 TYR cc_start: 0.8801 (m-80) cc_final: 0.8122 (m-80) REVERT: D 115 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7260 (p90) REVERT: D 137 MET cc_start: 0.8966 (ptt) cc_final: 0.8695 (ptm) REVERT: D 141 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: D 163 MET cc_start: 0.8921 (mmt) cc_final: 0.8578 (mmm) REVERT: D 197 CYS cc_start: 0.8450 (m) cc_final: 0.7955 (m) REVERT: D 332 LYS cc_start: 0.9062 (mtmm) cc_final: 0.8555 (mtmm) REVERT: E 132 ASN cc_start: 0.9075 (t0) cc_final: 0.8749 (t0) REVERT: E 179 LEU cc_start: 0.9038 (tp) cc_final: 0.8790 (tp) REVERT: E 222 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7745 (p90) REVERT: E 304 SER cc_start: 0.9073 (t) cc_final: 0.8603 (p) REVERT: E 731 MET cc_start: 0.6999 (tpp) cc_final: 0.6630 (tpp) REVERT: E 799 TYR cc_start: 0.7778 (t80) cc_final: 0.7127 (t80) REVERT: E 804 GLU cc_start: 0.8844 (mp0) cc_final: 0.8599 (mm-30) REVERT: E 1013 LEU cc_start: 0.9152 (tt) cc_final: 0.8943 (mp) REVERT: E 1392 PHE cc_start: 0.8344 (m-80) cc_final: 0.7979 (m-80) REVERT: E 1395 MET cc_start: 0.8444 (mmt) cc_final: 0.8162 (mmt) REVERT: E 1428 ASP cc_start: 0.8519 (t70) cc_final: 0.8293 (t0) outliers start: 103 outliers final: 75 residues processed: 408 average time/residue: 0.3052 time to fit residues: 197.5835 Evaluate side-chains 391 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 311 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 725 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 911 GLU Chi-restraints excluded: chain E residue 1022 LEU Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1166 VAL Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1232 ASP Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1337 LYS Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 160 optimal weight: 0.0980 chunk 103 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 chunk 235 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 398 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1123 ASN E1273 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21680 Z= 0.164 Angle : 0.615 11.744 29463 Z= 0.294 Chirality : 0.043 0.269 3482 Planarity : 0.003 0.047 3667 Dihedral : 5.781 144.411 2926 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.37 % Allowed : 23.03 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2674 helix: 1.26 (0.15), residues: 1268 sheet: 0.11 (0.34), residues: 254 loop : -1.08 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 52 HIS 0.011 0.001 HIS D 175 PHE 0.014 0.001 PHE E 537 TYR 0.022 0.001 TYR D 268 ARG 0.004 0.000 ARG E1246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 336 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8304 (m110) cc_final: 0.7816 (m110) REVERT: A 73 LEU cc_start: 0.8990 (mt) cc_final: 0.8731 (tp) REVERT: A 148 ILE cc_start: 0.9607 (tp) cc_final: 0.9346 (tp) REVERT: A 153 ASN cc_start: 0.8828 (m-40) cc_final: 0.8583 (m110) REVERT: A 160 ASN cc_start: 0.8711 (m-40) cc_final: 0.8438 (m110) REVERT: A 258 TYR cc_start: 0.8590 (p90) cc_final: 0.8274 (p90) REVERT: B 39 LYS cc_start: 0.8283 (tmtt) cc_final: 0.7916 (ttpt) REVERT: B 41 ASN cc_start: 0.8572 (p0) cc_final: 0.8096 (p0) REVERT: B 47 LYS cc_start: 0.8975 (ptpt) cc_final: 0.8766 (ptpt) REVERT: B 144 LEU cc_start: 0.9376 (tp) cc_final: 0.8949 (tp) REVERT: B 169 MET cc_start: 0.8805 (ttm) cc_final: 0.8504 (mtp) REVERT: B 288 GLU cc_start: 0.7779 (pm20) cc_final: 0.7373 (pm20) REVERT: C 86 PHE cc_start: 0.8759 (m-10) cc_final: 0.8520 (m-10) REVERT: C 173 GLN cc_start: 0.9385 (OUTLIER) cc_final: 0.9088 (pm20) REVERT: C 217 MET cc_start: 0.8742 (mtm) cc_final: 0.8529 (mtm) REVERT: C 303 SER cc_start: 0.8975 (t) cc_final: 0.8763 (t) REVERT: C 304 TYR cc_start: 0.8776 (m-80) cc_final: 0.8165 (m-80) REVERT: D 137 MET cc_start: 0.8953 (ptt) cc_final: 0.8686 (ptm) REVERT: D 141 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: D 163 MET cc_start: 0.8853 (mmt) cc_final: 0.8471 (mmm) REVERT: D 197 CYS cc_start: 0.8400 (m) cc_final: 0.7885 (m) REVERT: D 251 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8742 (tt) REVERT: D 332 LYS cc_start: 0.9055 (mtmm) cc_final: 0.8667 (mtmm) REVERT: E 179 LEU cc_start: 0.9012 (tp) cc_final: 0.8776 (tp) REVERT: E 222 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7611 (p90) REVERT: E 243 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7718 (mmtt) REVERT: E 304 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8549 (p) REVERT: E 309 LEU cc_start: 0.9317 (mt) cc_final: 0.9053 (mt) REVERT: E 731 MET cc_start: 0.6938 (tpp) cc_final: 0.6647 (tpp) REVERT: E 799 TYR cc_start: 0.7823 (t80) cc_final: 0.7203 (t80) REVERT: E 1033 TRP cc_start: 0.8131 (t-100) cc_final: 0.7629 (t-100) REVERT: E 1189 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9325 (mt) REVERT: E 1248 LEU cc_start: 0.9202 (tp) cc_final: 0.8766 (mp) REVERT: E 1392 PHE cc_start: 0.8318 (m-80) cc_final: 0.7862 (m-80) REVERT: E 1395 MET cc_start: 0.8434 (mmt) cc_final: 0.8169 (mmt) REVERT: E 1428 ASP cc_start: 0.8533 (t70) cc_final: 0.8327 (t0) REVERT: E 1505 MET cc_start: 0.7520 (mpp) cc_final: 0.7210 (mmp) outliers start: 101 outliers final: 69 residues processed: 410 average time/residue: 0.3324 time to fit residues: 216.0847 Evaluate side-chains 385 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 310 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 725 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 808 LEU Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 911 GLU Chi-restraints excluded: chain E residue 1022 LEU Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1166 VAL Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1337 LYS Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 248 optimal weight: 10.0000 chunk 226 optimal weight: 0.6980 chunk 241 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 240 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN C 97 HIS ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 398 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1348 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21680 Z= 0.271 Angle : 0.668 14.163 29463 Z= 0.328 Chirality : 0.044 0.272 3482 Planarity : 0.004 0.048 3667 Dihedral : 5.903 142.611 2926 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.90 % Allowed : 23.38 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2674 helix: 1.19 (0.15), residues: 1261 sheet: 0.05 (0.32), residues: 272 loop : -1.13 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 83 HIS 0.011 0.001 HIS D 175 PHE 0.026 0.002 PHE E1164 TYR 0.028 0.002 TYR D 268 ARG 0.003 0.000 ARG E1246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 316 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8571 (m110) cc_final: 0.7972 (m-40) REVERT: A 73 LEU cc_start: 0.9015 (mt) cc_final: 0.8748 (tp) REVERT: A 148 ILE cc_start: 0.9646 (tp) cc_final: 0.9375 (tp) REVERT: A 153 ASN cc_start: 0.8862 (m-40) cc_final: 0.8611 (m110) REVERT: A 160 ASN cc_start: 0.8700 (m-40) cc_final: 0.8462 (m110) REVERT: A 258 TYR cc_start: 0.8683 (p90) cc_final: 0.8294 (p90) REVERT: A 280 ASP cc_start: 0.7967 (p0) cc_final: 0.7616 (p0) REVERT: A 288 GLU cc_start: 0.7560 (pm20) cc_final: 0.7302 (pm20) REVERT: B 39 LYS cc_start: 0.8346 (tmtt) cc_final: 0.8010 (ttpt) REVERT: B 144 LEU cc_start: 0.9487 (tp) cc_final: 0.9131 (tp) REVERT: B 288 GLU cc_start: 0.7805 (pm20) cc_final: 0.7308 (pm20) REVERT: C 173 GLN cc_start: 0.9450 (OUTLIER) cc_final: 0.9157 (pm20) REVERT: C 217 MET cc_start: 0.8792 (mtm) cc_final: 0.8563 (mtm) REVERT: C 304 TYR cc_start: 0.8956 (m-80) cc_final: 0.8246 (m-80) REVERT: D 47 LYS cc_start: 0.8805 (tptt) cc_final: 0.8394 (ttpp) REVERT: D 115 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.7230 (p90) REVERT: D 137 MET cc_start: 0.9018 (ptt) cc_final: 0.8733 (ptm) REVERT: D 141 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: D 163 MET cc_start: 0.8865 (mmt) cc_final: 0.8495 (mmm) REVERT: D 197 CYS cc_start: 0.8465 (m) cc_final: 0.7967 (m) REVERT: D 222 LYS cc_start: 0.8848 (tmtt) cc_final: 0.8646 (tptp) REVERT: D 332 LYS cc_start: 0.9170 (mtmm) cc_final: 0.8658 (mtmm) REVERT: E 179 LEU cc_start: 0.9097 (tp) cc_final: 0.8869 (tp) REVERT: E 222 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7723 (p90) REVERT: E 304 SER cc_start: 0.9140 (t) cc_final: 0.8726 (p) REVERT: E 1033 TRP cc_start: 0.8160 (t-100) cc_final: 0.7725 (t-100) REVERT: E 1110 MET cc_start: 0.7508 (tpt) cc_final: 0.7276 (tpt) REVERT: E 1189 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9344 (mt) REVERT: E 1248 LEU cc_start: 0.9243 (tp) cc_final: 0.8752 (mp) REVERT: E 1392 PHE cc_start: 0.8315 (m-80) cc_final: 0.7812 (m-80) REVERT: E 1428 ASP cc_start: 0.8546 (t70) cc_final: 0.8322 (t0) outliers start: 90 outliers final: 69 residues processed: 386 average time/residue: 0.3365 time to fit residues: 204.0985 Evaluate side-chains 372 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 298 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 911 GLU Chi-restraints excluded: chain E residue 1022 LEU Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1166 VAL Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 255 optimal weight: 5.9990 chunk 155 optimal weight: 0.0470 chunk 121 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 267 optimal weight: 0.0010 chunk 246 optimal weight: 10.0000 chunk 213 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN ** E 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 398 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21680 Z= 0.160 Angle : 0.644 11.846 29463 Z= 0.310 Chirality : 0.043 0.250 3482 Planarity : 0.003 0.048 3667 Dihedral : 5.790 140.695 2926 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.38 % Allowed : 24.63 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2674 helix: 1.30 (0.15), residues: 1258 sheet: -0.22 (0.32), residues: 282 loop : -0.98 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 83 HIS 0.011 0.001 HIS D 175 PHE 0.040 0.001 PHE D 35 TYR 0.023 0.001 TYR D 268 ARG 0.005 0.000 ARG E1246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 325 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8504 (m110) cc_final: 0.7937 (m110) REVERT: A 73 LEU cc_start: 0.8981 (mt) cc_final: 0.8730 (tp) REVERT: A 148 ILE cc_start: 0.9608 (tp) cc_final: 0.9333 (tp) REVERT: A 153 ASN cc_start: 0.8844 (m-40) cc_final: 0.8585 (m110) REVERT: A 160 ASN cc_start: 0.8711 (m-40) cc_final: 0.8449 (m110) REVERT: A 258 TYR cc_start: 0.8607 (p90) cc_final: 0.8304 (p90) REVERT: B 39 LYS cc_start: 0.8242 (tmtt) cc_final: 0.7773 (ttpt) REVERT: B 144 LEU cc_start: 0.9370 (tp) cc_final: 0.8942 (tp) REVERT: B 288 GLU cc_start: 0.7788 (pm20) cc_final: 0.7355 (pm20) REVERT: C 173 GLN cc_start: 0.9409 (OUTLIER) cc_final: 0.9109 (pm20) REVERT: C 217 MET cc_start: 0.8758 (mtm) cc_final: 0.8527 (mtm) REVERT: D 47 LYS cc_start: 0.8739 (tptt) cc_final: 0.8394 (ttpp) REVERT: D 115 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.7128 (p90) REVERT: D 137 MET cc_start: 0.9023 (ptt) cc_final: 0.8759 (ptm) REVERT: D 141 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7371 (tt0) REVERT: D 163 MET cc_start: 0.8851 (mmt) cc_final: 0.8467 (mmm) REVERT: D 197 CYS cc_start: 0.8427 (m) cc_final: 0.7863 (m) REVERT: D 332 LYS cc_start: 0.9124 (mtmm) cc_final: 0.8684 (mtmm) REVERT: E 179 LEU cc_start: 0.9023 (tp) cc_final: 0.8770 (tp) REVERT: E 222 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7581 (p90) REVERT: E 243 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7545 (mmtt) REVERT: E 304 SER cc_start: 0.9057 (t) cc_final: 0.8598 (p) REVERT: E 1033 TRP cc_start: 0.8082 (t-100) cc_final: 0.7676 (t-100) REVERT: E 1110 MET cc_start: 0.7380 (tpt) cc_final: 0.7132 (tpt) REVERT: E 1189 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9288 (mt) REVERT: E 1392 PHE cc_start: 0.8277 (m-80) cc_final: 0.7832 (m-80) REVERT: E 1395 MET cc_start: 0.8395 (mmt) cc_final: 0.8188 (mmt) REVERT: E 1428 ASP cc_start: 0.8547 (t70) cc_final: 0.8339 (t0) REVERT: E 1505 MET cc_start: 0.7559 (mpp) cc_final: 0.7262 (mmp) outliers start: 78 outliers final: 60 residues processed: 384 average time/residue: 0.3311 time to fit residues: 200.1965 Evaluate side-chains 376 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 311 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 908 ILE Chi-restraints excluded: chain E residue 911 GLU Chi-restraints excluded: chain E residue 1022 LEU Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1166 VAL Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 196 optimal weight: 0.8980 chunk 31 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 187 optimal weight: 4.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN ** E 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 398 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.078847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.065179 restraints weight = 70051.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.067255 restraints weight = 32839.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.068636 restraints weight = 19789.645| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21680 Z= 0.183 Angle : 0.647 12.034 29463 Z= 0.313 Chirality : 0.044 0.281 3482 Planarity : 0.003 0.046 3667 Dihedral : 5.764 140.624 2926 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.25 % Allowed : 25.02 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2674 helix: 1.29 (0.15), residues: 1267 sheet: -0.28 (0.31), residues: 292 loop : -0.92 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 83 HIS 0.011 0.001 HIS D 175 PHE 0.035 0.001 PHE D 35 TYR 0.032 0.001 TYR E 799 ARG 0.004 0.000 ARG E1246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4691.21 seconds wall clock time: 91 minutes 56.50 seconds (5516.50 seconds total)