Starting phenix.real_space_refine on Mon Mar 18 12:57:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s61_24846/03_2024/7s61_24846_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s61_24846/03_2024/7s61_24846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s61_24846/03_2024/7s61_24846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s61_24846/03_2024/7s61_24846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s61_24846/03_2024/7s61_24846_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s61_24846/03_2024/7s61_24846_updated.pdb" } resolution = 4.0 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= 0.074 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 120 5.16 5 C 13564 2.51 5 N 3569 2.21 5 O 3725 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 GLU 51": "OE1" <-> "OE2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "C TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 351": "OE1" <-> "OE2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D ASP 58": "OD1" <-> "OD2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D ASP 323": "OD1" <-> "OD2" Residue "D TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 351": "OE1" <-> "OE2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E ASP 30": "OD1" <-> "OD2" Residue "E PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 249": "NH1" <-> "NH2" Residue "E ARG 259": "NH1" <-> "NH2" 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 PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 412": "OE1" <-> "OE2" Residue "E TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 491": "OE1" <-> "OE2" Residue "E TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 569": "OE1" <-> "OE2" 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 GLU 730": "OE1" <-> "OE2" Residue "E GLU 804": "OE1" <-> "OE2" Residue "E ARG 842": "NH1" <-> "NH2" Residue "E ASP 855": "OD1" <-> "OD2" Residue "E ASP 861": "OD1" <-> "OD2" Residue "E ASP 898": "OD1" <-> "OD2" Residue "E GLU 911": "OE1" <-> "OE2" Residue "E GLU 938": "OE1" <-> "OE2" Residue "E GLU 940": "OE1" <-> "OE2" Residue "E PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1087": "OE1" <-> "OE2" Residue "E ARG 1124": "NH1" <-> "NH2" Residue "E ASP 1133": "OD1" <-> "OD2" Residue "E GLU 1141": "OE1" <-> "OE2" Residue "E ASP 1193": "OD1" <-> "OD2" Residue "E GLU 1209": "OE1" <-> "OE2" Residue "E GLU 1220": "OE1" <-> "OE2" Residue "E ARG 1222": "NH1" <-> "NH2" Residue "E ASP 1232": "OD1" <-> "OD2" Residue "E TYR 1294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1304": "OD1" <-> "OD2" Residue "E GLU 1306": "OE1" <-> "OE2" Residue "E ARG 1314": "NH1" <-> "NH2" Residue "E TYR 1326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1392": "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 GLU 1443": "OE1" <-> "OE2" Residue "E ASP 1448": "OD1" <-> "OD2" Residue "E GLU 1456": "OE1" <-> "OE2" Residue "E GLU 1480": "OE1" <-> "OE2" Residue "E ARG 1487": "NH1" <-> "NH2" Residue "E ARG 1494": "NH1" <-> "NH2" Residue "E ARG 1498": "NH1" <-> "NH2" Residue "E GLU 1507": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20985 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: 10909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1396, 10909 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'peptide': 1392, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 43, 'TRANS': 1348, 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: 8 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 89 Time building chain proxies: 11.02, per 1000 atoms: 0.53 Number of scatterers: 20985 At special positions: 0 Unit cell: (133.9, 149.5, 136.5, 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 120 16.00 P 5 15.00 Mg 2 11.99 O 3725 8.00 N 3569 7.00 C 13564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.01 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.01 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.01 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.01 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 27 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.07 Conformation dependent library (CDL) restraints added in 3.7 seconds 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 24 sheets defined 44.2% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'A' and resid 53 through 56 No H-bonds generated for 'chain 'A' and resid 53 through 56' 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 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'B' and resid 53 through 56 No H-bonds generated for 'chain 'B' and resid 53 through 56' 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 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'C' and resid 53 through 56 No H-bonds generated for 'chain 'C' and resid 53 through 56' 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 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'D' and resid 53 through 56 No H-bonds generated for 'chain 'D' and resid 53 through 56' 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 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'E' and resid 10 through 13 No H-bonds generated for 'chain 'E' and resid 10 through 13' Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 26 through 33 Processing helix chain 'E' and resid 35 through 51 removed outlier: 3.959A pdb=" N PHE E 45 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 72 through 99 removed outlier: 3.866A pdb=" N TRP E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 Processing helix chain 'E' and resid 138 through 160 removed outlier: 3.594A pdb=" N VAL E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 192 removed outlier: 3.516A pdb=" N GLY E 181 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 229 Processing helix chain 'E' and resid 235 through 243 removed outlier: 3.921A pdb=" N HIS E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 263 No H-bonds generated for 'chain 'E' and resid 260 through 263' Processing helix chain 'E' and resid 285 through 295 Processing helix chain 'E' and resid 297 through 327 removed outlier: 3.850A pdb=" N PHE E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY E 317 " --> pdb=" O LEU E 313 " (cutoff:3.500A) Proline residue: E 318 - end of helix Processing helix chain 'E' and resid 349 through 354 Processing helix chain 'E' and resid 356 through 401 Processing helix chain 'E' and resid 406 through 409 No H-bonds generated for 'chain 'E' and resid 406 through 409' Processing helix chain 'E' and resid 415 through 456 removed outlier: 3.591A pdb=" N VAL E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR E 426 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASN E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) Proline residue: E 437 - end of helix Proline residue: E 443 - end of helix Processing helix chain 'E' and resid 459 through 512 removed outlier: 3.563A pdb=" N LEU E 462 " --> pdb=" O VAL E 459 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA E 466 " --> pdb=" O ILE E 463 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL E 467 " --> pdb=" O GLY E 464 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE E 469 " --> pdb=" O ALA E 466 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA E 472 " --> pdb=" O ILE E 469 " (cutoff:3.500A) Proline residue: E 473 - end of helix removed outlier: 3.741A pdb=" N VAL E 478 " --> pdb=" O GLN E 475 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS E 481 " --> pdb=" O VAL E 478 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU E 482 " --> pdb=" O ALA E 479 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA E 485 " --> pdb=" O LEU E 482 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER E 488 " --> pdb=" O ALA E 485 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU E 491 " --> pdb=" O SER E 488 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR E 492 " --> pdb=" O THR E 489 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER E 493 " --> pdb=" O LEU E 490 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 498 " --> pdb=" O GLU E 495 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN E 499 " --> pdb=" O ARG E 496 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN E 501 " --> pdb=" O LYS E 498 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG E 505 " --> pdb=" O GLU E 502 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE E 507 " --> pdb=" O LEU E 504 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS E 508 " --> pdb=" O ARG E 505 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 509 " --> pdb=" O GLY E 506 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS E 511 " --> pdb=" O LYS E 508 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 512 " --> pdb=" O LEU E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 564 Proline residue: E 552 - end of helix removed outlier: 4.069A pdb=" N VAL E 564 " --> pdb=" O PHE E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 590 Proline residue: E 590 - end of helix Processing helix chain 'E' and resid 594 through 616 Processing helix chain 'E' and resid 722 through 728 Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 796 through 806 Processing helix chain 'E' and resid 833 through 843 Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'E' and resid 892 through 895 Proline residue: E 895 - end of helix No H-bonds generated for 'chain 'E' and resid 892 through 895' Processing helix chain 'E' and resid 914 through 919 Processing helix chain 'E' and resid 922 through 931 removed outlier: 3.545A pdb=" N LEU E 931 " --> pdb=" O HIS E 927 " (cutoff:3.500A) Processing helix chain 'E' and resid 999 through 1008 Processing helix chain 'E' and resid 1010 through 1038 Processing helix chain 'E' and resid 1063 through 1096 removed outlier: 5.197A pdb=" N PHE E1068 " --> pdb=" O TYR E1064 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E1074 " --> pdb=" O VAL E1070 " (cutoff:3.500A) Processing helix chain 'E' and resid 1101 through 1105 Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1118 through 1160 removed outlier: 4.693A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE E1136 " --> pdb=" O ILE E1132 " (cutoff:3.500A) Proline residue: E1137 - end of helix Processing helix chain 'E' and resid 1163 through 1207 Proline residue: E1170 - end of helix removed outlier: 4.573A pdb=" N VAL E1184 " --> pdb=" O LYS E1180 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA E1185 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) Proline residue: E1199 - end of helix Processing helix chain 'E' and resid 1211 through 1216 Processing helix chain 'E' and resid 1220 through 1273 removed outlier: 3.695A pdb=" N VAL E1259 " --> pdb=" O ILE E1255 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL E1260 " --> pdb=" O GLY E1256 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS E1273 " --> pdb=" O SER E1269 " (cutoff:3.500A) Processing helix chain 'E' and resid 1280 through 1319 removed outlier: 5.627A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP E1297 " --> pdb=" O ASN E1293 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA E1311 " --> pdb=" O LEU E1307 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1385 through 1390 removed outlier: 3.713A pdb=" N SER E1389 " --> pdb=" O LYS E1385 " (cutoff:3.500A) Processing helix chain 'E' and resid 1415 through 1421 removed outlier: 3.791A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) Processing helix chain 'E' and resid 1436 through 1440 Processing helix chain 'E' and resid 1448 through 1457 Processing helix chain 'E' and resid 1461 through 1465 Processing helix chain 'E' and resid 1484 through 1497 Processing helix chain 'E' and resid 1514 through 1527 removed outlier: 3.514A pdb=" N ALA E1527 " --> pdb=" O VAL E1523 " (cutoff:3.500A) Processing helix chain 'E' and resid 1563 through 1569 Processing helix chain 'E' and resid 1573 through 1581 Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.615A pdb=" N VAL A 202 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 255 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.995A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 234 through 238 removed outlier: 3.723A pdb=" N ARG A 221 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= E, first strand: chain 'A' and resid 319 through 322 Processing sheet with id= F, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.614A pdb=" N VAL B 202 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 255 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 309 through 311 removed outlier: 6.996A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 234 through 238 removed outlier: 3.723A pdb=" N ARG B 221 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 313 through 315 Processing sheet with id= J, first strand: chain 'B' and resid 319 through 322 Processing sheet with id= K, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.615A pdb=" N VAL C 202 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 255 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 309 through 311 removed outlier: 6.996A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 234 through 238 removed outlier: 3.723A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= O, first strand: chain 'C' and resid 319 through 322 Processing sheet with id= P, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.614A pdb=" N VAL D 202 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 255 " --> pdb=" O VAL D 202 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 309 through 311 removed outlier: 6.996A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 234 through 238 removed outlier: 3.723A pdb=" N ARG D 221 " --> pdb=" O HIS D 234 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 313 through 315 Processing sheet with id= T, first strand: chain 'D' and resid 319 through 322 Processing sheet with id= U, first strand: chain 'E' and resid 899 through 902 removed outlier: 3.533A pdb=" N TRP E 899 " --> pdb=" O LEU E 709 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET E 711 " --> pdb=" O TRP E 899 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL E 884 " --> pdb=" O THR E 710 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ILE E 712 " --> pdb=" O VAL E 884 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU E 886 " --> pdb=" O ILE E 712 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 853 " --> pdb=" O VAL E 885 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 1402 through 1405 removed outlier: 5.392A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 1556 through 1561 removed outlier: 6.578A pdb=" N VAL E1551 " --> pdb=" O LEU E1558 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE E1560 " --> pdb=" O VAL E1549 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL E1549 " --> pdb=" O PHE E1560 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E1548 " --> pdb=" O LYS E1374 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL E1533 " --> pdb=" O ILE E1375 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE E1377 " --> pdb=" O VAL E1533 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N THR E1535 " --> pdb=" O ILE E1377 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N GLY E1379 " --> pdb=" O THR E1535 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N SER E1423 " --> pdb=" O ILE E1504 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 1351 through 1353 removed outlier: 3.792A pdb=" N GLU E1400 " --> pdb=" O SER E1351 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG E1353 " --> pdb=" O THR E1398 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR E1398 " --> pdb=" O ARG E1353 " (cutoff:3.500A) 983 hydrogen bonds defined for protein. 2799 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: 7.63 Time building geometry restraints manager: 8.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3601 1.32 - 1.45: 5540 1.45 - 1.57: 12097 1.57 - 1.70: 10 1.70 - 1.82: 192 Bond restraints: 21440 Sorted by residual: bond pdb=" C ILE E 551 " pdb=" N PRO E 552 " ideal model delta sigma weight residual 1.335 1.452 -0.116 1.36e-02 5.41e+03 7.32e+01 bond pdb=" C4 ATP E1604 " pdb=" C5 ATP E1604 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C5 ATP E1604 " pdb=" C6 ATP E1604 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.27e+01 bond pdb=" C TRP E1339 " pdb=" N PRO E1340 " ideal model delta sigma weight residual 1.340 1.490 -0.150 2.76e-02 1.31e+03 2.97e+01 bond pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 1.374 1.325 0.049 1.00e-02 1.00e+04 2.37e+01 ... (remaining 21435 not shown) Histogram of bond angle deviations from ideal: 95.74 - 104.52: 343 104.52 - 113.31: 11796 113.31 - 122.09: 12853 122.09 - 130.87: 3985 130.87 - 139.66: 162 Bond angle restraints: 29139 Sorted by residual: angle pdb=" PB ATP E1604 " pdb=" O3B ATP E1604 " pdb=" PG ATP E1604 " ideal model delta sigma weight residual 139.87 120.87 19.00 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PA ATP E1604 " pdb=" O3A ATP E1604 " pdb=" PB ATP E1604 " ideal model delta sigma weight residual 136.83 123.76 13.07 1.00e+00 1.00e+00 1.71e+02 angle pdb=" C LEU E 261 " pdb=" N THR E 262 " pdb=" CA THR E 262 " ideal model delta sigma weight residual 121.54 139.66 -18.12 1.91e+00 2.74e-01 9.00e+01 angle pdb=" N SER E1100 " pdb=" CA SER E1100 " pdb=" C SER E1100 " ideal model delta sigma weight residual 113.43 102.92 10.51 1.26e+00 6.30e-01 6.96e+01 angle pdb=" C ALA E 5 " pdb=" N PHE E 6 " pdb=" CA PHE E 6 " ideal model delta sigma weight residual 121.54 137.37 -15.83 1.91e+00 2.74e-01 6.87e+01 ... (remaining 29134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 12288 35.49 - 70.98: 436 70.98 - 106.47: 23 106.47 - 141.96: 0 141.96 - 177.45: 1 Dihedral angle restraints: 12748 sinusoidal: 4980 harmonic: 7768 Sorted by residual: dihedral pdb=" CA VAL E 193 " pdb=" C VAL E 193 " pdb=" N ARG E 194 " pdb=" CA ARG E 194 " ideal model delta harmonic sigma weight residual -180.00 -106.53 -73.47 0 5.00e+00 4.00e-02 2.16e+02 dihedral pdb=" CA GLY E 21 " pdb=" C GLY E 21 " pdb=" N VAL E 22 " pdb=" CA VAL E 22 " ideal model delta harmonic sigma weight residual 180.00 -132.58 -47.42 0 5.00e+00 4.00e-02 9.00e+01 dihedral pdb=" CA GLY E 411 " pdb=" C GLY E 411 " pdb=" N GLU E 412 " pdb=" CA GLU E 412 " ideal model delta harmonic sigma weight residual -180.00 -136.60 -43.40 0 5.00e+00 4.00e-02 7.53e+01 ... (remaining 12745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 3282 0.169 - 0.338: 156 0.338 - 0.508: 13 0.508 - 0.677: 2 0.677 - 0.846: 1 Chirality restraints: 3454 Sorted by residual: chirality pdb=" CG LEU E1227 " pdb=" CB LEU E1227 " pdb=" CD1 LEU E1227 " pdb=" CD2 LEU E1227 " both_signs ideal model delta sigma weight residual False -2.59 -1.74 -0.85 2.00e-01 2.50e+01 1.79e+01 chirality pdb=" CG LEU E 183 " pdb=" CB LEU E 183 " pdb=" CD1 LEU E 183 " pdb=" CD2 LEU E 183 " both_signs ideal model delta sigma weight residual False -2.59 -1.96 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CB VAL E 556 " pdb=" CA VAL E 556 " pdb=" CG1 VAL E 556 " pdb=" CG2 VAL E 556 " both_signs ideal model delta sigma weight residual False -2.63 -2.09 -0.54 2.00e-01 2.50e+01 7.25e+00 ... (remaining 3451 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 267 " 0.024 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C LEU E 267 " -0.081 2.00e-02 2.50e+03 pdb=" O LEU E 267 " 0.031 2.00e-02 2.50e+03 pdb=" N CYS E 268 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 589 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO E 590 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E1017 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C VAL E1017 " -0.067 2.00e-02 2.50e+03 pdb=" O VAL E1017 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE E1018 " 0.022 2.00e-02 2.50e+03 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1018 2.71 - 3.26: 18807 3.26 - 3.80: 36576 3.80 - 4.35: 43966 4.35 - 4.90: 72098 Nonbonded interactions: 172465 Sorted by model distance: nonbonded pdb=" O1B ADP E1601 " pdb="MG MG E1603 " model vdw 2.160 2.170 nonbonded pdb="MG MG E1602 " pdb=" O3B ATP E1604 " model vdw 2.162 2.170 nonbonded pdb="MG MG E1602 " pdb=" O2B ATP E1604 " model vdw 2.170 2.170 nonbonded pdb=" NE2 GLN E 775 " pdb="MG MG E1602 " model vdw 2.246 2.250 nonbonded pdb=" OE1 GLN E 775 " pdb="MG MG E1602 " model vdw 2.333 2.170 ... (remaining 172460 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: 2.830 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: 11.190 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 56.230 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 0.150 21440 Z= 0.629 Angle : 1.581 23.309 29139 Z= 0.870 Chirality : 0.083 0.846 3454 Planarity : 0.013 0.104 3624 Dihedral : 17.700 177.446 7685 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.57 % Favored : 95.32 % Rotamer: Outliers : 8.22 % Allowed : 10.60 % Favored : 81.18 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -4.86 (0.12), residues: 2650 helix: -4.05 (0.07), residues: 1289 sheet: -1.03 (0.30), residues: 275 loop : -2.51 (0.15), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP E1247 HIS 0.014 0.003 HIS E1098 PHE 0.047 0.004 PHE E1164 TYR 0.051 0.004 TYR E1287 ARG 0.017 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 619 time to evaluate : 2.591 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: 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 84 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8758 (tt) REVERT: A 129 VAL cc_start: 0.9139 (t) cc_final: 0.8589 (t) REVERT: A 130 THR cc_start: 0.9024 (p) cc_final: 0.8659 (t) REVERT: A 137 MET cc_start: 0.8511 (ptt) cc_final: 0.8254 (ptp) REVERT: A 148 ILE cc_start: 0.9469 (tp) cc_final: 0.9256 (tp) REVERT: A 160 ASN cc_start: 0.9323 (m-40) cc_final: 0.8316 (m-40) REVERT: A 170 LYS cc_start: 0.8989 (tptp) cc_final: 0.8700 (tppt) REVERT: A 199 MET cc_start: 0.9026 (mtm) cc_final: 0.8725 (mtt) REVERT: A 211 ILE cc_start: 0.9323 (mp) cc_final: 0.8755 (mp) REVERT: A 265 SER cc_start: 0.9335 (OUTLIER) cc_final: 0.9053 (p) REVERT: A 279 GLN cc_start: 0.9020 (tp40) cc_final: 0.8527 (tm-30) REVERT: A 330 TYR cc_start: 0.8993 (m-80) cc_final: 0.8358 (m-80) REVERT: A 332 LYS cc_start: 0.9425 (mttt) cc_final: 0.8972 (mttm) REVERT: B 43 ASN cc_start: 0.8753 (m110) cc_final: 0.8353 (m-40) REVERT: B 44 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8569 (t) REVERT: B 52 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7572 (mm110) REVERT: B 67 LYS cc_start: 0.7998 (tptt) cc_final: 0.7634 (tptt) REVERT: B 77 MET cc_start: 0.8323 (tpp) cc_final: 0.8014 (tmm) REVERT: B 166 SER cc_start: 0.9296 (OUTLIER) cc_final: 0.9058 (p) REVERT: B 170 LYS cc_start: 0.9053 (tptp) cc_final: 0.8469 (tppt) REVERT: B 191 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8908 (tp) REVERT: B 218 GLN cc_start: 0.8562 (mt0) cc_final: 0.8236 (mt0) REVERT: B 281 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8923 (tt) REVERT: B 288 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 305 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8119 (mt) REVERT: B 343 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8511 (tt) REVERT: C 39 LYS cc_start: 0.9237 (mmtt) cc_final: 0.8939 (tppt) REVERT: C 162 ILE cc_start: 0.9280 (mt) cc_final: 0.9053 (mt) REVERT: C 166 SER cc_start: 0.9564 (OUTLIER) cc_final: 0.9348 (p) REVERT: C 170 LYS cc_start: 0.9247 (tptp) cc_final: 0.8947 (tptm) REVERT: C 237 ASP cc_start: 0.8287 (p0) cc_final: 0.7190 (p0) REVERT: C 258 TYR cc_start: 0.8958 (p90) cc_final: 0.8741 (p90) REVERT: C 287 LEU cc_start: 0.9751 (tp) cc_final: 0.9524 (tt) REVERT: C 288 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8446 (mt-10) REVERT: C 293 THR cc_start: 0.9308 (p) cc_final: 0.9027 (t) REVERT: C 316 VAL cc_start: 0.9645 (OUTLIER) cc_final: 0.9420 (m) REVERT: C 332 LYS cc_start: 0.9563 (mttt) cc_final: 0.9338 (mmmt) REVERT: C 335 ASN cc_start: 0.9266 (m-40) cc_final: 0.8553 (m-40) REVERT: D 44 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.8931 (t) REVERT: D 66 LEU cc_start: 0.9280 (mt) cc_final: 0.8993 (mt) REVERT: D 77 MET cc_start: 0.8504 (tpp) cc_final: 0.8104 (tmm) REVERT: D 86 PHE cc_start: 0.9019 (m-80) cc_final: 0.8276 (m-80) REVERT: D 91 TRP cc_start: 0.8797 (t60) cc_final: 0.8533 (t60) REVERT: D 130 THR cc_start: 0.8871 (p) cc_final: 0.8657 (t) REVERT: D 147 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9261 (mm) REVERT: D 163 MET cc_start: 0.8962 (mmm) cc_final: 0.8723 (mmm) REVERT: D 166 SER cc_start: 0.9661 (OUTLIER) cc_final: 0.9427 (p) REVERT: D 183 PHE cc_start: 0.9088 (m-80) cc_final: 0.8616 (m-10) REVERT: D 191 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8125 (tp) REVERT: D 202 VAL cc_start: 0.9369 (OUTLIER) cc_final: 0.9017 (p) REVERT: D 209 MET cc_start: 0.7624 (mmp) cc_final: 0.6949 (mmp) REVERT: D 211 ILE cc_start: 0.9494 (mp) cc_final: 0.8370 (mp) REVERT: D 235 GLN cc_start: 0.8748 (mt0) cc_final: 0.8417 (pm20) REVERT: D 240 MET cc_start: 0.7932 (tmm) cc_final: 0.7562 (tmm) REVERT: D 244 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8727 (m) REVERT: D 247 ASN cc_start: 0.8445 (p0) cc_final: 0.7780 (p0) REVERT: D 250 PHE cc_start: 0.8846 (t80) cc_final: 0.8635 (t80) REVERT: D 265 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.7929 (p) REVERT: D 305 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9138 (mt) REVERT: D 348 GLN cc_start: 0.8998 (mt0) cc_final: 0.8552 (mt0) REVERT: E 33 ASN cc_start: 0.8895 (t0) cc_final: 0.8646 (t0) REVERT: E 43 ILE cc_start: 0.9643 (tp) cc_final: 0.9394 (pt) REVERT: E 45 PHE cc_start: 0.8603 (t80) cc_final: 0.8272 (t80) REVERT: E 79 THR cc_start: 0.9466 (OUTLIER) cc_final: 0.9265 (m) REVERT: E 113 MET cc_start: 0.8948 (mmt) cc_final: 0.8659 (mmp) REVERT: E 128 ILE cc_start: 0.9642 (tp) cc_final: 0.9354 (tp) REVERT: E 225 LEU cc_start: 0.9279 (tp) cc_final: 0.9051 (tt) REVERT: E 320 CYS cc_start: 0.8993 (m) cc_final: 0.8763 (m) REVERT: E 324 ILE cc_start: 0.9423 (mt) cc_final: 0.9125 (mm) REVERT: E 359 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9043 (tt) REVERT: E 369 LEU cc_start: 0.9383 (tp) cc_final: 0.9115 (tp) REVERT: E 382 ILE cc_start: 0.9659 (mm) cc_final: 0.9440 (mm) REVERT: E 430 MET cc_start: 0.9148 (ttp) cc_final: 0.8920 (ttp) REVERT: E 584 PHE cc_start: 0.8824 (m-10) cc_final: 0.8613 (m-80) REVERT: E 886 LEU cc_start: 0.9208 (tp) cc_final: 0.8447 (tp) REVERT: E 891 LEU cc_start: 0.9073 (mt) cc_final: 0.8816 (mp) REVERT: E 1021 LEU cc_start: 0.9577 (mm) cc_final: 0.9375 (pp) REVERT: E 1031 ASP cc_start: 0.8722 (p0) cc_final: 0.8518 (p0) REVERT: E 1110 MET cc_start: 0.8423 (tpp) cc_final: 0.7989 (tpp) REVERT: E 1130 ASN cc_start: 0.9290 (t0) cc_final: 0.9061 (t0) REVERT: E 1173 ILE cc_start: 0.9058 (tp) cc_final: 0.8842 (tp) REVERT: E 1261 LEU cc_start: 0.9480 (tp) cc_final: 0.9160 (tp) REVERT: E 1276 LEU cc_start: 0.8203 (mp) cc_final: 0.7908 (tt) REVERT: E 1298 MET cc_start: 0.8780 (ttt) cc_final: 0.8483 (ttt) REVERT: E 1305 MET cc_start: 0.9141 (tpp) cc_final: 0.8863 (tpp) REVERT: E 1514 MET cc_start: 0.9066 (mtp) cc_final: 0.8859 (mtm) outliers start: 187 outliers final: 38 residues processed: 742 average time/residue: 0.3311 time to fit residues: 383.2776 Evaluate side-chains 492 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 434 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 359 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 209 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 348 GLN B 57 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS C 277 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 175 HIS D 277 HIS E 72 HIS E 265 GLN E 407 ASN E 438 ASN E 548 ASN E 563 HIS E 795 ASN E 836 GLN E 846 GLN E1197 GLN ** E1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21440 Z= 0.188 Angle : 0.716 10.574 29139 Z= 0.365 Chirality : 0.045 0.259 3454 Planarity : 0.006 0.084 3624 Dihedral : 8.581 168.561 2975 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 3.96 % Allowed : 19.79 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.18 (0.14), residues: 2650 helix: -1.16 (0.13), residues: 1280 sheet: -0.71 (0.30), residues: 283 loop : -1.86 (0.16), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 90 HIS 0.004 0.001 HIS C 278 PHE 0.027 0.001 PHE D 86 TYR 0.023 0.002 TYR D 268 ARG 0.004 0.000 ARG E1300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 440 time to evaluate : 2.224 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8684 (m-40) cc_final: 0.8304 (t0) REVERT: A 47 LYS cc_start: 0.9242 (mmmt) cc_final: 0.8971 (ptpt) REVERT: A 66 LEU cc_start: 0.9337 (mt) cc_final: 0.9092 (mt) REVERT: A 77 MET cc_start: 0.8711 (tpp) cc_final: 0.7591 (tmm) REVERT: A 84 LEU cc_start: 0.9222 (tp) cc_final: 0.9018 (mp) REVERT: A 137 MET cc_start: 0.8307 (ptt) cc_final: 0.8034 (ptp) REVERT: A 170 LYS cc_start: 0.8866 (tptp) cc_final: 0.8543 (tppt) REVERT: A 173 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8593 (pt0) REVERT: A 209 MET cc_start: 0.8536 (mmp) cc_final: 0.7923 (mmp) REVERT: A 211 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.8968 (mm) REVERT: A 279 GLN cc_start: 0.9139 (tp40) cc_final: 0.8398 (tm-30) REVERT: A 332 LYS cc_start: 0.9396 (mttt) cc_final: 0.9081 (mttp) REVERT: B 43 ASN cc_start: 0.8742 (m110) cc_final: 0.8466 (m-40) REVERT: B 81 CYS cc_start: 0.8327 (t) cc_final: 0.8071 (t) REVERT: B 88 MET cc_start: 0.8999 (ttm) cc_final: 0.8684 (ttm) REVERT: B 169 MET cc_start: 0.9251 (mmm) cc_final: 0.8811 (ttm) REVERT: B 170 LYS cc_start: 0.9020 (tptp) cc_final: 0.8613 (tptm) REVERT: B 240 MET cc_start: 0.8292 (tmm) cc_final: 0.8076 (tmm) REVERT: B 288 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 305 LEU cc_start: 0.8792 (mt) cc_final: 0.8420 (mt) REVERT: B 330 TYR cc_start: 0.8678 (m-80) cc_final: 0.8474 (m-80) REVERT: C 39 LYS cc_start: 0.9372 (mmtt) cc_final: 0.9012 (tptt) REVERT: C 86 PHE cc_start: 0.9332 (m-80) cc_final: 0.9039 (m-10) REVERT: C 88 MET cc_start: 0.8860 (ttt) cc_final: 0.7961 (tmm) REVERT: C 152 GLN cc_start: 0.8812 (tt0) cc_final: 0.8431 (tt0) REVERT: C 170 LYS cc_start: 0.9146 (tptp) cc_final: 0.8691 (tptm) REVERT: C 288 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8111 (mt-10) REVERT: C 293 THR cc_start: 0.9584 (p) cc_final: 0.9246 (t) REVERT: C 296 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8875 (tt) REVERT: C 313 GLN cc_start: 0.8649 (mt0) cc_final: 0.8383 (mt0) REVERT: D 44 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8905 (t) REVERT: D 47 LYS cc_start: 0.8902 (mmmt) cc_final: 0.7997 (mptt) REVERT: D 77 MET cc_start: 0.8733 (tpp) cc_final: 0.8427 (tmm) REVERT: D 86 PHE cc_start: 0.8969 (m-80) cc_final: 0.8341 (m-10) REVERT: D 128 GLN cc_start: 0.8858 (tt0) cc_final: 0.8651 (tm-30) REVERT: D 183 PHE cc_start: 0.9096 (m-80) cc_final: 0.8579 (m-10) REVERT: D 202 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.8974 (p) REVERT: D 211 ILE cc_start: 0.9361 (mp) cc_final: 0.8747 (mp) REVERT: D 217 MET cc_start: 0.8395 (mtm) cc_final: 0.7890 (mtm) REVERT: D 218 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8934 (mm-40) REVERT: D 240 MET cc_start: 0.8179 (tmm) cc_final: 0.7698 (tmm) REVERT: D 247 ASN cc_start: 0.8190 (p0) cc_final: 0.7674 (p0) REVERT: D 299 GLN cc_start: 0.9477 (tt0) cc_final: 0.8666 (tm-30) REVERT: D 332 LYS cc_start: 0.9540 (mttt) cc_final: 0.9095 (mmmt) REVERT: E 43 ILE cc_start: 0.9569 (tp) cc_final: 0.9319 (pt) REVERT: E 89 GLU cc_start: 0.9038 (tp30) cc_final: 0.8768 (tm-30) REVERT: E 105 LEU cc_start: 0.9256 (tp) cc_final: 0.9021 (tp) REVERT: E 109 MET cc_start: 0.8100 (tpp) cc_final: 0.7435 (tpp) REVERT: E 113 MET cc_start: 0.9193 (mmt) cc_final: 0.8727 (mmp) REVERT: E 128 ILE cc_start: 0.9574 (tp) cc_final: 0.9323 (tp) REVERT: E 182 MET cc_start: 0.9317 (mmm) cc_final: 0.8760 (mmm) REVERT: E 369 LEU cc_start: 0.9402 (tp) cc_final: 0.9157 (tp) REVERT: E 410 MET cc_start: 0.7783 (ptt) cc_final: 0.7520 (mmp) REVERT: E 584 PHE cc_start: 0.8629 (m-10) cc_final: 0.8338 (m-80) REVERT: E 711 MET cc_start: 0.8992 (mmm) cc_final: 0.8529 (mpp) REVERT: E 1021 LEU cc_start: 0.9627 (mm) cc_final: 0.9347 (pp) REVERT: E 1298 MET cc_start: 0.9085 (ttt) cc_final: 0.8554 (tmm) outliers start: 90 outliers final: 38 residues processed: 503 average time/residue: 0.2977 time to fit residues: 237.2805 Evaluate side-chains 409 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 366 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1474 ILE Chi-restraints excluded: chain E residue 1524 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 201 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 240 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 128 GLN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN D 46 HIS D 97 HIS D 160 ASN D 175 HIS E 235 ASN E 820 GLN ** E1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1427 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21440 Z= 0.279 Angle : 0.713 10.384 29139 Z= 0.364 Chirality : 0.045 0.193 3454 Planarity : 0.005 0.068 3624 Dihedral : 7.105 131.426 2913 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 3.83 % Allowed : 23.09 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.99 (0.16), residues: 2650 helix: 0.06 (0.14), residues: 1317 sheet: -0.52 (0.30), residues: 287 loop : -1.54 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E1247 HIS 0.017 0.001 HIS A 277 PHE 0.028 0.002 PHE C 86 TYR 0.028 0.002 TYR D 268 ARG 0.004 0.000 ARG E 798 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 364 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8773 (m-40) cc_final: 0.8056 (t0) REVERT: A 47 LYS cc_start: 0.9343 (mmmt) cc_final: 0.9112 (mmmt) REVERT: A 77 MET cc_start: 0.8775 (tpp) cc_final: 0.7998 (tmm) REVERT: A 84 LEU cc_start: 0.9309 (tp) cc_final: 0.9086 (mp) REVERT: A 137 MET cc_start: 0.8514 (ptt) cc_final: 0.8100 (ptp) REVERT: A 173 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8724 (pt0) REVERT: A 199 MET cc_start: 0.8003 (mtp) cc_final: 0.7644 (mtp) REVERT: A 209 MET cc_start: 0.8295 (mmp) cc_final: 0.7673 (mmp) REVERT: A 211 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9170 (mp) REVERT: A 279 GLN cc_start: 0.9079 (tp40) cc_final: 0.8463 (tm-30) REVERT: A 332 LYS cc_start: 0.9430 (mttt) cc_final: 0.9091 (mttp) REVERT: B 38 LYS cc_start: 0.9588 (mmmm) cc_final: 0.9371 (mmmm) REVERT: B 39 LYS cc_start: 0.9548 (mmmm) cc_final: 0.9313 (mmmm) REVERT: B 43 ASN cc_start: 0.8726 (m110) cc_final: 0.8508 (m-40) REVERT: B 52 GLN cc_start: 0.8096 (mm110) cc_final: 0.7817 (mm110) REVERT: B 66 LEU cc_start: 0.9359 (mt) cc_final: 0.9105 (mp) REVERT: B 77 MET cc_start: 0.8723 (tmm) cc_final: 0.7256 (tpt) REVERT: B 169 MET cc_start: 0.9183 (mmm) cc_final: 0.8736 (ttm) REVERT: B 170 LYS cc_start: 0.9008 (tptp) cc_final: 0.8382 (tptm) REVERT: B 175 HIS cc_start: 0.8986 (OUTLIER) cc_final: 0.8707 (p90) REVERT: B 185 LYS cc_start: 0.9141 (pptt) cc_final: 0.8576 (ptmm) REVERT: B 288 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8255 (mt-10) REVERT: B 305 LEU cc_start: 0.8939 (mt) cc_final: 0.8476 (mt) REVERT: B 330 TYR cc_start: 0.8847 (m-80) cc_final: 0.8527 (m-80) REVERT: C 39 LYS cc_start: 0.9377 (mmtt) cc_final: 0.9022 (tptt) REVERT: C 170 LYS cc_start: 0.9075 (tptp) cc_final: 0.8815 (tptm) REVERT: C 207 LYS cc_start: 0.9347 (mmmm) cc_final: 0.8984 (mmmm) REVERT: C 209 MET cc_start: 0.8589 (tpp) cc_final: 0.8220 (tpt) REVERT: C 288 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8113 (mt-10) REVERT: C 296 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8924 (tt) REVERT: C 332 LYS cc_start: 0.9351 (mtpp) cc_final: 0.9140 (ttpp) REVERT: D 77 MET cc_start: 0.8896 (tpp) cc_final: 0.8549 (tmm) REVERT: D 128 GLN cc_start: 0.9000 (tt0) cc_final: 0.8778 (tm-30) REVERT: D 163 MET cc_start: 0.9072 (mmm) cc_final: 0.8594 (mmm) REVERT: D 183 PHE cc_start: 0.9184 (m-80) cc_final: 0.8524 (m-10) REVERT: D 185 LYS cc_start: 0.9003 (ttpp) cc_final: 0.8571 (tptt) REVERT: D 202 VAL cc_start: 0.9313 (OUTLIER) cc_final: 0.8948 (p) REVERT: D 207 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8055 (tmtt) REVERT: D 211 ILE cc_start: 0.9367 (mp) cc_final: 0.8374 (mp) REVERT: D 218 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8832 (mm-40) REVERT: D 240 MET cc_start: 0.8325 (tmm) cc_final: 0.7555 (tmm) REVERT: D 247 ASN cc_start: 0.8305 (p0) cc_final: 0.7905 (p0) REVERT: D 299 GLN cc_start: 0.9623 (tt0) cc_final: 0.8793 (tm-30) REVERT: D 332 LYS cc_start: 0.9507 (mttt) cc_final: 0.9096 (mmmt) REVERT: E 43 ILE cc_start: 0.9491 (tp) cc_final: 0.9278 (pt) REVERT: E 45 PHE cc_start: 0.8616 (t80) cc_final: 0.8282 (t80) REVERT: E 89 GLU cc_start: 0.9120 (tp30) cc_final: 0.8653 (tm-30) REVERT: E 105 LEU cc_start: 0.9329 (tp) cc_final: 0.9111 (tp) REVERT: E 109 MET cc_start: 0.8289 (tpp) cc_final: 0.7822 (tpp) REVERT: E 113 MET cc_start: 0.9257 (mmt) cc_final: 0.8783 (mmp) REVERT: E 182 MET cc_start: 0.9332 (mmm) cc_final: 0.8684 (mmm) REVERT: E 185 LEU cc_start: 0.9159 (pp) cc_final: 0.8518 (pp) REVERT: E 369 LEU cc_start: 0.9463 (tp) cc_final: 0.9232 (tp) REVERT: E 430 MET cc_start: 0.9071 (ttp) cc_final: 0.8763 (ttm) REVERT: E 510 LEU cc_start: 0.9456 (mt) cc_final: 0.8959 (mt) REVERT: E 584 PHE cc_start: 0.8626 (m-10) cc_final: 0.8286 (m-80) REVERT: E 711 MET cc_start: 0.8971 (mmm) cc_final: 0.8561 (mpp) REVERT: E 731 MET cc_start: 0.9029 (mmt) cc_final: 0.8070 (mmt) REVERT: E 1021 LEU cc_start: 0.9640 (mm) cc_final: 0.9374 (pp) REVERT: E 1276 LEU cc_start: 0.8043 (mp) cc_final: 0.7388 (tt) REVERT: E 1289 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9214 (tt) REVERT: E 1298 MET cc_start: 0.9117 (ttt) cc_final: 0.8612 (tmm) REVERT: E 1301 ASN cc_start: 0.9253 (m-40) cc_final: 0.8784 (m-40) outliers start: 87 outliers final: 49 residues processed: 424 average time/residue: 0.3026 time to fit residues: 203.7959 Evaluate side-chains 390 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 335 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1130 ASN Chi-restraints excluded: chain E residue 1161 THR Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1289 LEU Chi-restraints excluded: chain E residue 1368 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 126 optimal weight: 0.0470 chunk 26 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 243 optimal weight: 9.9990 chunk 258 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS D 160 ASN ** E 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 809 GLN ** E1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21440 Z= 0.221 Angle : 0.669 10.428 29139 Z= 0.335 Chirality : 0.044 0.235 3454 Planarity : 0.004 0.059 3624 Dihedral : 6.503 122.490 2905 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 4.44 % Allowed : 23.70 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 2650 helix: 0.47 (0.14), residues: 1325 sheet: -0.66 (0.30), residues: 305 loop : -1.21 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E1247 HIS 0.017 0.001 HIS B 175 PHE 0.025 0.001 PHE E 364 TYR 0.012 0.001 TYR E 379 ARG 0.004 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 354 time to evaluate : 2.350 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: symmetry clash REVERT: A 43 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8174 (t0) REVERT: A 77 MET cc_start: 0.8848 (tpp) cc_final: 0.7840 (tmm) REVERT: A 137 MET cc_start: 0.8454 (ptt) cc_final: 0.8145 (ptp) REVERT: A 199 MET cc_start: 0.7994 (mtp) cc_final: 0.7612 (mtp) REVERT: A 211 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9205 (mp) REVERT: A 279 GLN cc_start: 0.9120 (tp40) cc_final: 0.8383 (tm-30) REVERT: A 332 LYS cc_start: 0.9428 (mttt) cc_final: 0.9121 (mttp) REVERT: B 38 LYS cc_start: 0.9608 (mmmm) cc_final: 0.9376 (mmmm) REVERT: B 39 LYS cc_start: 0.9550 (mmmm) cc_final: 0.9289 (mmmm) REVERT: B 43 ASN cc_start: 0.8756 (m110) cc_final: 0.6286 (p0) REVERT: B 52 GLN cc_start: 0.8185 (mm110) cc_final: 0.7938 (mm110) REVERT: B 146 ILE cc_start: 0.9818 (mt) cc_final: 0.9575 (mp) REVERT: B 169 MET cc_start: 0.9046 (mmm) cc_final: 0.8751 (ttm) REVERT: B 170 LYS cc_start: 0.9044 (tptp) cc_final: 0.8457 (tptp) REVERT: B 175 HIS cc_start: 0.8949 (OUTLIER) cc_final: 0.8515 (p90) REVERT: B 305 LEU cc_start: 0.8969 (mt) cc_final: 0.8466 (mt) REVERT: B 330 TYR cc_start: 0.8771 (m-80) cc_final: 0.8570 (m-80) REVERT: B 332 LYS cc_start: 0.9273 (mmtt) cc_final: 0.8948 (mmtt) REVERT: C 39 LYS cc_start: 0.9388 (mmtt) cc_final: 0.9122 (mppt) REVERT: C 142 CYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7566 (m) REVERT: C 170 LYS cc_start: 0.8976 (tptp) cc_final: 0.8741 (tptm) REVERT: C 207 LYS cc_start: 0.9345 (mmmm) cc_final: 0.8974 (mmmm) REVERT: C 209 MET cc_start: 0.8635 (tpp) cc_final: 0.8335 (tpt) REVERT: C 296 ILE cc_start: 0.9283 (mt) cc_final: 0.8886 (tt) REVERT: C 326 TYR cc_start: 0.8632 (m-80) cc_final: 0.7524 (m-80) REVERT: C 332 LYS cc_start: 0.9375 (mtpp) cc_final: 0.9157 (mmmt) REVERT: D 77 MET cc_start: 0.8898 (tpp) cc_final: 0.8546 (tmm) REVERT: D 86 PHE cc_start: 0.9040 (m-80) cc_final: 0.8540 (m-10) REVERT: D 183 PHE cc_start: 0.9125 (m-80) cc_final: 0.8509 (m-10) REVERT: D 202 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.8883 (p) REVERT: D 240 MET cc_start: 0.8157 (tmm) cc_final: 0.7346 (tmm) REVERT: D 247 ASN cc_start: 0.8268 (p0) cc_final: 0.7892 (p0) REVERT: D 250 PHE cc_start: 0.9227 (t80) cc_final: 0.8259 (t80) REVERT: D 332 LYS cc_start: 0.9500 (mttt) cc_final: 0.9142 (mmmt) REVERT: E 109 MET cc_start: 0.8339 (tpp) cc_final: 0.7569 (tpp) REVERT: E 113 MET cc_start: 0.9235 (mmt) cc_final: 0.8670 (mmp) REVERT: E 182 MET cc_start: 0.9321 (mmm) cc_final: 0.8912 (mmm) REVERT: E 234 MET cc_start: 0.9149 (mmm) cc_final: 0.8853 (tpp) REVERT: E 315 PHE cc_start: 0.8909 (m-10) cc_final: 0.8679 (m-10) REVERT: E 369 LEU cc_start: 0.9448 (tp) cc_final: 0.9217 (tp) REVERT: E 430 MET cc_start: 0.9064 (ttp) cc_final: 0.8705 (ttm) REVERT: E 503 MET cc_start: 0.9337 (tpp) cc_final: 0.9059 (tpp) REVERT: E 584 PHE cc_start: 0.8626 (m-10) cc_final: 0.8244 (m-80) REVERT: E 711 MET cc_start: 0.8941 (mmm) cc_final: 0.8595 (mpp) REVERT: E 731 MET cc_start: 0.9024 (mmt) cc_final: 0.7636 (tpp) REVERT: E 1021 LEU cc_start: 0.9645 (mm) cc_final: 0.9359 (pp) REVERT: E 1298 MET cc_start: 0.9179 (ttt) cc_final: 0.8605 (tmm) REVERT: E 1301 ASN cc_start: 0.9139 (m-40) cc_final: 0.8706 (m-40) outliers start: 101 outliers final: 55 residues processed: 426 average time/residue: 0.2981 time to fit residues: 202.0948 Evaluate side-chains 388 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 328 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 142 CYS Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1130 ASN Chi-restraints excluded: chain E residue 1161 THR Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1368 LEU Chi-restraints excluded: chain E residue 1435 THR Chi-restraints excluded: chain E residue 1474 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 3 optimal weight: 0.0980 chunk 192 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS C 279 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** E 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1459 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21440 Z= 0.326 Angle : 0.727 10.697 29139 Z= 0.371 Chirality : 0.046 0.268 3454 Planarity : 0.004 0.056 3624 Dihedral : 6.529 122.156 2901 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 5.19 % Allowed : 24.14 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2650 helix: 0.65 (0.14), residues: 1330 sheet: -0.57 (0.30), residues: 287 loop : -1.04 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E1033 HIS 0.030 0.001 HIS C 175 PHE 0.027 0.002 PHE E1164 TYR 0.027 0.002 TYR E1064 ARG 0.013 0.001 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 316 time to evaluate : 2.456 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: symmetry clash REVERT: A 77 MET cc_start: 0.8752 (tpp) cc_final: 0.7925 (tmm) REVERT: A 137 MET cc_start: 0.8610 (ptt) cc_final: 0.8279 (ptp) REVERT: A 199 MET cc_start: 0.7919 (mtp) cc_final: 0.7624 (mtp) REVERT: A 209 MET cc_start: 0.7764 (mmp) cc_final: 0.7516 (mmp) REVERT: A 279 GLN cc_start: 0.8769 (tp40) cc_final: 0.8392 (tm-30) REVERT: A 313 GLN cc_start: 0.8217 (mt0) cc_final: 0.7910 (mp10) REVERT: A 332 LYS cc_start: 0.9425 (mttt) cc_final: 0.9212 (mttp) REVERT: B 38 LYS cc_start: 0.9564 (mmmm) cc_final: 0.9146 (mmmm) REVERT: B 39 LYS cc_start: 0.9571 (mmmm) cc_final: 0.9281 (mmmm) REVERT: B 52 GLN cc_start: 0.8299 (mm110) cc_final: 0.8012 (mm110) REVERT: B 77 MET cc_start: 0.9133 (tpt) cc_final: 0.8078 (tpt) REVERT: B 81 CYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8356 (m) REVERT: B 146 ILE cc_start: 0.9757 (mt) cc_final: 0.9553 (mp) REVERT: B 169 MET cc_start: 0.9043 (mmm) cc_final: 0.8689 (ttm) REVERT: B 170 LYS cc_start: 0.9036 (tptp) cc_final: 0.8468 (tptm) REVERT: B 218 GLN cc_start: 0.8628 (mt0) cc_final: 0.7676 (tt0) REVERT: B 288 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8219 (mt-10) REVERT: B 305 LEU cc_start: 0.9085 (mt) cc_final: 0.8554 (mt) REVERT: B 330 TYR cc_start: 0.8825 (m-80) cc_final: 0.8605 (m-80) REVERT: B 332 LYS cc_start: 0.9278 (mmtt) cc_final: 0.9016 (mptt) REVERT: C 39 LYS cc_start: 0.9406 (mmtt) cc_final: 0.9155 (mppt) REVERT: C 47 LYS cc_start: 0.8957 (tppt) cc_final: 0.8397 (tptp) REVERT: C 142 CYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7606 (m) REVERT: C 170 LYS cc_start: 0.9062 (tptp) cc_final: 0.8832 (tptm) REVERT: C 185 LYS cc_start: 0.9419 (tppp) cc_final: 0.9202 (tppp) REVERT: C 207 LYS cc_start: 0.9378 (mmmm) cc_final: 0.9063 (mmmm) REVERT: C 279 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: C 296 ILE cc_start: 0.9404 (mt) cc_final: 0.9096 (tt) REVERT: D 77 MET cc_start: 0.9006 (tpp) cc_final: 0.8536 (tmm) REVERT: D 88 MET cc_start: 0.9111 (tpp) cc_final: 0.8903 (tpt) REVERT: D 137 MET cc_start: 0.8599 (ttp) cc_final: 0.8322 (ttm) REVERT: D 183 PHE cc_start: 0.9169 (m-80) cc_final: 0.8483 (m-10) REVERT: D 202 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.8928 (p) REVERT: D 240 MET cc_start: 0.8132 (tmm) cc_final: 0.7491 (tmm) REVERT: D 247 ASN cc_start: 0.8290 (p0) cc_final: 0.8047 (p0) REVERT: D 332 LYS cc_start: 0.9572 (mttt) cc_final: 0.9218 (mmmt) REVERT: E 109 MET cc_start: 0.8436 (tpp) cc_final: 0.7696 (tpp) REVERT: E 113 MET cc_start: 0.9257 (mmt) cc_final: 0.8667 (mmp) REVERT: E 144 TRP cc_start: 0.9065 (m100) cc_final: 0.8289 (m100) REVERT: E 151 LYS cc_start: 0.9637 (OUTLIER) cc_final: 0.9375 (mmmm) REVERT: E 182 MET cc_start: 0.9353 (mmm) cc_final: 0.8912 (mmm) REVERT: E 369 LEU cc_start: 0.9449 (tp) cc_final: 0.9171 (tp) REVERT: E 430 MET cc_start: 0.9113 (ttp) cc_final: 0.8823 (ttm) REVERT: E 584 PHE cc_start: 0.8632 (m-10) cc_final: 0.8272 (m-80) REVERT: E 711 MET cc_start: 0.8953 (mmm) cc_final: 0.8669 (mpp) REVERT: E 731 MET cc_start: 0.9152 (mmt) cc_final: 0.7681 (tpp) REVERT: E 1021 LEU cc_start: 0.9657 (mm) cc_final: 0.9384 (pp) REVERT: E 1298 MET cc_start: 0.9199 (ttt) cc_final: 0.8675 (tmm) REVERT: E 1301 ASN cc_start: 0.9125 (m-40) cc_final: 0.8687 (m110) REVERT: E 1505 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.9035 (mmm) outliers start: 118 outliers final: 72 residues processed: 407 average time/residue: 0.3075 time to fit residues: 200.2460 Evaluate side-chains 384 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 306 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 142 CYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1130 ASN Chi-restraints excluded: chain E residue 1139 THR Chi-restraints excluded: chain E residue 1161 THR Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1368 LEU Chi-restraints excluded: chain E residue 1435 THR Chi-restraints excluded: chain E residue 1450 THR Chi-restraints excluded: chain E residue 1505 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 6.9990 chunk 232 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 258 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 119 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN C 235 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 933 ASN E1293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21440 Z= 0.215 Angle : 0.683 12.428 29139 Z= 0.337 Chirality : 0.045 0.256 3454 Planarity : 0.004 0.054 3624 Dihedral : 6.355 124.370 2900 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.08 % Rotamer: Outliers : 4.13 % Allowed : 25.29 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 2650 helix: 0.83 (0.14), residues: 1331 sheet: -0.63 (0.30), residues: 299 loop : -0.91 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E1033 HIS 0.005 0.001 HIS D 175 PHE 0.023 0.001 PHE E1164 TYR 0.013 0.001 TYR E1004 ARG 0.003 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 339 time to evaluate : 2.410 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: A 47 LYS cc_start: 0.9478 (mmmt) cc_final: 0.9160 (mmmt) REVERT: A 77 MET cc_start: 0.8772 (tpp) cc_final: 0.7928 (tmm) REVERT: A 137 MET cc_start: 0.8553 (ptt) cc_final: 0.8233 (ptp) REVERT: A 199 MET cc_start: 0.7878 (mtp) cc_final: 0.7618 (mtp) REVERT: A 279 GLN cc_start: 0.8651 (tp40) cc_final: 0.8340 (tm-30) REVERT: A 313 GLN cc_start: 0.8170 (mt0) cc_final: 0.7960 (mp10) REVERT: A 332 LYS cc_start: 0.9429 (mttt) cc_final: 0.9206 (mttp) REVERT: B 38 LYS cc_start: 0.9543 (mmmm) cc_final: 0.9329 (mmmm) REVERT: B 39 LYS cc_start: 0.9571 (mmmm) cc_final: 0.9268 (mmmm) REVERT: B 44 VAL cc_start: 0.8703 (t) cc_final: 0.8473 (t) REVERT: B 77 MET cc_start: 0.8971 (tpt) cc_final: 0.8630 (tpt) REVERT: B 146 ILE cc_start: 0.9791 (mt) cc_final: 0.9582 (mp) REVERT: B 169 MET cc_start: 0.9003 (mmm) cc_final: 0.8671 (ttm) REVERT: B 170 LYS cc_start: 0.9012 (tptp) cc_final: 0.8460 (tptm) REVERT: B 181 LEU cc_start: 0.9541 (mm) cc_final: 0.9184 (mm) REVERT: B 218 GLN cc_start: 0.8635 (mt0) cc_final: 0.7776 (tt0) REVERT: B 288 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 296 ILE cc_start: 0.8719 (mp) cc_final: 0.8380 (pt) REVERT: B 305 LEU cc_start: 0.9151 (mt) cc_final: 0.8651 (mt) REVERT: B 330 TYR cc_start: 0.8800 (m-80) cc_final: 0.8576 (m-80) REVERT: B 332 LYS cc_start: 0.9270 (mmtt) cc_final: 0.9021 (mptt) REVERT: C 39 LYS cc_start: 0.9400 (mmtt) cc_final: 0.9153 (mppt) REVERT: C 47 LYS cc_start: 0.8943 (tppt) cc_final: 0.8256 (tptp) REVERT: C 142 CYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7565 (m) REVERT: C 163 MET cc_start: 0.9166 (mmm) cc_final: 0.8501 (mmm) REVERT: C 185 LYS cc_start: 0.9406 (tppp) cc_final: 0.9205 (tppp) REVERT: C 207 LYS cc_start: 0.9336 (mmmm) cc_final: 0.9132 (mmmm) REVERT: C 268 TYR cc_start: 0.9159 (t80) cc_final: 0.8578 (t80) REVERT: C 296 ILE cc_start: 0.9389 (mt) cc_final: 0.9073 (tt) REVERT: C 332 LYS cc_start: 0.9459 (ttpp) cc_final: 0.9117 (ttpp) REVERT: D 77 MET cc_start: 0.9011 (tpp) cc_final: 0.8442 (tpp) REVERT: D 137 MET cc_start: 0.8455 (ttp) cc_final: 0.8196 (ttm) REVERT: D 183 PHE cc_start: 0.9134 (m-80) cc_final: 0.8428 (m-10) REVERT: D 185 LYS cc_start: 0.9115 (ttpp) cc_final: 0.8676 (tptt) REVERT: D 202 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.8901 (p) REVERT: D 240 MET cc_start: 0.8052 (tmm) cc_final: 0.7312 (tmm) REVERT: D 247 ASN cc_start: 0.8292 (p0) cc_final: 0.8015 (p0) REVERT: D 250 PHE cc_start: 0.9060 (t80) cc_final: 0.8351 (t80) REVERT: D 268 TYR cc_start: 0.8617 (t80) cc_final: 0.8194 (m-80) REVERT: D 332 LYS cc_start: 0.9562 (mttt) cc_final: 0.9203 (mmmt) REVERT: E 109 MET cc_start: 0.8496 (tpp) cc_final: 0.7901 (tpp) REVERT: E 113 MET cc_start: 0.9224 (mmt) cc_final: 0.8622 (mmp) REVERT: E 144 TRP cc_start: 0.8987 (m100) cc_final: 0.8284 (m100) REVERT: E 151 LYS cc_start: 0.9624 (OUTLIER) cc_final: 0.9345 (mmmm) REVERT: E 182 MET cc_start: 0.9337 (mmm) cc_final: 0.8868 (mmm) REVERT: E 183 LEU cc_start: 0.9599 (mm) cc_final: 0.7949 (mm) REVERT: E 368 LEU cc_start: 0.9427 (tp) cc_final: 0.9105 (tp) REVERT: E 369 LEU cc_start: 0.9389 (tp) cc_final: 0.9134 (tp) REVERT: E 430 MET cc_start: 0.9056 (ttp) cc_final: 0.8758 (ttm) REVERT: E 503 MET cc_start: 0.9366 (tpp) cc_final: 0.9104 (tpp) REVERT: E 584 PHE cc_start: 0.8617 (m-10) cc_final: 0.8224 (m-80) REVERT: E 711 MET cc_start: 0.8921 (mmm) cc_final: 0.8640 (mpp) REVERT: E 731 MET cc_start: 0.9165 (mmt) cc_final: 0.7875 (tpp) REVERT: E 1021 LEU cc_start: 0.9588 (mm) cc_final: 0.9321 (pp) REVERT: E 1066 MET cc_start: 0.8286 (mmm) cc_final: 0.7806 (mmm) REVERT: E 1188 ASP cc_start: 0.9221 (t70) cc_final: 0.8800 (t0) REVERT: E 1293 ASN cc_start: 0.9441 (OUTLIER) cc_final: 0.9237 (t0) REVERT: E 1298 MET cc_start: 0.9191 (ttt) cc_final: 0.8626 (tmm) REVERT: E 1301 ASN cc_start: 0.9036 (m-40) cc_final: 0.8598 (m110) REVERT: E 1505 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.9052 (mmm) outliers start: 94 outliers final: 66 residues processed: 407 average time/residue: 0.3010 time to fit residues: 196.3958 Evaluate side-chains 390 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 319 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 142 CYS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1130 ASN Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1293 ASN Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1368 LEU Chi-restraints excluded: chain E residue 1406 ASP Chi-restraints excluded: chain E residue 1435 THR Chi-restraints excluded: chain E residue 1474 ILE Chi-restraints excluded: chain E residue 1505 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 146 optimal weight: 0.8980 chunk 217 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN D 175 HIS ** E 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21440 Z= 0.273 Angle : 0.706 11.946 29139 Z= 0.352 Chirality : 0.045 0.235 3454 Planarity : 0.004 0.052 3624 Dihedral : 6.306 122.702 2900 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.06 % Rotamer: Outliers : 4.79 % Allowed : 25.73 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.05 (0.16), residues: 2650 helix: 0.90 (0.14), residues: 1319 sheet: -0.63 (0.29), residues: 295 loop : -0.81 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 83 HIS 0.005 0.001 HIS E 867 PHE 0.024 0.002 PHE C 86 TYR 0.015 0.001 TYR D 268 ARG 0.003 0.000 ARG E 798 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 317 time to evaluate : 2.578 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: 0.9392 (mmmt) cc_final: 0.9151 (mmmt) REVERT: A 77 MET cc_start: 0.8674 (tpp) cc_final: 0.7886 (tmm) REVERT: A 137 MET cc_start: 0.8634 (ptt) cc_final: 0.8283 (ptp) REVERT: A 199 MET cc_start: 0.7905 (mtp) cc_final: 0.7635 (mtp) REVERT: A 279 GLN cc_start: 0.8685 (tp40) cc_final: 0.8359 (tm-30) REVERT: A 313 GLN cc_start: 0.8243 (mt0) cc_final: 0.8011 (mp10) REVERT: A 332 LYS cc_start: 0.9450 (mttt) cc_final: 0.9211 (mttp) REVERT: B 39 LYS cc_start: 0.9589 (mmmm) cc_final: 0.9294 (mmmm) REVERT: B 77 MET cc_start: 0.9051 (tpt) cc_final: 0.8585 (tpt) REVERT: B 141 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: B 169 MET cc_start: 0.9055 (mmm) cc_final: 0.8690 (ttm) REVERT: B 181 LEU cc_start: 0.9545 (mm) cc_final: 0.9192 (mm) REVERT: B 218 GLN cc_start: 0.8662 (mt0) cc_final: 0.7768 (tt0) REVERT: B 288 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8128 (mt-10) REVERT: B 296 ILE cc_start: 0.8722 (mp) cc_final: 0.8386 (pt) REVERT: B 305 LEU cc_start: 0.9184 (mt) cc_final: 0.8660 (mp) REVERT: B 330 TYR cc_start: 0.8782 (m-80) cc_final: 0.8539 (m-80) REVERT: B 332 LYS cc_start: 0.9278 (mmtt) cc_final: 0.9057 (mptt) REVERT: C 39 LYS cc_start: 0.9405 (mmtt) cc_final: 0.9143 (mppt) REVERT: C 47 LYS cc_start: 0.8940 (tppt) cc_final: 0.8555 (tppt) REVERT: C 142 CYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7600 (m) REVERT: C 185 LYS cc_start: 0.9436 (tppp) cc_final: 0.9222 (tppp) REVERT: C 207 LYS cc_start: 0.9368 (mmmm) cc_final: 0.9160 (mmmm) REVERT: C 268 TYR cc_start: 0.9145 (t80) cc_final: 0.8571 (t80) REVERT: C 296 ILE cc_start: 0.9419 (mt) cc_final: 0.9139 (tt) REVERT: C 332 LYS cc_start: 0.9457 (ttpp) cc_final: 0.9102 (ttpp) REVERT: D 77 MET cc_start: 0.9038 (tpp) cc_final: 0.8487 (tpp) REVERT: D 137 MET cc_start: 0.8503 (ttp) cc_final: 0.8210 (ttm) REVERT: D 163 MET cc_start: 0.9092 (mmm) cc_final: 0.8503 (mmt) REVERT: D 183 PHE cc_start: 0.9083 (m-80) cc_final: 0.8860 (m-80) REVERT: D 202 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.8997 (p) REVERT: D 240 MET cc_start: 0.8073 (tmm) cc_final: 0.7423 (tmm) REVERT: D 247 ASN cc_start: 0.8420 (p0) cc_final: 0.8130 (p0) REVERT: D 250 PHE cc_start: 0.9070 (t80) cc_final: 0.8321 (t80) REVERT: D 332 LYS cc_start: 0.9570 (mttt) cc_final: 0.9239 (mmmt) REVERT: E 89 GLU cc_start: 0.9087 (tp30) cc_final: 0.8621 (tm-30) REVERT: E 109 MET cc_start: 0.8532 (tpp) cc_final: 0.7932 (tpp) REVERT: E 113 MET cc_start: 0.9242 (mmt) cc_final: 0.8629 (mmp) REVERT: E 144 TRP cc_start: 0.9061 (m100) cc_final: 0.8290 (m100) REVERT: E 151 LYS cc_start: 0.9624 (OUTLIER) cc_final: 0.9359 (mmmm) REVERT: E 182 MET cc_start: 0.9345 (mmm) cc_final: 0.8887 (mmm) REVERT: E 183 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.8050 (mm) REVERT: E 368 LEU cc_start: 0.9388 (tp) cc_final: 0.9113 (tp) REVERT: E 369 LEU cc_start: 0.9398 (tp) cc_final: 0.9140 (tp) REVERT: E 430 MET cc_start: 0.9091 (ttp) cc_final: 0.8876 (ttp) REVERT: E 584 PHE cc_start: 0.8659 (m-10) cc_final: 0.8263 (m-80) REVERT: E 711 MET cc_start: 0.8921 (mmm) cc_final: 0.8626 (mpp) REVERT: E 731 MET cc_start: 0.9145 (mmt) cc_final: 0.7874 (tpp) REVERT: E 1021 LEU cc_start: 0.9580 (mm) cc_final: 0.9358 (pp) REVERT: E 1066 MET cc_start: 0.8496 (mmm) cc_final: 0.7994 (mmm) REVERT: E 1298 MET cc_start: 0.9181 (ttt) cc_final: 0.8658 (tmm) REVERT: E 1301 ASN cc_start: 0.9099 (m-40) cc_final: 0.8670 (m-40) REVERT: E 1313 LYS cc_start: 0.9128 (tppt) cc_final: 0.8852 (tppt) REVERT: E 1505 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.9044 (mmm) outliers start: 109 outliers final: 83 residues processed: 401 average time/residue: 0.3045 time to fit residues: 195.4822 Evaluate side-chains 398 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 309 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 142 CYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1130 ASN Chi-restraints excluded: chain E residue 1161 THR Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1280 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1368 LEU Chi-restraints excluded: chain E residue 1435 THR Chi-restraints excluded: chain E residue 1474 ILE Chi-restraints excluded: chain E residue 1505 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 279 GLN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 175 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21440 Z= 0.234 Angle : 0.705 14.753 29139 Z= 0.345 Chirality : 0.045 0.240 3454 Planarity : 0.004 0.051 3624 Dihedral : 6.243 123.920 2900 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 4.75 % Allowed : 25.81 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2650 helix: 0.96 (0.14), residues: 1329 sheet: -0.62 (0.30), residues: 295 loop : -0.71 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 83 HIS 0.005 0.001 HIS B 46 PHE 0.023 0.001 PHE E1164 TYR 0.013 0.001 TYR E 379 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 330 time to evaluate : 2.342 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: 0.9415 (mmmt) cc_final: 0.9161 (mmmt) REVERT: A 77 MET cc_start: 0.8597 (tpp) cc_final: 0.7847 (tmm) REVERT: A 137 MET cc_start: 0.8606 (ptt) cc_final: 0.8291 (ptp) REVERT: A 199 MET cc_start: 0.7872 (mtp) cc_final: 0.7611 (mtp) REVERT: A 279 GLN cc_start: 0.8675 (tp40) cc_final: 0.8352 (tm-30) REVERT: A 332 LYS cc_start: 0.9427 (mttt) cc_final: 0.9210 (mttp) REVERT: B 77 MET cc_start: 0.9045 (tpt) cc_final: 0.8553 (tpt) REVERT: B 169 MET cc_start: 0.8928 (mmm) cc_final: 0.8680 (ttm) REVERT: B 170 LYS cc_start: 0.9391 (tptm) cc_final: 0.9036 (tptm) REVERT: B 181 LEU cc_start: 0.9526 (mm) cc_final: 0.9185 (mm) REVERT: B 218 GLN cc_start: 0.8652 (mt0) cc_final: 0.8251 (mt0) REVERT: B 288 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8063 (mt-10) REVERT: B 305 LEU cc_start: 0.9150 (mt) cc_final: 0.8626 (mt) REVERT: B 330 TYR cc_start: 0.8772 (m-80) cc_final: 0.8554 (m-80) REVERT: C 39 LYS cc_start: 0.9394 (mmtt) cc_final: 0.9127 (mppt) REVERT: C 47 LYS cc_start: 0.8981 (tppt) cc_final: 0.8605 (tppt) REVERT: C 185 LYS cc_start: 0.9434 (tppp) cc_final: 0.9216 (tppp) REVERT: C 207 LYS cc_start: 0.9377 (mmmm) cc_final: 0.9045 (mmmm) REVERT: C 211 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9197 (mp) REVERT: C 268 TYR cc_start: 0.9111 (t80) cc_final: 0.8568 (t80) REVERT: C 296 ILE cc_start: 0.9411 (mt) cc_final: 0.9138 (tt) REVERT: C 332 LYS cc_start: 0.9424 (ttpp) cc_final: 0.9054 (ttpp) REVERT: D 77 MET cc_start: 0.9032 (tpp) cc_final: 0.8647 (tpp) REVERT: D 183 PHE cc_start: 0.9085 (m-80) cc_final: 0.8869 (m-80) REVERT: D 185 LYS cc_start: 0.9150 (ttpp) cc_final: 0.8737 (tptt) REVERT: D 202 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.8963 (p) REVERT: D 240 MET cc_start: 0.8017 (tmm) cc_final: 0.7295 (tmm) REVERT: D 250 PHE cc_start: 0.9061 (t80) cc_final: 0.8306 (t80) REVERT: D 332 LYS cc_start: 0.9568 (mttt) cc_final: 0.9236 (mmmt) REVERT: E 89 GLU cc_start: 0.9082 (tp30) cc_final: 0.8592 (tm-30) REVERT: E 109 MET cc_start: 0.8462 (tpp) cc_final: 0.7837 (tpp) REVERT: E 113 MET cc_start: 0.9241 (mmt) cc_final: 0.8784 (mmp) REVERT: E 144 TRP cc_start: 0.8997 (m100) cc_final: 0.8335 (m100) REVERT: E 182 MET cc_start: 0.9332 (mmm) cc_final: 0.8861 (mmm) REVERT: E 183 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.8047 (mm) REVERT: E 369 LEU cc_start: 0.9400 (tp) cc_final: 0.9063 (tp) REVERT: E 430 MET cc_start: 0.9076 (ttp) cc_final: 0.8870 (ttp) REVERT: E 503 MET cc_start: 0.9338 (tpp) cc_final: 0.9071 (tpp) REVERT: E 584 PHE cc_start: 0.8649 (m-10) cc_final: 0.8202 (m-80) REVERT: E 711 MET cc_start: 0.8904 (mmm) cc_final: 0.8619 (mpp) REVERT: E 731 MET cc_start: 0.9104 (mmt) cc_final: 0.7889 (tpp) REVERT: E 877 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8674 (tt) REVERT: E 1066 MET cc_start: 0.8515 (mmm) cc_final: 0.8003 (mmm) REVERT: E 1088 TRP cc_start: 0.7902 (OUTLIER) cc_final: 0.7539 (t-100) REVERT: E 1110 MET cc_start: 0.8732 (mmm) cc_final: 0.8412 (mmt) REVERT: E 1298 MET cc_start: 0.9160 (ttt) cc_final: 0.8361 (tmm) REVERT: E 1301 ASN cc_start: 0.9043 (m-40) cc_final: 0.8609 (m-40) REVERT: E 1313 LYS cc_start: 0.9125 (tppt) cc_final: 0.8807 (tppt) REVERT: E 1525 MET cc_start: 0.9227 (mmm) cc_final: 0.8855 (mmm) outliers start: 108 outliers final: 84 residues processed: 410 average time/residue: 0.2968 time to fit residues: 194.4026 Evaluate side-chains 404 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 315 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 337 VAL 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 138 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 877 LEU Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1088 TRP Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1130 ASN Chi-restraints excluded: chain E residue 1161 THR Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1171 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1280 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1368 LEU Chi-restraints excluded: chain E residue 1435 THR Chi-restraints excluded: chain E residue 1450 THR Chi-restraints excluded: chain E residue 1474 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 188 optimal weight: 0.0570 chunk 73 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 226 optimal weight: 0.5980 chunk 238 optimal weight: 0.8980 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 335 ASN D 160 ASN D 175 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21440 Z= 0.186 Angle : 0.721 14.469 29139 Z= 0.344 Chirality : 0.046 0.257 3454 Planarity : 0.003 0.052 3624 Dihedral : 6.107 125.268 2900 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 3.78 % Allowed : 26.87 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 2650 helix: 1.06 (0.14), residues: 1307 sheet: -0.58 (0.30), residues: 295 loop : -0.62 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 83 HIS 0.007 0.001 HIS D 175 PHE 0.021 0.001 PHE E 364 TYR 0.012 0.001 TYR D 268 ARG 0.004 0.000 ARG D 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 349 time to evaluate : 2.257 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: A 47 LYS cc_start: 0.9418 (mmmt) cc_final: 0.9120 (mmmt) REVERT: A 77 MET cc_start: 0.8572 (tpp) cc_final: 0.7757 (tmm) REVERT: A 199 MET cc_start: 0.7954 (mtp) cc_final: 0.7688 (mtp) REVERT: A 279 GLN cc_start: 0.8659 (tp40) cc_final: 0.8339 (tm-30) REVERT: A 332 LYS cc_start: 0.9426 (mttt) cc_final: 0.9204 (mttp) REVERT: B 38 LYS cc_start: 0.9357 (mmmm) cc_final: 0.9078 (mmtp) REVERT: B 63 LEU cc_start: 0.9680 (tt) cc_final: 0.9449 (pp) REVERT: B 77 MET cc_start: 0.9031 (tpt) cc_final: 0.8563 (tpt) REVERT: B 169 MET cc_start: 0.8917 (mmm) cc_final: 0.8643 (ttm) REVERT: B 170 LYS cc_start: 0.9360 (tptm) cc_final: 0.8972 (tptm) REVERT: B 181 LEU cc_start: 0.9512 (mm) cc_final: 0.9148 (mm) REVERT: B 288 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8037 (mt-10) REVERT: B 305 LEU cc_start: 0.9110 (mt) cc_final: 0.8592 (mt) REVERT: B 332 LYS cc_start: 0.9265 (mmtt) cc_final: 0.8960 (mptt) REVERT: C 39 LYS cc_start: 0.9378 (mmtt) cc_final: 0.9119 (mppt) REVERT: C 47 LYS cc_start: 0.8957 (tppt) cc_final: 0.8590 (tppt) REVERT: C 163 MET cc_start: 0.8924 (mmm) cc_final: 0.8552 (mmm) REVERT: C 185 LYS cc_start: 0.9411 (tppp) cc_final: 0.9157 (tppp) REVERT: C 207 LYS cc_start: 0.9384 (mmmm) cc_final: 0.9056 (mmmm) REVERT: C 211 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9136 (mp) REVERT: C 235 GLN cc_start: 0.8713 (mt0) cc_final: 0.8303 (mt0) REVERT: C 268 TYR cc_start: 0.9079 (t80) cc_final: 0.8579 (t80) REVERT: C 296 ILE cc_start: 0.9406 (mt) cc_final: 0.9008 (tt) REVERT: C 332 LYS cc_start: 0.9394 (ttpp) cc_final: 0.9012 (ttpp) REVERT: D 77 MET cc_start: 0.8984 (tpp) cc_final: 0.8596 (tpp) REVERT: D 185 LYS cc_start: 0.9177 (ttpp) cc_final: 0.8781 (tptt) REVERT: D 240 MET cc_start: 0.8026 (tmm) cc_final: 0.7306 (tmm) REVERT: D 247 ASN cc_start: 0.7730 (p0) cc_final: 0.7514 (p0) REVERT: D 250 PHE cc_start: 0.9021 (t80) cc_final: 0.7884 (t80) REVERT: D 257 ILE cc_start: 0.9462 (mt) cc_final: 0.9213 (mp) REVERT: D 332 LYS cc_start: 0.9560 (mttt) cc_final: 0.9255 (mmmt) REVERT: E 89 GLU cc_start: 0.9203 (tp30) cc_final: 0.8665 (tm-30) REVERT: E 109 MET cc_start: 0.8432 (tpp) cc_final: 0.7810 (tpp) REVERT: E 113 MET cc_start: 0.9236 (mmt) cc_final: 0.8791 (mmp) REVERT: E 144 TRP cc_start: 0.8970 (m100) cc_final: 0.8367 (m100) REVERT: E 182 MET cc_start: 0.9287 (mmm) cc_final: 0.8792 (mmm) REVERT: E 183 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.8055 (mm) REVERT: E 369 LEU cc_start: 0.9360 (tp) cc_final: 0.9033 (tp) REVERT: E 413 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8187 (ptm) REVERT: E 430 MET cc_start: 0.9060 (ttp) cc_final: 0.8857 (ttp) REVERT: E 503 MET cc_start: 0.9341 (tpp) cc_final: 0.9061 (tpp) REVERT: E 584 PHE cc_start: 0.8739 (m-10) cc_final: 0.8285 (m-80) REVERT: E 586 ILE cc_start: 0.9541 (pt) cc_final: 0.9322 (pt) REVERT: E 711 MET cc_start: 0.8899 (mmm) cc_final: 0.8613 (mpp) REVERT: E 731 MET cc_start: 0.9079 (mmt) cc_final: 0.7878 (tpp) REVERT: E 877 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8719 (tt) REVERT: E 1021 LEU cc_start: 0.9576 (mm) cc_final: 0.9354 (pp) REVERT: E 1066 MET cc_start: 0.8397 (mmm) cc_final: 0.7898 (mmm) REVERT: E 1088 TRP cc_start: 0.7905 (OUTLIER) cc_final: 0.7536 (t-100) REVERT: E 1110 MET cc_start: 0.8652 (mmm) cc_final: 0.8290 (mmt) REVERT: E 1261 LEU cc_start: 0.9536 (tp) cc_final: 0.9074 (mt) REVERT: E 1298 MET cc_start: 0.9117 (ttt) cc_final: 0.8303 (tmm) REVERT: E 1301 ASN cc_start: 0.9023 (m-40) cc_final: 0.8621 (m-40) REVERT: E 1525 MET cc_start: 0.9236 (mmm) cc_final: 0.8904 (mmm) outliers start: 86 outliers final: 67 residues processed: 414 average time/residue: 0.2954 time to fit residues: 194.4383 Evaluate side-chains 395 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 323 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 877 LEU Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1088 TRP Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1130 ASN Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1171 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1280 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1368 LEU Chi-restraints excluded: chain E residue 1435 THR Chi-restraints excluded: chain E residue 1450 THR Chi-restraints excluded: chain E residue 1474 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 3.9990 chunk 253 optimal weight: 0.3980 chunk 154 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN E 132 ASN ** E 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21440 Z= 0.248 Angle : 0.745 14.160 29139 Z= 0.361 Chirality : 0.046 0.266 3454 Planarity : 0.004 0.055 3624 Dihedral : 6.049 122.330 2899 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.28 % Rotamer: Outliers : 3.30 % Allowed : 28.41 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 2650 helix: 1.01 (0.14), residues: 1304 sheet: -0.52 (0.29), residues: 299 loop : -0.57 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 52 HIS 0.005 0.001 HIS D 175 PHE 0.028 0.002 PHE D 183 TYR 0.012 0.001 TYR D 268 ARG 0.002 0.000 ARG B 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 323 time to evaluate : 2.784 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: A 47 LYS cc_start: 0.9437 (mmmt) cc_final: 0.9075 (mmmt) REVERT: A 77 MET cc_start: 0.8565 (tpp) cc_final: 0.7786 (tmm) REVERT: A 199 MET cc_start: 0.7961 (mtp) cc_final: 0.7683 (mtp) REVERT: A 279 GLN cc_start: 0.8694 (tp40) cc_final: 0.8343 (tm-30) REVERT: A 332 LYS cc_start: 0.9446 (mttt) cc_final: 0.9225 (mttp) REVERT: B 38 LYS cc_start: 0.9370 (mmmm) cc_final: 0.9123 (mmtp) REVERT: B 77 MET cc_start: 0.9053 (tpt) cc_final: 0.8586 (tpt) REVERT: B 169 MET cc_start: 0.8916 (mmm) cc_final: 0.8698 (ttm) REVERT: B 181 LEU cc_start: 0.9521 (mm) cc_final: 0.9165 (mm) REVERT: B 288 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8056 (mt-10) REVERT: B 305 LEU cc_start: 0.9135 (mt) cc_final: 0.8607 (mt) REVERT: B 332 LYS cc_start: 0.9304 (mmtt) cc_final: 0.8963 (mptt) REVERT: C 39 LYS cc_start: 0.9370 (mmtt) cc_final: 0.9136 (mppt) REVERT: C 47 LYS cc_start: 0.8881 (tppt) cc_final: 0.8495 (tppt) REVERT: C 185 LYS cc_start: 0.9417 (tppp) cc_final: 0.9186 (tppp) REVERT: C 207 LYS cc_start: 0.9384 (mmmm) cc_final: 0.9064 (mmmm) REVERT: C 211 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9187 (mp) REVERT: C 235 GLN cc_start: 0.8781 (mt0) cc_final: 0.8452 (mt0) REVERT: C 268 TYR cc_start: 0.9083 (t80) cc_final: 0.8541 (t80) REVERT: C 296 ILE cc_start: 0.9425 (mt) cc_final: 0.9093 (tt) REVERT: C 332 LYS cc_start: 0.9412 (ttpp) cc_final: 0.8976 (ttpp) REVERT: D 77 MET cc_start: 0.9047 (tpp) cc_final: 0.8659 (tpp) REVERT: D 137 MET cc_start: 0.8567 (ttp) cc_final: 0.8228 (ttm) REVERT: D 185 LYS cc_start: 0.9165 (ttpp) cc_final: 0.8785 (tptt) REVERT: D 240 MET cc_start: 0.7987 (tmm) cc_final: 0.7208 (tmm) REVERT: D 257 ILE cc_start: 0.9450 (mt) cc_final: 0.9214 (mp) REVERT: D 332 LYS cc_start: 0.9577 (mttt) cc_final: 0.9277 (mmmt) REVERT: E 39 PHE cc_start: 0.9172 (t80) cc_final: 0.8783 (t80) REVERT: E 89 GLU cc_start: 0.9181 (tp30) cc_final: 0.8666 (tm-30) REVERT: E 109 MET cc_start: 0.8471 (tpp) cc_final: 0.7834 (tpp) REVERT: E 113 MET cc_start: 0.9265 (mmt) cc_final: 0.8784 (mmp) REVERT: E 144 TRP cc_start: 0.9040 (m100) cc_final: 0.8398 (m100) REVERT: E 182 MET cc_start: 0.9332 (mmm) cc_final: 0.8857 (mmm) REVERT: E 183 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.8097 (mm) REVERT: E 369 LEU cc_start: 0.9377 (tp) cc_final: 0.9054 (tp) REVERT: E 413 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8195 (ptm) REVERT: E 503 MET cc_start: 0.9348 (tpp) cc_final: 0.9069 (tpp) REVERT: E 584 PHE cc_start: 0.8719 (m-10) cc_final: 0.8279 (m-80) REVERT: E 711 MET cc_start: 0.8877 (mmm) cc_final: 0.8583 (mpp) REVERT: E 731 MET cc_start: 0.9080 (mmt) cc_final: 0.7884 (tpp) REVERT: E 801 MET cc_start: 0.8889 (ptp) cc_final: 0.8646 (ptp) REVERT: E 877 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8695 (tt) REVERT: E 1066 MET cc_start: 0.8474 (mmm) cc_final: 0.7968 (mmm) REVERT: E 1088 TRP cc_start: 0.7912 (OUTLIER) cc_final: 0.7590 (t-100) REVERT: E 1110 MET cc_start: 0.8667 (mmm) cc_final: 0.8314 (mmt) REVERT: E 1298 MET cc_start: 0.9121 (ttt) cc_final: 0.8327 (tmm) REVERT: E 1301 ASN cc_start: 0.9104 (m-40) cc_final: 0.8699 (m-40) REVERT: E 1313 LYS cc_start: 0.9039 (tppt) cc_final: 0.8699 (tppt) outliers start: 75 outliers final: 65 residues processed: 381 average time/residue: 0.2957 time to fit residues: 179.2188 Evaluate side-chains 387 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 317 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 877 LEU Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1088 TRP Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1130 ASN Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1171 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1280 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1368 LEU Chi-restraints excluded: chain E residue 1435 THR Chi-restraints excluded: chain E residue 1450 THR Chi-restraints excluded: chain E residue 1474 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 195 optimal weight: 1.9990 chunk 31 optimal weight: 0.0000 chunk 58 optimal weight: 0.6980 chunk 212 optimal weight: 5.9990 chunk 88 optimal weight: 0.1980 chunk 217 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 175 HIS D 247 ASN ** E 732 GLN ** 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 = 0.3169 r_free = 0.3169 target = 0.058434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.048899 restraints weight = 108775.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.050429 restraints weight = 58017.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.051463 restraints weight = 37220.664| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21440 Z= 0.173 Angle : 0.732 13.738 29139 Z= 0.344 Chirality : 0.046 0.288 3454 Planarity : 0.003 0.053 3624 Dihedral : 5.824 125.457 2899 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 3.17 % Allowed : 28.50 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.16), residues: 2650 helix: 1.12 (0.14), residues: 1298 sheet: -0.46 (0.31), residues: 287 loop : -0.52 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP E 52 HIS 0.008 0.001 HIS B 46 PHE 0.020 0.001 PHE E 364 TYR 0.010 0.001 TYR E 379 ARG 0.002 0.000 ARG C 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4559.52 seconds wall clock time: 83 minutes 16.44 seconds (4996.44 seconds total)