Starting phenix.real_space_refine on Sat Feb 17 19:42:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd7_29004/02_2024/8fd7_29004_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd7_29004/02_2024/8fd7_29004.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd7_29004/02_2024/8fd7_29004_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd7_29004/02_2024/8fd7_29004_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd7_29004/02_2024/8fd7_29004_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd7_29004/02_2024/8fd7_29004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd7_29004/02_2024/8fd7_29004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd7_29004/02_2024/8fd7_29004_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd7_29004/02_2024/8fd7_29004_updated.pdb" } resolution = 3.1 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= -0.008 sd= 1.079 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 2 5.49 5 S 105 5.16 5 Na 1 4.78 5 C 12761 2.51 5 N 3234 2.21 5 O 3595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1479": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19701 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 7630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7630 Classifications: {'peptide': 955} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 912} Chain breaks: 4 Chain: "K" Number of atoms: 10227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 10227 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1227} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 181} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 126 Unusual residues: {' CA': 1, ' NA': 1, 'GBN': 1, 'NAG': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 172 Unusual residues: {' CA': 2, 'CLR': 3, 'WO9': 1, 'YSW': 1} Classifications: {'undetermined': 7, 'water': 3} Link IDs: {None: 9} Time building chain proxies: 10.22, per 1000 atoms: 0.52 Number of scatterers: 19701 At special positions: 0 Unit cell: (126.085, 142.785, 199.565, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 105 16.00 P 2 15.00 Na 1 11.00 O 3595 8.00 N 3234 7.00 C 12761 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 305 " - pdb=" SG CYS D1046 " distance=2.03 Simple disulfide: pdb=" SG CYS D 356 " - pdb=" SG CYS D1061 " distance=2.03 Simple disulfide: pdb=" SG CYS D 406 " - pdb=" SG CYS D1073 " distance=2.03 Simple disulfide: pdb=" SG CYS D 669 " - pdb=" SG CYS D 699 " distance=2.03 Simple disulfide: pdb=" SG CYS D 906 " - pdb=" SG CYS D 976 " distance=2.03 Simple disulfide: pdb=" SG CYS D 998 " - pdb=" SG CYS D1028 " distance=2.03 Simple disulfide: pdb=" SG CYS D1001 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS K 316 " - pdb=" SG CYS K 332 " distance=2.03 Simple disulfide: pdb=" SG CYS K1058 " - pdb=" SG CYS K1069 " distance=2.03 Simple disulfide: pdb=" SG CYS K1431 " - pdb=" SG CYS K1447 " 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=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG D1203 " - " ASN D 94 " " NAG D1204 " - " ASN D 470 " Time building additional restraints: 8.63 Conformation dependent library (CDL) restraints added in 3.6 seconds 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4582 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 15 sheets defined 48.2% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'D' and resid 32 through 54 Processing helix chain 'D' and resid 56 through 66 removed outlier: 4.193A pdb=" N TYR D 66 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 111 Processing helix chain 'D' and resid 179 through 201 removed outlier: 5.083A pdb=" N ALA D 190 " --> pdb=" O ASN D 186 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU D 191 " --> pdb=" O TRP D 187 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ASP D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 244 through 250 removed outlier: 4.148A pdb=" N GLY D 249 " --> pdb=" O TRP D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.626A pdb=" N THR D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 326 removed outlier: 3.961A pdb=" N ASN D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 345 Processing helix chain 'D' and resid 372 through 378 Processing helix chain 'D' and resid 399 through 407 Processing helix chain 'D' and resid 418 through 420 No H-bonds generated for 'chain 'D' and resid 418 through 420' Processing helix chain 'D' and resid 427 through 431 Processing helix chain 'D' and resid 434 through 443 removed outlier: 5.703A pdb=" N ASP D 441 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LYS D 442 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 484 No H-bonds generated for 'chain 'D' and resid 482 through 484' Processing helix chain 'D' and resid 496 through 502 removed outlier: 3.687A pdb=" N LEU D 502 " --> pdb=" O ASP D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 566 No H-bonds generated for 'chain 'D' and resid 563 through 566' Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 627 through 629 No H-bonds generated for 'chain 'D' and resid 627 through 629' Processing helix chain 'D' and resid 640 through 650 removed outlier: 4.285A pdb=" N LEU D 650 " --> pdb=" O TYR D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 658 removed outlier: 3.741A pdb=" N PHE D 655 " --> pdb=" O PRO D 652 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU D 656 " --> pdb=" O ASP D 653 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER D 658 " --> pdb=" O PHE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 691 Processing helix chain 'D' and resid 701 through 720 Processing helix chain 'D' and resid 748 through 753 removed outlier: 3.625A pdb=" N GLU D 752 " --> pdb=" O GLU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 762 No H-bonds generated for 'chain 'D' and resid 760 through 762' Processing helix chain 'D' and resid 764 through 771 Processing helix chain 'D' and resid 820 through 828 Processing helix chain 'D' and resid 882 through 888 Processing helix chain 'D' and resid 1023 through 1025 No H-bonds generated for 'chain 'D' and resid 1023 through 1025' Processing helix chain 'D' and resid 1045 through 1048 No H-bonds generated for 'chain 'D' and resid 1045 through 1048' Processing helix chain 'K' and resid 113 through 119 Processing helix chain 'K' and resid 124 through 143 removed outlier: 3.641A pdb=" N ILE K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 181 removed outlier: 3.717A pdb=" N TYR K 164 " --> pdb=" O GLU K 160 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU K 165 " --> pdb=" O ARG K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 210 Processing helix chain 'K' and resid 235 through 250 Proline residue: K 244 - end of helix Processing helix chain 'K' and resid 255 through 289 Proline residue: K 267 - end of helix removed outlier: 5.779A pdb=" N HIS K 270 " --> pdb=" O VAL K 266 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILE K 271 " --> pdb=" O PRO K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 360 Processing helix chain 'K' and resid 365 through 376 Processing helix chain 'K' and resid 381 through 412 Processing helix chain 'K' and resid 421 through 446 removed outlier: 3.936A pdb=" N GLU K 445 " --> pdb=" O ILE K 441 " (cutoff:3.500A) Processing helix chain 'K' and resid 521 through 523 No H-bonds generated for 'chain 'K' and resid 521 through 523' Processing helix chain 'K' and resid 526 through 541 Processing helix chain 'K' and resid 553 through 577 removed outlier: 3.536A pdb=" N ALA K 565 " --> pdb=" O LYS K 561 " (cutoff:3.500A) Processing helix chain 'K' and resid 580 through 584 Processing helix chain 'K' and resid 590 through 608 removed outlier: 3.689A pdb=" N PHE K 594 " --> pdb=" O ARG K 590 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL K 595 " --> pdb=" O PHE K 591 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS K 597 " --> pdb=" O CYS K 593 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY K 598 " --> pdb=" O PHE K 594 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE K 604 " --> pdb=" O ILE K 600 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU K 607 " --> pdb=" O THR K 603 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR K 608 " --> pdb=" O ILE K 604 " (cutoff:3.500A) Processing helix chain 'K' and resid 613 through 630 removed outlier: 4.353A pdb=" N VAL K 618 " --> pdb=" O GLY K 615 " (cutoff:3.500A) Processing helix chain 'K' and resid 638 through 672 removed outlier: 5.543A pdb=" N SER K 653 " --> pdb=" O ARG K 649 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU K 654 " --> pdb=" O SER K 650 " (cutoff:3.500A) Processing helix chain 'K' and resid 692 through 704 Processing helix chain 'K' and resid 709 through 718 Processing helix chain 'K' and resid 724 through 762 removed outlier: 4.268A pdb=" N LEU K 728 " --> pdb=" O PHE K 724 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL K 729 " --> pdb=" O PRO K 725 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N CYS K 730 " --> pdb=" O GLY K 726 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE K 731 " --> pdb=" O MET K 727 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR K 732 " --> pdb=" O LEU K 728 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE K 733 " --> pdb=" O VAL K 729 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY K 740 " --> pdb=" O LEU K 736 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN K 741 " --> pdb=" O PHE K 737 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE K 751 " --> pdb=" O VAL K 747 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU K 760 " --> pdb=" O LEU K 756 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER K 761 " --> pdb=" O ALA K 757 " (cutoff:3.500A) Processing helix chain 'K' and resid 890 through 897 Processing helix chain 'K' and resid 901 through 918 removed outlier: 3.675A pdb=" N LEU K 917 " --> pdb=" O SER K 913 " (cutoff:3.500A) Processing helix chain 'K' and resid 929 through 950 Processing helix chain 'K' and resid 966 through 979 Processing helix chain 'K' and resid 997 through 999 No H-bonds generated for 'chain 'K' and resid 997 through 999' Processing helix chain 'K' and resid 1003 through 1010 Processing helix chain 'K' and resid 1018 through 1029 removed outlier: 3.627A pdb=" N ILE K1029 " --> pdb=" O ALA K1025 " (cutoff:3.500A) Processing helix chain 'K' and resid 1031 through 1050 Processing helix chain 'K' and resid 1105 through 1112 Processing helix chain 'K' and resid 1117 through 1125 Processing helix chain 'K' and resid 1141 through 1170 removed outlier: 4.804A pdb=" N MET K1158 " --> pdb=" O PHE K1155 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE K1160 " --> pdb=" O MET K1157 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE K1161 " --> pdb=" O MET K1158 " (cutoff:3.500A) Processing helix chain 'K' and resid 1184 through 1192 Processing helix chain 'K' and resid 1218 through 1239 removed outlier: 4.154A pdb=" N LEU K1224 " --> pdb=" O TYR K1220 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET K1225 " --> pdb=" O PHE K1221 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU K1230 " --> pdb=" O PHE K1226 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU K1236 " --> pdb=" O ASN K1232 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ALA K1237 " --> pdb=" O THR K1233 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N MET K1238 " --> pdb=" O ILE K1234 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN K1239 " --> pdb=" O CYS K1235 " (cutoff:3.500A) Processing helix chain 'K' and resid 1245 through 1270 Processing helix chain 'K' and resid 1275 through 1280 removed outlier: 4.383A pdb=" N PHE K1279 " --> pdb=" O PRO K1275 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N CYS K1280 " --> pdb=" O LYS K1276 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1275 through 1280' Processing helix chain 'K' and resid 1282 through 1300 Processing helix chain 'K' and resid 1329 through 1342 removed outlier: 3.778A pdb=" N VAL K1333 " --> pdb=" O LEU K1330 " (cutoff:3.500A) Processing helix chain 'K' and resid 1345 through 1354 Processing helix chain 'K' and resid 1360 through 1381 Processing helix chain 'K' and resid 1402 through 1414 Processing helix chain 'K' and resid 1418 through 1424 Processing helix chain 'K' and resid 1452 through 1482 removed outlier: 3.968A pdb=" N PHE K1459 " --> pdb=" O TYR K1455 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP K1480 " --> pdb=" O MET K1476 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TYR K1481 " --> pdb=" O ASP K1477 " (cutoff:3.500A) Processing helix chain 'K' and resid 1486 through 1489 No H-bonds generated for 'chain 'K' and resid 1486 through 1489' Processing helix chain 'K' and resid 1491 through 1503 removed outlier: 3.683A pdb=" N ASP K1495 " --> pdb=" O PRO K1491 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA K1502 " --> pdb=" O LYS K1498 " (cutoff:3.500A) Processing helix chain 'K' and resid 1514 through 1517 No H-bonds generated for 'chain 'K' and resid 1514 through 1517' Processing helix chain 'K' and resid 1520 through 1522 No H-bonds generated for 'chain 'K' and resid 1520 through 1522' Processing helix chain 'K' and resid 1540 through 1542 No H-bonds generated for 'chain 'K' and resid 1540 through 1542' Processing helix chain 'K' and resid 1558 through 1569 Processing helix chain 'K' and resid 1578 through 1590 removed outlier: 4.799A pdb=" N GLU K1583 " --> pdb=" O GLU K1579 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA K1587 " --> pdb=" O GLU K1583 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE K1588 " --> pdb=" O GLU K1584 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE K1589 " --> pdb=" O LEU K1585 " (cutoff:3.500A) Processing helix chain 'K' and resid 1599 through 1608 removed outlier: 4.106A pdb=" N VAL K1604 " --> pdb=" O LEU K1601 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL K1605 " --> pdb=" O ASP K1602 " (cutoff:3.500A) Proline residue: K1606 - end of helix Processing helix chain 'C' and resid 191 through 207 Processing helix chain 'C' and resid 241 through 244 No H-bonds generated for 'chain 'C' and resid 241 through 244' Processing helix chain 'C' and resid 247 through 262 Processing helix chain 'C' and resid 277 through 280 Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 311 through 326 removed outlier: 4.406A pdb=" N THR C 316 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N MET C 319 " --> pdb=" O THR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 360 removed outlier: 3.535A pdb=" N TYR C 352 " --> pdb=" O HIS C 348 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 70 through 74 Processing sheet with id= B, first strand: chain 'D' and resid 124 through 126 Processing sheet with id= C, first strand: chain 'D' and resid 167 through 169 removed outlier: 7.049A pdb=" N VAL D 468 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL D 489 " --> pdb=" O LEU D 466 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 466 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY D 491 " --> pdb=" O GLY D 464 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY D 464 " --> pdb=" O GLY D 491 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP D 493 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE D 462 " --> pdb=" O ASP D 493 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 411 through 415 removed outlier: 3.598A pdb=" N TYR D 411 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU D 257 " --> pdb=" O MET D 361 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE D 363 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU D 259 " --> pdb=" O PHE D 363 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN D 292 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL D 260 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA D 294 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 513 through 518 removed outlier: 3.575A pdb=" N PHE D 515 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 586 through 595 Processing sheet with id= G, first strand: chain 'D' and resid 743 through 745 removed outlier: 6.603A pdb=" N LYS D 817 " --> pdb=" O LYS D 732 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG D 734 " --> pdb=" O GLY D 815 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLY D 815 " --> pdb=" O ARG D 734 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL D 736 " --> pdb=" O VAL D 813 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL D 813 " --> pdb=" O VAL D 736 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA D 812 " --> pdb=" O VAL D 800 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET D 795 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 850 through 856 Processing sheet with id= I, first strand: chain 'D' and resid 895 through 901 removed outlier: 4.321A pdb=" N ILE D 977 " --> pdb=" O SER D1040 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 904 through 907 removed outlier: 3.761A pdb=" N SER D 904 " --> pdb=" O CYS D 976 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 994 through 996 removed outlier: 3.647A pdb=" N GLY D 994 " --> pdb=" O PHE D1005 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE D1005 " --> pdb=" O GLY D 994 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 1056 through 1058 Processing sheet with id= M, first strand: chain 'K' and resid 1072 through 1075 Processing sheet with id= N, first strand: chain 'C' and resid 180 through 183 removed outlier: 5.665A pdb=" N ILE C 288 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 183 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL C 290 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL C 335 " --> pdb=" O PHE C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 213 through 216 841 hydrogen bonds defined for protein. 2211 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: 6.27 Time building geometry restraints manager: 9.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3174 1.30 - 1.43: 5184 1.43 - 1.56: 11546 1.56 - 1.69: 66 1.69 - 1.82: 162 Bond restraints: 20132 Sorted by residual: bond pdb=" C10 YSW K1702 " pdb=" C11 YSW K1702 " ideal model delta sigma weight residual 1.527 1.437 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C12 YSW K1702 " pdb=" O14 YSW K1702 " ideal model delta sigma weight residual 1.398 1.311 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C07 YSW K1702 " pdb=" C08 YSW K1702 " ideal model delta sigma weight residual 1.528 1.442 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C08 YSW K1702 " pdb=" C09 YSW K1702 " ideal model delta sigma weight residual 1.527 1.442 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C04 YSW K1702 " pdb=" C05 YSW K1702 " ideal model delta sigma weight residual 1.527 1.443 0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 20127 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.35: 516 106.35 - 113.27: 10958 113.27 - 120.20: 7139 120.20 - 127.12: 8497 127.12 - 134.05: 188 Bond angle restraints: 27298 Sorted by residual: angle pdb=" C16 YSW K1702 " pdb=" C17 YSW K1702 " pdb=" O18 YSW K1702 " ideal model delta sigma weight residual 109.47 119.92 -10.45 3.00e+00 1.11e-01 1.21e+01 angle pdb=" O20 YSW K1702 " pdb=" P19 YSW K1702 " pdb=" O21 YSW K1702 " ideal model delta sigma weight residual 109.47 119.90 -10.43 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C37 YSW K1702 " pdb=" C38 YSW K1702 " pdb=" C39 YSW K1702 " ideal model delta sigma weight residual 109.47 119.61 -10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C11 YSW K1702 " pdb=" C12 YSW K1702 " pdb=" O14 YSW K1702 " ideal model delta sigma weight residual 120.00 111.05 8.95 3.00e+00 1.11e-01 8.89e+00 angle pdb=" O21 YSW K1702 " pdb=" P19 YSW K1702 " pdb=" O22 YSW K1702 " ideal model delta sigma weight residual 109.47 118.36 -8.89 3.00e+00 1.11e-01 8.78e+00 ... (remaining 27293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.55: 12107 33.55 - 67.09: 205 67.09 - 100.64: 8 100.64 - 134.18: 10 134.18 - 167.73: 2 Dihedral angle restraints: 12332 sinusoidal: 5250 harmonic: 7082 Sorted by residual: dihedral pdb=" C10 YSW K1702 " pdb=" C11 YSW K1702 " pdb=" C12 YSW K1702 " pdb=" O13 YSW K1702 " ideal model delta sinusoidal sigma weight residual -38.44 129.29 -167.73 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C08 WO9 K1701 " pdb=" C09 WO9 K1701 " pdb=" C10 WO9 K1701 " pdb=" C11 WO9 K1701 " ideal model delta sinusoidal sigma weight residual 192.43 45.68 146.75 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C2 GBN D1202 " pdb=" C1R GBN D1202 " pdb=" C6R GBN D1202 " pdb=" C5R GBN D1202 " ideal model delta sinusoidal sigma weight residual -66.69 67.09 -133.78 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 12329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.106: 3115 1.106 - 2.212: 0 2.212 - 3.318: 0 3.318 - 4.424: 0 4.424 - 5.531: 1 Chirality restraints: 3116 Sorted by residual: chirality pdb=" C1R GBN D1202 " pdb=" C2R GBN D1202 " pdb=" C3 GBN D1202 " pdb=" C6R GBN D1202 " both_signs ideal model delta sigma weight residual False -2.69 2.84 -5.53 2.00e-01 2.50e+01 7.65e+02 chirality pdb=" C22 WO9 K1701 " pdb=" C21 WO9 K1701 " pdb=" C23 WO9 K1701 " pdb=" O32 WO9 K1701 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.42e+00 ... (remaining 3113 not shown) Planarity restraints: 3428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K1526 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.22e+00 pdb=" N PRO K1527 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO K1527 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO K1527 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K1606 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO K1607 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO K1607 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO K1607 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 693 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO D 694 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 694 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 694 " 0.024 5.00e-02 4.00e+02 ... (remaining 3425 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3054 2.76 - 3.29: 20042 3.29 - 3.83: 31815 3.83 - 4.36: 37431 4.36 - 4.90: 62944 Nonbonded interactions: 155286 Sorted by model distance: nonbonded pdb=" OD1 ASP D 598 " pdb=" OG SER D 764 " model vdw 2.223 2.440 nonbonded pdb=" O LEU C 303 " pdb=" OG SER C 306 " model vdw 2.268 2.440 nonbonded pdb=" OG SER C 186 " pdb=" OE1 GLN C 318 " model vdw 2.269 2.440 nonbonded pdb=" NH2 ARG D 768 " pdb=" OD2 ASP D 857 " model vdw 2.276 2.520 nonbonded pdb=" O LEU K1230 " pdb=" OG1 THR K1233 " model vdw 2.280 2.440 ... (remaining 155281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 4.970 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: 18.350 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 54.000 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 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 : 0.005 0.090 20132 Z= 0.339 Angle : 0.551 10.453 27298 Z= 0.262 Chirality : 0.108 5.531 3116 Planarity : 0.004 0.045 3426 Dihedral : 12.605 167.726 7720 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.14 % Favored : 93.73 % Rotamer: Outliers : 2.76 % Allowed : 7.24 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2394 helix: 1.07 (0.16), residues: 1178 sheet: -0.18 (0.35), residues: 221 loop : -1.99 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 123 HIS 0.004 0.000 HIS K1240 PHE 0.012 0.001 PHE D 515 TYR 0.014 0.001 TYR D1070 ARG 0.002 0.000 ARG K1511 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 161 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7234 (ttpt) REVERT: D 272 LYS cc_start: 0.8463 (tttp) cc_final: 0.8129 (tppt) REVERT: D 726 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7757 (mmtp) REVERT: D 773 ASP cc_start: 0.8169 (t0) cc_final: 0.7848 (t0) REVERT: D 996 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8262 (tp) REVERT: K 570 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7235 (mm-30) REVERT: K 571 MET cc_start: 0.7063 (ttt) cc_final: 0.5891 (tmm) REVERT: K 656 LEU cc_start: 0.7838 (pp) cc_final: 0.7467 (mp) REVERT: K 1098 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8573 (t80) REVERT: K 1223 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.8466 (t80) REVERT: K 1226 PHE cc_start: 0.7633 (m-80) cc_final: 0.7407 (m-80) REVERT: K 1278 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.7004 (t80) REVERT: K 1379 MET cc_start: 0.7905 (ptp) cc_final: 0.7618 (ptm) REVERT: K 1399 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.5846 (t80) REVERT: K 1494 LEU cc_start: 0.8019 (mp) cc_final: 0.7714 (tt) REVERT: K 1586 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.5371 (mmp80) REVERT: C 312 MET cc_start: 0.4571 (mtt) cc_final: 0.3880 (ttm) outliers start: 59 outliers final: 24 residues processed: 213 average time/residue: 0.3537 time to fit residues: 114.4171 Evaluate side-chains 133 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 671 ASP Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 748 PHE Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1100 ASN Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1586 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 62 optimal weight: 0.0170 chunk 123 optimal weight: 30.0000 chunk 97 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 73 optimal weight: 0.0170 chunk 114 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 218 optimal weight: 20.0000 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 GLN D 165 HIS D 186 ASN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN D 528 ASN D 696 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 556 GLN ** K 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 892 GLN K 898 ASN ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1083 HIS K1087 GLN ** K1232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1358 GLN ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1580 GLN C 276 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20132 Z= 0.169 Angle : 0.580 24.435 27298 Z= 0.275 Chirality : 0.053 1.959 3116 Planarity : 0.004 0.046 3426 Dihedral : 10.661 178.957 3154 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.43 % Favored : 93.44 % Rotamer: Outliers : 2.57 % Allowed : 9.35 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2394 helix: 1.13 (0.16), residues: 1183 sheet: -0.23 (0.35), residues: 230 loop : -1.98 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 123 HIS 0.002 0.000 HIS D1006 PHE 0.015 0.001 PHE D 29 TYR 0.021 0.001 TYR K1223 ARG 0.004 0.000 ARG D 501 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 103 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7273 (ttpt) REVERT: D 272 LYS cc_start: 0.8501 (tttp) cc_final: 0.8154 (tppt) REVERT: D 726 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7779 (mmtp) REVERT: D 773 ASP cc_start: 0.8275 (t0) cc_final: 0.7866 (t0) REVERT: D 1011 MET cc_start: 0.8089 (tpp) cc_final: 0.7840 (tpp) REVERT: K 570 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7151 (mm-30) REVERT: K 571 MET cc_start: 0.6976 (ttt) cc_final: 0.6676 (ttp) REVERT: K 656 LEU cc_start: 0.7893 (pp) cc_final: 0.7542 (mp) REVERT: K 1098 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8465 (t80) REVERT: K 1278 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6918 (t80) REVERT: K 1379 MET cc_start: 0.7923 (ptp) cc_final: 0.7616 (ptm) REVERT: K 1399 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.5800 (t80) REVERT: K 1476 MET cc_start: 0.8378 (ttm) cc_final: 0.7769 (tpp) REVERT: K 1494 LEU cc_start: 0.8025 (mp) cc_final: 0.7693 (tt) REVERT: K 1586 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.5911 (mmp80) REVERT: C 312 MET cc_start: 0.4608 (mtt) cc_final: 0.3883 (ttm) outliers start: 55 outliers final: 34 residues processed: 152 average time/residue: 0.3153 time to fit residues: 76.0278 Evaluate side-chains 134 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 94 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 671 ASP Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 987 ASN Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 748 PHE Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1100 ASN Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1233 THR Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1240 HIS Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1422 MET Chi-restraints excluded: chain K residue 1486 TRP Chi-restraints excluded: chain K residue 1586 ARG Chi-restraints excluded: chain K residue 1600 LEU Chi-restraints excluded: chain C residue 181 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 182 optimal weight: 0.4980 chunk 149 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 219 optimal weight: 20.0000 chunk 236 optimal weight: 8.9990 chunk 195 optimal weight: 0.0370 chunk 217 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN D 974 GLN D 987 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 935 ASN ** K1232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20132 Z= 0.249 Angle : 0.613 25.152 27298 Z= 0.293 Chirality : 0.053 1.819 3116 Planarity : 0.004 0.050 3426 Dihedral : 10.192 177.964 3150 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.98 % Favored : 92.90 % Rotamer: Outliers : 3.13 % Allowed : 10.75 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2394 helix: 1.09 (0.16), residues: 1184 sheet: -0.33 (0.35), residues: 228 loop : -2.05 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 187 HIS 0.004 0.001 HIS D1006 PHE 0.024 0.001 PHE D 688 TYR 0.018 0.001 TYR D 514 ARG 0.004 0.000 ARG D 501 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 106 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8358 (tptt) REVERT: D 272 LYS cc_start: 0.8590 (tttp) cc_final: 0.8180 (tppt) REVERT: D 773 ASP cc_start: 0.8324 (t0) cc_final: 0.7828 (t0) REVERT: K 570 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: K 571 MET cc_start: 0.6914 (ttt) cc_final: 0.6624 (ptm) REVERT: K 575 MET cc_start: 0.5894 (mmm) cc_final: 0.5408 (mpp) REVERT: K 656 LEU cc_start: 0.7954 (pp) cc_final: 0.7573 (mp) REVERT: K 1098 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8550 (t80) REVERT: K 1238 MET cc_start: 0.6810 (tmm) cc_final: 0.6219 (ttt) REVERT: K 1278 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.6870 (t80) REVERT: K 1379 MET cc_start: 0.7940 (ptp) cc_final: 0.7630 (ptm) REVERT: K 1399 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.5888 (t80) REVERT: K 1476 MET cc_start: 0.8415 (ttm) cc_final: 0.7825 (tpp) REVERT: K 1494 LEU cc_start: 0.8033 (mp) cc_final: 0.7737 (tt) REVERT: K 1548 MET cc_start: 0.5407 (mpp) cc_final: 0.2950 (ptm) REVERT: K 1586 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.5660 (mmp80) REVERT: C 312 MET cc_start: 0.4650 (mtt) cc_final: 0.3916 (ttm) outliers start: 67 outliers final: 41 residues processed: 166 average time/residue: 0.3039 time to fit residues: 80.7044 Evaluate side-chains 144 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 97 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 987 ASN Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1066 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 258 LEU Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 969 PHE Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1233 THR Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1486 TRP Chi-restraints excluded: chain K residue 1586 ARG Chi-restraints excluded: chain K residue 1600 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 0.0870 chunk 164 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 220 optimal weight: 30.0000 chunk 232 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 428 GLN ** K 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1100 ASN ** K1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 20132 Z= 0.400 Angle : 0.683 26.531 27298 Z= 0.333 Chirality : 0.055 1.774 3116 Planarity : 0.005 0.056 3426 Dihedral : 9.997 177.227 3144 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.81 % Favored : 92.06 % Rotamer: Outliers : 3.46 % Allowed : 11.78 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.18), residues: 2394 helix: 0.98 (0.16), residues: 1174 sheet: -0.64 (0.35), residues: 227 loop : -2.16 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K1501 HIS 0.006 0.001 HIS D1006 PHE 0.019 0.002 PHE D 515 TYR 0.023 0.002 TYR D1070 ARG 0.004 0.001 ARG D 501 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 98 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8378 (tptt) REVERT: D 370 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6488 (mtp180) REVERT: D 603 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8003 (p0) REVERT: D 773 ASP cc_start: 0.8391 (t0) cc_final: 0.7921 (t0) REVERT: D 1073 CYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7188 (p) REVERT: K 570 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7126 (mm-30) REVERT: K 656 LEU cc_start: 0.8075 (pp) cc_final: 0.7653 (mp) REVERT: K 1098 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8530 (t80) REVERT: K 1238 MET cc_start: 0.7018 (tmm) cc_final: 0.6370 (tpp) REVERT: K 1278 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.6830 (t80) REVERT: K 1379 MET cc_start: 0.7925 (ptp) cc_final: 0.7529 (ptm) REVERT: K 1399 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.5960 (t80) REVERT: K 1476 MET cc_start: 0.8436 (ttm) cc_final: 0.7954 (tpp) REVERT: K 1494 LEU cc_start: 0.8083 (mp) cc_final: 0.7808 (tt) REVERT: K 1548 MET cc_start: 0.5387 (mpp) cc_final: 0.2566 (ptm) REVERT: K 1586 ARG cc_start: 0.6066 (OUTLIER) cc_final: 0.5460 (mmp80) REVERT: C 312 MET cc_start: 0.4594 (mtt) cc_final: 0.3907 (ttm) outliers start: 74 outliers final: 51 residues processed: 165 average time/residue: 0.3136 time to fit residues: 82.3014 Evaluate side-chains 152 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 92 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 671 ASP Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 873 ILE Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1066 VAL Chi-restraints excluded: chain D residue 1073 CYS Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 258 LEU Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 396 VAL Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 683 GLN Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 969 PHE Chi-restraints excluded: chain K residue 977 VAL Chi-restraints excluded: chain K residue 1002 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1233 THR Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1240 HIS Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1401 THR Chi-restraints excluded: chain K residue 1486 TRP Chi-restraints excluded: chain K residue 1586 ARG Chi-restraints excluded: chain K residue 1600 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 173 optimal weight: 6.9990 chunk 96 optimal weight: 0.0980 chunk 198 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 209 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 987 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 428 GLN ** K 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 931 HIS K 935 ASN ** K1232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1559 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20132 Z= 0.224 Angle : 0.609 26.739 27298 Z= 0.291 Chirality : 0.052 1.777 3116 Planarity : 0.004 0.055 3426 Dihedral : 9.543 164.095 3143 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.18 % Favored : 92.69 % Rotamer: Outliers : 3.32 % Allowed : 12.66 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.17), residues: 2394 helix: 1.06 (0.16), residues: 1174 sheet: -0.44 (0.35), residues: 218 loop : -2.13 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 187 HIS 0.004 0.001 HIS D1006 PHE 0.020 0.001 PHE K1226 TYR 0.020 0.001 TYR D1070 ARG 0.004 0.000 ARG D 501 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 97 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8382 (tptt) REVERT: D 199 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6562 (mmm-85) REVERT: D 370 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6088 (mtp85) REVERT: D 603 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7915 (p0) REVERT: D 773 ASP cc_start: 0.8319 (t0) cc_final: 0.7890 (t0) REVERT: K 570 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7073 (mm-30) REVERT: K 656 LEU cc_start: 0.8040 (pp) cc_final: 0.7623 (mp) REVERT: K 1098 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8511 (t80) REVERT: K 1225 MET cc_start: 0.8505 (ptp) cc_final: 0.8215 (ptp) REVERT: K 1226 PHE cc_start: 0.8255 (t80) cc_final: 0.8025 (t80) REVERT: K 1238 MET cc_start: 0.6943 (tmm) cc_final: 0.6335 (tpp) REVERT: K 1278 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6835 (t80) REVERT: K 1379 MET cc_start: 0.7911 (ptp) cc_final: 0.7516 (ptm) REVERT: K 1399 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.5938 (t80) REVERT: K 1476 MET cc_start: 0.8487 (ttm) cc_final: 0.8040 (tpp) REVERT: K 1494 LEU cc_start: 0.8124 (mp) cc_final: 0.7844 (tt) REVERT: K 1548 MET cc_start: 0.5418 (mpp) cc_final: 0.2486 (ptm) REVERT: K 1586 ARG cc_start: 0.6039 (OUTLIER) cc_final: 0.5446 (mmp80) REVERT: C 312 MET cc_start: 0.4600 (mtt) cc_final: 0.3912 (ttm) outliers start: 71 outliers final: 50 residues processed: 164 average time/residue: 0.3119 time to fit residues: 82.3981 Evaluate side-chains 152 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 93 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 ARG Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 671 ASP Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 873 ILE Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 987 ASN Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 258 LEU Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 683 GLN Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 969 PHE Chi-restraints excluded: chain K residue 977 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1233 THR Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1240 HIS Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1486 TRP Chi-restraints excluded: chain K residue 1586 ARG Chi-restraints excluded: chain K residue 1600 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 343 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 0.0970 chunk 209 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 136 optimal weight: 0.0010 chunk 57 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 193 optimal weight: 0.1980 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 428 GLN ** K 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20132 Z= 0.128 Angle : 0.568 24.952 27298 Z= 0.269 Chirality : 0.051 1.846 3116 Planarity : 0.004 0.052 3426 Dihedral : 9.110 163.099 3143 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.43 % Favored : 93.44 % Rotamer: Outliers : 2.90 % Allowed : 13.36 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.18), residues: 2394 helix: 1.19 (0.16), residues: 1180 sheet: -0.23 (0.35), residues: 221 loop : -2.04 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 440 HIS 0.004 0.000 HIS D1006 PHE 0.020 0.001 PHE K1161 TYR 0.018 0.001 TYR D1070 ARG 0.007 0.000 ARG D 501 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 100 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8376 (tptt) REVERT: D 199 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6724 (mmm-85) REVERT: D 272 LYS cc_start: 0.8523 (tttp) cc_final: 0.8095 (tppt) REVERT: D 370 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6055 (mtp85) REVERT: D 773 ASP cc_start: 0.8228 (t0) cc_final: 0.7881 (t0) REVERT: K 570 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6986 (mm-30) REVERT: K 571 MET cc_start: 0.6634 (ptm) cc_final: 0.6287 (ptt) REVERT: K 656 LEU cc_start: 0.7988 (pp) cc_final: 0.7584 (mp) REVERT: K 1098 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8500 (t80) REVERT: K 1157 MET cc_start: 0.8966 (mmp) cc_final: 0.8704 (mmp) REVERT: K 1238 MET cc_start: 0.6854 (tmm) cc_final: 0.6264 (tpp) REVERT: K 1278 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6897 (t80) REVERT: K 1379 MET cc_start: 0.7904 (ptp) cc_final: 0.7514 (ptm) REVERT: K 1399 PHE cc_start: 0.6640 (OUTLIER) cc_final: 0.5884 (t80) REVERT: K 1476 MET cc_start: 0.8462 (ttm) cc_final: 0.7840 (tpp) REVERT: K 1494 LEU cc_start: 0.8114 (mp) cc_final: 0.7837 (tt) REVERT: K 1546 MET cc_start: 0.4683 (ppp) cc_final: 0.4330 (ppp) REVERT: K 1548 MET cc_start: 0.5239 (mpp) cc_final: 0.2437 (ptm) REVERT: K 1586 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.5644 (mmp80) REVERT: C 312 MET cc_start: 0.4649 (mtt) cc_final: 0.3902 (ttm) outliers start: 62 outliers final: 44 residues processed: 158 average time/residue: 0.3121 time to fit residues: 77.7868 Evaluate side-chains 147 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 95 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 ARG Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 987 ASN Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 683 GLN Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 969 PHE Chi-restraints excluded: chain K residue 977 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1233 THR Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1240 HIS Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1475 ILE Chi-restraints excluded: chain K residue 1486 TRP Chi-restraints excluded: chain K residue 1586 ARG Chi-restraints excluded: chain K residue 1600 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 343 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 30.0000 chunk 26 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 170 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 130 optimal weight: 0.7980 chunk 232 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 987 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 428 GLN ** K 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20132 Z= 0.173 Angle : 0.590 25.370 27298 Z= 0.278 Chirality : 0.052 1.837 3116 Planarity : 0.004 0.052 3426 Dihedral : 8.993 163.687 3143 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.89 % Favored : 92.98 % Rotamer: Outliers : 2.94 % Allowed : 13.64 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2394 helix: 1.21 (0.16), residues: 1180 sheet: -0.21 (0.35), residues: 218 loop : -2.05 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 440 HIS 0.003 0.000 HIS D1006 PHE 0.016 0.001 PHE K1161 TYR 0.019 0.001 TYR D1070 ARG 0.008 0.000 ARG D 501 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 97 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8349 (tptt) REVERT: D 199 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6647 (mmm-85) REVERT: D 272 LYS cc_start: 0.8563 (tttp) cc_final: 0.8141 (tppt) REVERT: D 370 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6116 (mtp85) REVERT: D 603 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7869 (p0) REVERT: D 773 ASP cc_start: 0.8303 (t0) cc_final: 0.7933 (t0) REVERT: K 570 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6984 (mm-30) REVERT: K 571 MET cc_start: 0.6640 (ptm) cc_final: 0.6356 (ptt) REVERT: K 656 LEU cc_start: 0.8028 (pp) cc_final: 0.7616 (mp) REVERT: K 1098 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8478 (t80) REVERT: K 1223 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.8094 (p90) REVERT: K 1238 MET cc_start: 0.6810 (tmm) cc_final: 0.6246 (tpp) REVERT: K 1278 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.6887 (t80) REVERT: K 1379 MET cc_start: 0.7925 (ptp) cc_final: 0.7536 (ptm) REVERT: K 1399 PHE cc_start: 0.6680 (OUTLIER) cc_final: 0.5897 (t80) REVERT: K 1476 MET cc_start: 0.8483 (ttm) cc_final: 0.7817 (tpp) REVERT: K 1494 LEU cc_start: 0.8082 (mp) cc_final: 0.7816 (tt) REVERT: K 1546 MET cc_start: 0.4694 (ppp) cc_final: 0.4364 (ppp) REVERT: K 1548 MET cc_start: 0.5258 (mpp) cc_final: 0.2376 (ptm) REVERT: K 1586 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5699 (mmp80) REVERT: C 312 MET cc_start: 0.4642 (mtt) cc_final: 0.3909 (ttm) outliers start: 63 outliers final: 46 residues processed: 156 average time/residue: 0.3159 time to fit residues: 77.9915 Evaluate side-chains 153 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 97 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 ARG Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 671 ASP Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 726 LYS Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 873 ILE Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 639 ASN Chi-restraints excluded: chain K residue 683 GLN Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 969 PHE Chi-restraints excluded: chain K residue 977 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1233 THR Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1240 HIS Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1486 TRP Chi-restraints excluded: chain K residue 1586 ARG Chi-restraints excluded: chain K residue 1600 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 343 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 143 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 428 GLN ** K 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20132 Z= 0.218 Angle : 0.606 25.752 27298 Z= 0.286 Chirality : 0.053 1.830 3116 Planarity : 0.004 0.052 3426 Dihedral : 9.002 162.876 3143 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 3.32 % Allowed : 13.60 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2394 helix: 1.18 (0.16), residues: 1179 sheet: -0.27 (0.35), residues: 218 loop : -2.07 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP K 440 HIS 0.003 0.001 HIS D1006 PHE 0.014 0.001 PHE D 515 TYR 0.019 0.001 TYR D1070 ARG 0.006 0.000 ARG D 501 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 96 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8363 (tptt) REVERT: D 199 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6569 (mmm-85) REVERT: D 370 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6105 (mtp85) REVERT: D 603 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7918 (p0) REVERT: D 773 ASP cc_start: 0.8342 (t0) cc_final: 0.7943 (t0) REVERT: K 570 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7033 (mm-30) REVERT: K 571 MET cc_start: 0.6679 (ptm) cc_final: 0.6395 (ptt) REVERT: K 656 LEU cc_start: 0.8050 (pp) cc_final: 0.7630 (mp) REVERT: K 1098 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8476 (t80) REVERT: K 1223 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.8086 (p90) REVERT: K 1238 MET cc_start: 0.6840 (tmm) cc_final: 0.6331 (tpp) REVERT: K 1278 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.6855 (t80) REVERT: K 1379 MET cc_start: 0.7890 (ptp) cc_final: 0.7491 (ptm) REVERT: K 1399 PHE cc_start: 0.6638 (OUTLIER) cc_final: 0.5872 (t80) REVERT: K 1476 MET cc_start: 0.8466 (ttm) cc_final: 0.7949 (tpp) REVERT: K 1479 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.7077 (m-80) REVERT: K 1494 LEU cc_start: 0.8118 (mp) cc_final: 0.7853 (tt) REVERT: K 1546 MET cc_start: 0.4700 (ppp) cc_final: 0.4431 (ppp) REVERT: K 1548 MET cc_start: 0.5237 (mpp) cc_final: 0.2353 (ptm) REVERT: K 1586 ARG cc_start: 0.6250 (OUTLIER) cc_final: 0.5786 (mmp80) REVERT: C 312 MET cc_start: 0.4640 (mtt) cc_final: 0.3908 (ttm) outliers start: 71 outliers final: 51 residues processed: 163 average time/residue: 0.3231 time to fit residues: 83.8298 Evaluate side-chains 159 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 97 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 ARG Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 671 ASP Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 726 LYS Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 873 ILE Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1066 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 683 GLN Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 969 PHE Chi-restraints excluded: chain K residue 977 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1233 THR Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1240 HIS Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1479 PHE Chi-restraints excluded: chain K residue 1486 TRP Chi-restraints excluded: chain K residue 1586 ARG Chi-restraints excluded: chain K residue 1600 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 222 optimal weight: 0.6980 chunk 203 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 130 optimal weight: 0.0980 chunk 94 optimal weight: 0.0570 chunk 169 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20132 Z= 0.157 Angle : 0.585 25.150 27298 Z= 0.273 Chirality : 0.052 1.841 3116 Planarity : 0.004 0.052 3426 Dihedral : 8.744 164.042 3143 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.43 % Favored : 93.44 % Rotamer: Outliers : 2.90 % Allowed : 14.16 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.18), residues: 2394 helix: 1.19 (0.16), residues: 1186 sheet: -0.12 (0.35), residues: 220 loop : -2.01 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP K 440 HIS 0.003 0.000 HIS D1006 PHE 0.022 0.001 PHE K1226 TYR 0.018 0.001 TYR D1070 ARG 0.008 0.000 ARG D 501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 101 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8354 (tptt) REVERT: D 199 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6629 (mmm-85) REVERT: D 272 LYS cc_start: 0.8548 (tttp) cc_final: 0.8120 (tppt) REVERT: D 370 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6080 (mtp85) REVERT: D 603 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7848 (p0) REVERT: D 773 ASP cc_start: 0.8266 (t0) cc_final: 0.7931 (t0) REVERT: K 570 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7003 (mm-30) REVERT: K 571 MET cc_start: 0.6644 (ptm) cc_final: 0.6386 (ptt) REVERT: K 656 LEU cc_start: 0.8031 (pp) cc_final: 0.7615 (mp) REVERT: K 1098 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8425 (t80) REVERT: K 1223 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.8086 (p90) REVERT: K 1238 MET cc_start: 0.6812 (tmm) cc_final: 0.6394 (tpp) REVERT: K 1278 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6911 (t80) REVERT: K 1334 MET cc_start: 0.8931 (mmm) cc_final: 0.8427 (mmm) REVERT: K 1379 MET cc_start: 0.7917 (ptp) cc_final: 0.7529 (ptm) REVERT: K 1399 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.5778 (t80) REVERT: K 1476 MET cc_start: 0.8432 (ttm) cc_final: 0.7856 (tpp) REVERT: K 1479 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: K 1494 LEU cc_start: 0.8164 (mp) cc_final: 0.7899 (tt) REVERT: K 1546 MET cc_start: 0.4666 (ppp) cc_final: 0.4406 (ppp) REVERT: K 1548 MET cc_start: 0.5180 (mpp) cc_final: 0.2291 (ptm) REVERT: K 1586 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.6043 (mmp80) REVERT: C 312 MET cc_start: 0.4608 (mtt) cc_final: 0.3877 (ttm) outliers start: 62 outliers final: 46 residues processed: 160 average time/residue: 0.3131 time to fit residues: 79.6321 Evaluate side-chains 155 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 98 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 ARG Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 671 ASP Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 726 LYS Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 873 ILE Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 683 GLN Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 969 PHE Chi-restraints excluded: chain K residue 977 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1233 THR Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1240 HIS Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1479 PHE Chi-restraints excluded: chain K residue 1486 TRP Chi-restraints excluded: chain K residue 1586 ARG Chi-restraints excluded: chain K residue 1600 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 108 optimal weight: 0.0570 chunk 159 optimal weight: 7.9990 chunk 240 optimal weight: 40.0000 chunk 220 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20132 Z= 0.190 Angle : 0.596 25.490 27298 Z= 0.280 Chirality : 0.052 1.835 3116 Planarity : 0.004 0.052 3426 Dihedral : 8.721 163.417 3143 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.93 % Favored : 92.94 % Rotamer: Outliers : 2.80 % Allowed : 14.44 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2394 helix: 1.18 (0.16), residues: 1185 sheet: -0.17 (0.35), residues: 218 loop : -2.00 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP K 440 HIS 0.003 0.000 HIS D1006 PHE 0.018 0.001 PHE K 395 TYR 0.020 0.001 TYR D1070 ARG 0.008 0.000 ARG D 501 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 100 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8352 (tptt) REVERT: D 199 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6580 (mmm-85) REVERT: D 272 LYS cc_start: 0.8580 (tttp) cc_final: 0.8152 (tppt) REVERT: D 370 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6131 (mtp85) REVERT: D 603 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7872 (p0) REVERT: D 773 ASP cc_start: 0.8302 (t0) cc_final: 0.7943 (t0) REVERT: D 1031 ARG cc_start: 0.6061 (ptm-80) cc_final: 0.5801 (ptm-80) REVERT: K 570 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: K 656 LEU cc_start: 0.8046 (pp) cc_final: 0.7622 (mp) REVERT: K 1098 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8375 (t80) REVERT: K 1223 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.8133 (p90) REVERT: K 1238 MET cc_start: 0.6806 (tmm) cc_final: 0.6419 (tpp) REVERT: K 1278 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.6871 (t80) REVERT: K 1379 MET cc_start: 0.7901 (ptp) cc_final: 0.7501 (ptm) REVERT: K 1399 PHE cc_start: 0.6677 (OUTLIER) cc_final: 0.5891 (t80) REVERT: K 1476 MET cc_start: 0.8424 (ttm) cc_final: 0.7817 (tpp) REVERT: K 1479 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7006 (m-80) REVERT: K 1494 LEU cc_start: 0.8159 (mp) cc_final: 0.7891 (tt) REVERT: K 1546 MET cc_start: 0.4663 (ppp) cc_final: 0.4432 (ppp) REVERT: K 1548 MET cc_start: 0.5163 (mpp) cc_final: 0.2279 (ptm) REVERT: K 1586 ARG cc_start: 0.6408 (OUTLIER) cc_final: 0.6192 (mmp80) REVERT: C 312 MET cc_start: 0.4604 (mtt) cc_final: 0.3876 (ttm) outliers start: 60 outliers final: 46 residues processed: 156 average time/residue: 0.3274 time to fit residues: 81.4885 Evaluate side-chains 154 residues out of total 2141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 97 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 ARG Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 671 ASP Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 726 LYS Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 873 ILE Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 987 ASN Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 969 PHE Chi-restraints excluded: chain K residue 977 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1233 THR Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1240 HIS Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1479 PHE Chi-restraints excluded: chain K residue 1486 TRP Chi-restraints excluded: chain K residue 1586 ARG Chi-restraints excluded: chain K residue 1600 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.161976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.102871 restraints weight = 37160.673| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.29 r_work: 0.3196 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20132 Z= 0.166 Angle : 0.592 25.236 27298 Z= 0.277 Chirality : 0.052 1.842 3116 Planarity : 0.004 0.052 3426 Dihedral : 8.622 163.738 3143 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.68 % Favored : 93.19 % Rotamer: Outliers : 2.85 % Allowed : 14.39 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2394 helix: 1.20 (0.16), residues: 1181 sheet: -0.12 (0.35), residues: 218 loop : -1.97 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP K 440 HIS 0.003 0.000 HIS D1006 PHE 0.038 0.001 PHE K1226 TYR 0.019 0.001 TYR D1070 ARG 0.008 0.000 ARG D 501 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4992.48 seconds wall clock time: 91 minutes 14.32 seconds (5474.32 seconds total)