Starting phenix.real_space_refine on Tue Mar 19 12:39:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9j_15284/03_2024/8a9j_15284_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9j_15284/03_2024/8a9j_15284.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9j_15284/03_2024/8a9j_15284_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9j_15284/03_2024/8a9j_15284_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9j_15284/03_2024/8a9j_15284_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9j_15284/03_2024/8a9j_15284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9j_15284/03_2024/8a9j_15284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9j_15284/03_2024/8a9j_15284_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9j_15284/03_2024/8a9j_15284_updated.pdb" } resolution = 2.8 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= 0.000 sd= 0.131 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 58 5.49 5 S 136 5.16 5 C 15412 2.51 5 N 3972 2.21 5 O 4654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24233 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 999, 7966 Classifications: {'peptide': 999} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 966} Chain breaks: 12 Conformer: "B" Number of residues, atoms: 999, 7966 Classifications: {'peptide': 999} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 966} Chain breaks: 12 bond proxies already assigned to first conformer: 8085 Chain: "B" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7705 Classifications: {'peptide': 960} Link IDs: {'PTRANS': 32, 'TRANS': 927} Chain breaks: 10 Chain: "C" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 607 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2655 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 316} Chain breaks: 5 Chain: "E" Number of atoms: 4655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4655 Classifications: {'peptide': 586} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 564} Chain breaks: 5 Chain: "S" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 319 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 87 Chain: "T" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 319 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 87 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17470 SG CYS D 440 54.235 95.774 37.097 1.00 17.92 S ATOM 17493 SG CYS D 443 55.880 96.401 33.827 1.00 17.92 S ATOM 17868 SG CYS D 506 57.931 95.306 36.386 1.00 17.92 S ATOM 17891 SG CYS D 509 56.789 98.908 36.305 1.00 17.92 S Time building chain proxies: 15.26, per 1000 atoms: 0.63 Number of scatterers: 24233 At special positions: 0 Unit cell: (119.78, 167.48, 164.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 136 16.00 P 58 15.00 O 4654 8.00 N 3972 7.00 C 15412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 469 " distance=2.04 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 Time building additional restraints: 9.56 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 443 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 506 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 509 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 440 " Number of angles added : 6 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5686 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 18 sheets defined 54.3% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.76 Creating SS restraints... Processing helix chain 'A' and resid 189 through 203 removed outlier: 4.065A pdb=" N SER A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 223 Proline residue: A 211 - end of helix removed outlier: 3.825A pdb=" N SER A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 248 Processing helix chain 'A' and resid 261 through 282 removed outlier: 3.686A pdb=" N LEU A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 307 through 318 removed outlier: 4.304A pdb=" N ARG A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 345 removed outlier: 4.939A pdb=" N ASP A 324 " --> pdb=" O ARG A 321 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 325 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 326 " --> pdb=" O GLN A 323 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 327 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 328 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 334 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 336 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 345 " --> pdb=" O GLN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.670A pdb=" N LEU A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 353' Processing helix chain 'A' and resid 360 through 372 removed outlier: 3.965A pdb=" N VAL A 372 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 392 removed outlier: 4.610A pdb=" N GLN A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLY A 381 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 432 Proline residue: A 414 - end of helix Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 457 through 466 Processing helix chain 'A' and resid 470 through 476 removed outlier: 4.471A pdb=" N SER A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 487 removed outlier: 3.549A pdb=" N TYR A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 502 Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.851A pdb=" N VAL A 509 " --> pdb=" O PRO A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 526 removed outlier: 3.554A pdb=" N LYS A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 544 Processing helix chain 'A' and resid 577 through 596 removed outlier: 3.792A pdb=" N CYS A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 615 removed outlier: 4.368A pdb=" N TYR A 610 " --> pdb=" O TYR A 606 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 632 Processing helix chain 'A' and resid 647 through 650 removed outlier: 3.504A pdb=" N CYS A 650 " --> pdb=" O LEU A 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 664 through 681 Processing helix chain 'A' and resid 699 through 715 removed outlier: 3.845A pdb=" N ASP A 704 " --> pdb=" O GLU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 759 removed outlier: 3.843A pdb=" N SER A 759 " --> pdb=" O GLU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 788 Processing helix chain 'A' and resid 807 through 819 Processing helix chain 'A' and resid 823 through 834 removed outlier: 3.864A pdb=" N GLU A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 856 Processing helix chain 'A' and resid 867 through 887 Processing helix chain 'A' and resid 904 through 922 Processing helix chain 'A' and resid 927 through 932 Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.503A pdb=" N SER A 965 " --> pdb=" O GLN A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 994 Processing helix chain 'A' and resid 1001 through 1016 Processing helix chain 'A' and resid 1022 through 1037 Processing helix chain 'A' and resid 1043 through 1057 Processing helix chain 'A' and resid 1084 through 1109 Processing helix chain 'A' and resid 1127 through 1150 removed outlier: 3.691A pdb=" N THR A1143 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1183 Processing helix chain 'A' and resid 1192 through 1204 Processing helix chain 'A' and resid 1206 through 1218 Processing helix chain 'A' and resid 1237 through 1246 Processing helix chain 'A' and resid 1248 through 1270 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 277 through 287 removed outlier: 3.693A pdb=" N HIS B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.694A pdb=" N ILE B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 344 " --> pdb=" O GLN B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 removed outlier: 3.608A pdb=" N ILE B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 391 removed outlier: 3.531A pdb=" N TYR B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 408 removed outlier: 3.644A pdb=" N LYS B 396 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS B 397 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 398 " --> pdb=" O THR B 395 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B 399 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 401 " --> pdb=" O TYR B 398 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 402 " --> pdb=" O ILE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 423 Processing helix chain 'B' and resid 425 through 444 removed outlier: 4.263A pdb=" N ASP B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N MET B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N SER B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER B 434 " --> pdb=" O ASP B 430 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 Processing helix chain 'B' and resid 467 through 481 Processing helix chain 'B' and resid 486 through 502 Processing helix chain 'B' and resid 504 through 520 removed outlier: 3.879A pdb=" N MET B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 511 " --> pdb=" O MET B 507 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE B 513 " --> pdb=" O MET B 509 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP B 519 " --> pdb=" O LYS B 515 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 540 Processing helix chain 'B' and resid 546 through 563 Processing helix chain 'B' and resid 568 through 585 removed outlier: 3.528A pdb=" N ILE B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 625 through 641 Processing helix chain 'B' and resid 646 through 663 Processing helix chain 'B' and resid 699 through 705 Processing helix chain 'B' and resid 727 through 745 removed outlier: 4.992A pdb=" N ALA B 731 " --> pdb=" O LEU B 728 " (cutoff:3.500A) Proline residue: B 732 - end of helix removed outlier: 3.596A pdb=" N ARG B 735 " --> pdb=" O PRO B 732 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 739 " --> pdb=" O LEU B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 757 removed outlier: 5.029A pdb=" N GLY B 754 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP B 757 " --> pdb=" O GLY B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 799 Processing helix chain 'B' and resid 806 through 831 removed outlier: 3.561A pdb=" N VAL B 812 " --> pdb=" O MET B 808 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 828 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 829 " --> pdb=" O ILE B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 924 No H-bonds generated for 'chain 'B' and resid 921 through 924' Processing helix chain 'B' and resid 930 through 937 removed outlier: 3.596A pdb=" N PHE B 933 " --> pdb=" O ILE B 930 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS B 937 " --> pdb=" O SER B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 979 removed outlier: 3.517A pdb=" N MET B 979 " --> pdb=" O LYS B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1005 No H-bonds generated for 'chain 'B' and resid 1002 through 1005' Processing helix chain 'B' and resid 1009 through 1038 removed outlier: 3.716A pdb=" N LEU B1019 " --> pdb=" O CYS B1015 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR B1021 " --> pdb=" O PHE B1017 " (cutoff:3.500A) Proline residue: B1022 - end of helix removed outlier: 3.525A pdb=" N CYS B1036 " --> pdb=" O ASN B1032 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B1037 " --> pdb=" O TYR B1033 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA B1038 " --> pdb=" O PHE B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1073 Processing helix chain 'B' and resid 1076 through 1079 Processing helix chain 'B' and resid 1084 through 1097 removed outlier: 3.598A pdb=" N LEU B1094 " --> pdb=" O ALA B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1107 through 1122 removed outlier: 3.506A pdb=" N ASN B1120 " --> pdb=" O HIS B1116 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE B1121 " --> pdb=" O TYR B1117 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N HIS B1122 " --> pdb=" O LEU B1118 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1144 removed outlier: 4.047A pdb=" N LYS B1144 " --> pdb=" O VAL B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1164 Processing helix chain 'B' and resid 1179 through 1192 Processing helix chain 'B' and resid 1196 through 1205 Processing helix chain 'B' and resid 1207 through 1213 Processing helix chain 'B' and resid 1231 through 1248 removed outlier: 3.668A pdb=" N LYS B1248 " --> pdb=" O LYS B1244 " (cutoff:3.500A) Processing helix chain 'B' and resid 1258 through 1282 removed outlier: 4.379A pdb=" N ILE B1282 " --> pdb=" O LEU B1278 " (cutoff:3.500A) Processing helix chain 'B' and resid 1288 through 1308 removed outlier: 3.703A pdb=" N ARG B1299 " --> pdb=" O LEU B1295 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B1300 " --> pdb=" O LYS B1296 " (cutoff:3.500A) Processing helix chain 'B' and resid 1310 through 1315 Processing helix chain 'B' and resid 1322 through 1348 removed outlier: 3.593A pdb=" N ASP B1334 " --> pdb=" O THR B1330 " (cutoff:3.500A) Processing helix chain 'B' and resid 1351 through 1354 No H-bonds generated for 'chain 'B' and resid 1351 through 1354' Processing helix chain 'B' and resid 1357 through 1377 Processing helix chain 'B' and resid 1381 through 1383 No H-bonds generated for 'chain 'B' and resid 1381 through 1383' Processing helix chain 'C' and resid 23 through 34 Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.528A pdb=" N ILE D 95 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 121 Processing helix chain 'D' and resid 144 through 165 Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'D' and resid 179 through 188 Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing helix chain 'D' and resid 200 through 221 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 485 through 493 Processing helix chain 'D' and resid 500 through 502 No H-bonds generated for 'chain 'D' and resid 500 through 502' Processing helix chain 'D' and resid 565 through 567 No H-bonds generated for 'chain 'D' and resid 565 through 567' Processing helix chain 'D' and resid 739 through 743 removed outlier: 3.690A pdb=" N GLU D 742 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 767 Processing helix chain 'E' and resid 146 through 150 Processing helix chain 'E' and resid 403 through 410 Processing helix chain 'E' and resid 462 through 470 Processing helix chain 'E' and resid 475 through 477 No H-bonds generated for 'chain 'E' and resid 475 through 477' Processing helix chain 'E' and resid 530 through 534 removed outlier: 3.681A pdb=" N SER E 533 " --> pdb=" O CYS E 530 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY E 534 " --> pdb=" O ARG E 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 530 through 534' Processing helix chain 'E' and resid 536 through 545 removed outlier: 3.774A pdb=" N GLU E 544 " --> pdb=" O MET E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 554 removed outlier: 4.303A pdb=" N ILE E 553 " --> pdb=" O TRP E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 603 Processing helix chain 'E' and resid 635 through 638 No H-bonds generated for 'chain 'E' and resid 635 through 638' Processing helix chain 'E' and resid 654 through 659 Processing sheet with id= A, first strand: chain 'B' and resid 665 through 667 Processing sheet with id= B, first strand: chain 'B' and resid 680 through 683 Processing sheet with id= C, first strand: chain 'C' and resid 12 through 17 Processing sheet with id= D, first strand: chain 'D' and resid 446 through 453 removed outlier: 6.360A pdb=" N VAL D 435 " --> pdb=" O PHE D 521 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE D 521 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG D 437 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU D 519 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ARG D 439 " --> pdb=" O ARG D 517 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG D 517 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 455 through 459 removed outlier: 7.965A pdb=" N ILE D 456 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR D 529 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL D 458 " --> pdb=" O THR D 529 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N HIS D 531 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 580 " --> pdb=" O PHE D 781 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LYS D 783 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LEU D 578 " --> pdb=" O LYS D 783 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE D 579 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 749 " --> pdb=" O LYS D 756 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 504 through 506 Processing sheet with id= G, first strand: chain 'D' and resid 583 through 585 Processing sheet with id= H, first strand: chain 'E' and resid 421 through 423 removed outlier: 4.071A pdb=" N LEU E 429 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU E 519 " --> pdb=" O THR E 524 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR E 524 " --> pdb=" O GLU E 519 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 33 through 39 removed outlier: 6.639A pdb=" N ALA E 48 " --> pdb=" O ASN E 34 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU E 36 " --> pdb=" O PHE E 46 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE E 46 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU E 38 " --> pdb=" O ARG E 44 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG E 44 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA E 69 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N SER E 58 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR E 67 " --> pdb=" O SER E 58 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 78 through 84 removed outlier: 6.614A pdb=" N ALA E 93 " --> pdb=" O ASN E 79 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE E 81 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE E 91 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU E 83 " --> pdb=" O THR E 89 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR E 89 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN E 103 " --> pdb=" O CYS E 109 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N CYS E 109 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 162 through 164 removed outlier: 4.195A pdb=" N SER E 162 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE E 141 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 171 through 176 removed outlier: 6.731A pdb=" N GLY E 186 " --> pdb=" O TYR E 172 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU E 174 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL E 184 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER E 187 " --> pdb=" O VAL E 191 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL E 191 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET E 204 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASP E 196 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS E 202 " --> pdb=" O ASP E 196 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 213 through 218 removed outlier: 6.854A pdb=" N GLY E 228 " --> pdb=" O LYS E 214 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU E 216 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU E 226 " --> pdb=" O LEU E 216 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU E 218 " --> pdb=" O GLN E 224 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLN E 224 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER E 238 " --> pdb=" O CYS E 244 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N CYS E 244 " --> pdb=" O SER E 238 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 255 through 260 removed outlier: 6.729A pdb=" N GLY E 270 " --> pdb=" O TRP E 256 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU E 258 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR E 268 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL E 260 " --> pdb=" O HIS E 266 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N HIS E 266 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY E 271 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS E 291 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N CYS E 278 " --> pdb=" O LEU E 289 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU E 289 " --> pdb=" O CYS E 278 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASP E 280 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG E 287 " --> pdb=" O ASP E 280 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 355 through 357 removed outlier: 3.514A pdb=" N ASN E 322 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 363 through 368 removed outlier: 6.702A pdb=" N LYS E 378 " --> pdb=" O ILE E 364 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N CYS E 366 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU E 376 " --> pdb=" O CYS E 366 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE E 368 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS E 374 " --> pdb=" O ILE E 368 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP E 388 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYS E 394 " --> pdb=" O ASP E 388 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 442 through 444 Processing sheet with id= R, first strand: chain 'E' and resid 584 through 588 removed outlier: 6.846A pdb=" N LEU E 668 " --> pdb=" O TYR E 568 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLN E 570 " --> pdb=" O LEU E 668 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU E 670 " --> pdb=" O GLN E 570 " (cutoff:3.500A) 1207 hydrogen bonds defined for protein. 3440 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: 9.27 Time building geometry restraints manager: 10.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7591 1.34 - 1.46: 5492 1.46 - 1.58: 11312 1.58 - 1.70: 114 1.70 - 1.82: 201 Bond restraints: 24710 Sorted by residual: bond pdb=" C3' DN S 7 " pdb=" C4' DN S 7 " ideal model delta sigma weight residual 1.270 1.539 -0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C3' DN T 46 " pdb=" C4' DN T 46 " ideal model delta sigma weight residual 1.270 1.537 -0.267 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C3' DN T 58 " pdb=" C4' DN T 58 " ideal model delta sigma weight residual 1.270 1.537 -0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C3' DN S 1 " pdb=" C4' DN S 1 " ideal model delta sigma weight residual 1.270 1.537 -0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C3' DN S 23 " pdb=" C4' DN S 23 " ideal model delta sigma weight residual 1.270 1.536 -0.266 2.00e-02 2.50e+03 1.77e+02 ... (remaining 24705 not shown) Histogram of bond angle deviations from ideal: 97.52 - 104.83: 527 104.83 - 112.13: 13143 112.13 - 119.43: 7937 119.43 - 126.74: 11602 126.74 - 134.04: 285 Bond angle restraints: 33494 Sorted by residual: angle pdb=" C2' DN S 7 " pdb=" C3' DN S 7 " pdb=" O3' DN S 7 " ideal model delta sigma weight residual 110.08 121.89 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" N VAL B 832 " pdb=" CA VAL B 832 " pdb=" C VAL B 832 " ideal model delta sigma weight residual 112.80 108.51 4.29 1.15e+00 7.56e-01 1.39e+01 angle pdb=" OP1 DN T 35 " pdb=" P DN T 35 " pdb=" OP2 DN T 35 " ideal model delta sigma weight residual 109.59 120.26 -10.67 3.00e+00 1.11e-01 1.26e+01 angle pdb=" OP1 DN T 58 " pdb=" P DN T 58 " pdb=" OP2 DN T 58 " ideal model delta sigma weight residual 109.59 119.94 -10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" OP1 DN T 50 " pdb=" P DN T 50 " pdb=" OP2 DN T 50 " ideal model delta sigma weight residual 109.59 119.89 -10.30 3.00e+00 1.11e-01 1.18e+01 ... (remaining 33489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 13425 17.78 - 35.55: 1222 35.55 - 53.33: 399 53.33 - 71.11: 91 71.11 - 88.88: 21 Dihedral angle restraints: 15158 sinusoidal: 6475 harmonic: 8683 Sorted by residual: dihedral pdb=" CA ILE B 945 " pdb=" C ILE B 945 " pdb=" N LEU B 946 " pdb=" CA LEU B 946 " ideal model delta harmonic sigma weight residual 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CG ARG D 437 " pdb=" CD ARG D 437 " pdb=" NE ARG D 437 " pdb=" CZ ARG D 437 " ideal model delta sinusoidal sigma weight residual 90.00 134.98 -44.98 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CB GLU A1195 " pdb=" CG GLU A1195 " pdb=" CD GLU A1195 " pdb=" OE1 GLU A1195 " ideal model delta sinusoidal sigma weight residual 0.00 -88.88 88.88 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 15155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3735 0.098 - 0.195: 142 0.195 - 0.293: 17 0.293 - 0.390: 27 0.390 - 0.488: 9 Chirality restraints: 3930 Sorted by residual: chirality pdb=" C3' DN S 27 " pdb=" C2' DN S 27 " pdb=" C4' DN S 27 " pdb=" O3' DN S 27 " both_signs ideal model delta sigma weight residual False -2.33 -2.82 0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" C3' DN T 43 " pdb=" C2' DN T 43 " pdb=" C4' DN T 43 " pdb=" O3' DN T 43 " both_signs ideal model delta sigma weight residual False -2.33 -2.81 0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" C3' DN S 26 " pdb=" C2' DN S 26 " pdb=" C4' DN S 26 " pdb=" O3' DN S 26 " both_signs ideal model delta sigma weight residual False -2.33 -2.78 0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 3927 not shown) Planarity restraints: 4066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 833 " 0.061 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO B 834 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO B 834 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 834 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 306 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 307 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 638 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 639 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 639 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 639 " -0.021 5.00e-02 4.00e+02 ... (remaining 4063 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 1 2.02 - 2.74: 1646 2.74 - 3.46: 34790 3.46 - 4.18: 57863 4.18 - 4.90: 104545 Nonbonded interactions: 198845 Sorted by model distance: nonbonded pdb=" NZ LYS B 561 " pdb=" C GLY C 76 " model vdw 1.301 3.350 nonbonded pdb=" NH2 ARG A 321 " pdb=" OE2 GLU B 488 " model vdw 2.172 2.520 nonbonded pdb=" NZ LYS B 561 " pdb=" O GLY C 76 " model vdw 2.194 2.520 nonbonded pdb=" O PHE A1287 " pdb=" NE2 GLN B1332 " model vdw 2.202 2.520 nonbonded pdb=" CE LYS B 561 " pdb=" C GLY C 76 " model vdw 2.217 3.670 ... (remaining 198840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.510 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: 8.600 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 74.680 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.018 0.269 24710 Z= 1.163 Angle : 0.781 11.806 33494 Z= 0.343 Chirality : 0.055 0.488 3930 Planarity : 0.004 0.092 4066 Dihedral : 15.877 88.882 9469 Min Nonbonded Distance : 1.301 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.07 % Allowed : 0.30 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 2879 helix: 0.91 (0.12), residues: 1628 sheet: 0.82 (0.30), residues: 286 loop : -0.28 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 567 HIS 0.007 0.001 HIS B 641 PHE 0.022 0.001 PHE D 535 TYR 0.019 0.001 TYR A 283 ARG 0.008 0.001 ARG B 779 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 3.007 Fit side-chains REVERT: B 486 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6671 (tp30) REVERT: B 509 MET cc_start: 0.7502 (ptm) cc_final: 0.7270 (ptt) REVERT: D 166 ASN cc_start: 0.7161 (m110) cc_final: 0.6456 (p0) REVERT: D 423 PHE cc_start: 0.7636 (m-80) cc_final: 0.7207 (m-80) REVERT: E 14 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7876 (pttt) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 1.1939 time to fit residues: 473.5955 Evaluate side-chains 267 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 139 optimal weight: 0.0270 chunk 170 optimal weight: 1.9990 chunk 266 optimal weight: 4.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1076 ASN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN B 418 GLN B 654 HIS B 706 GLN B 818 HIS B1005 GLN C 25 ASN C 60 ASN E 330 HIS E 563 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24710 Z= 0.320 Angle : 0.649 10.500 33494 Z= 0.316 Chirality : 0.044 0.172 3930 Planarity : 0.005 0.057 4066 Dihedral : 10.462 66.857 3630 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.48 % Allowed : 7.59 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.15), residues: 2879 helix: 1.49 (0.12), residues: 1640 sheet: 0.63 (0.29), residues: 294 loop : -0.34 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 195 HIS 0.009 0.001 HIS B 654 PHE 0.023 0.002 PHE B 635 TYR 0.019 0.002 TYR B1062 ARG 0.010 0.001 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 279 time to evaluate : 2.859 Fit side-chains REVERT: A 475 GLN cc_start: 0.7616 (tt0) cc_final: 0.7367 (tt0) REVERT: B 502 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8172 (tp) REVERT: B 1018 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7720 (mp10) REVERT: B 1244 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8184 (mtmm) REVERT: C 39 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7892 (p0) REVERT: E 14 LYS cc_start: 0.8277 (mtmm) cc_final: 0.7869 (pttt) REVERT: E 165 SER cc_start: 0.8669 (p) cc_final: 0.8422 (m) REVERT: E 423 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6931 (p0) outliers start: 38 outliers final: 12 residues processed: 295 average time/residue: 1.2450 time to fit residues: 428.6470 Evaluate side-chains 267 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 250 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 758 CYS Chi-restraints excluded: chain B residue 1018 GLN Chi-restraints excluded: chain B residue 1244 LYS Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 421 SER Chi-restraints excluded: chain E residue 423 ASP Chi-restraints excluded: chain E residue 590 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 147 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 221 optimal weight: 0.4980 chunk 181 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 266 optimal weight: 5.9990 chunk 287 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS A 618 GLN A 968 ASN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 HIS B 706 GLN B1005 GLN C 60 ASN E 461 ASN E 563 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24710 Z= 0.196 Angle : 0.548 9.381 33494 Z= 0.268 Chirality : 0.040 0.151 3930 Planarity : 0.004 0.045 4066 Dihedral : 10.334 61.368 3630 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.41 % Allowed : 9.96 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.16), residues: 2879 helix: 1.81 (0.13), residues: 1646 sheet: 0.68 (0.29), residues: 298 loop : -0.27 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 102 HIS 0.009 0.001 HIS B 654 PHE 0.014 0.001 PHE A 237 TYR 0.012 0.001 TYR A 283 ARG 0.008 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 280 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 GLN cc_start: 0.7613 (tt0) cc_final: 0.7391 (tt0) REVERT: A 586 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7558 (tm-30) REVERT: B 502 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8179 (tp) REVERT: C 39 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7781 (p0) REVERT: D 159 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8080 (mp) REVERT: D 423 PHE cc_start: 0.7759 (m-80) cc_final: 0.7290 (m-80) REVERT: D 424 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6099 (mt-10) REVERT: D 761 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7375 (ptpp) REVERT: E 14 LYS cc_start: 0.8264 (mtmm) cc_final: 0.7853 (pttt) REVERT: E 165 SER cc_start: 0.8669 (p) cc_final: 0.8441 (m) REVERT: E 423 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.6886 (p0) outliers start: 36 outliers final: 14 residues processed: 297 average time/residue: 1.2005 time to fit residues: 418.2823 Evaluate side-chains 281 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 261 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 618 GLN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 GLN Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 424 GLU Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 761 LYS Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 421 SER Chi-restraints excluded: chain E residue 423 ASP Chi-restraints excluded: chain E residue 590 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 263 optimal weight: 0.8980 chunk 200 optimal weight: 0.5980 chunk 138 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 267 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 chunk 253 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A 618 GLN A 968 ASN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 HIS B1005 GLN C 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24710 Z= 0.166 Angle : 0.526 7.786 33494 Z= 0.255 Chirality : 0.039 0.146 3930 Planarity : 0.004 0.040 4066 Dihedral : 10.110 59.772 3630 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.59 % Allowed : 10.78 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.16), residues: 2879 helix: 1.97 (0.13), residues: 1644 sheet: 0.58 (0.29), residues: 307 loop : -0.23 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 102 HIS 0.009 0.001 HIS B 654 PHE 0.013 0.001 PHE A 237 TYR 0.011 0.001 TYR B1088 ARG 0.009 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 277 time to evaluate : 2.928 Fit side-chains REVERT: A 475 GLN cc_start: 0.7600 (tt0) cc_final: 0.7389 (tm-30) REVERT: A 586 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 618 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.7108 (pt0) REVERT: B 765 LEU cc_start: 0.5679 (OUTLIER) cc_final: 0.5332 (pp) REVERT: B 1018 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7736 (mm-40) REVERT: C 34 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7558 (mm-30) REVERT: C 39 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7795 (p0) REVERT: D 159 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8102 (mp) REVERT: D 423 PHE cc_start: 0.7688 (m-80) cc_final: 0.7238 (m-80) REVERT: D 424 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6199 (mt-10) REVERT: E 14 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7861 (pttt) REVERT: E 165 SER cc_start: 0.8636 (p) cc_final: 0.8435 (m) REVERT: E 220 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7544 (ttt90) REVERT: E 423 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.6865 (p0) outliers start: 41 outliers final: 13 residues processed: 295 average time/residue: 1.2026 time to fit residues: 415.3193 Evaluate side-chains 279 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 258 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 618 GLN Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 1018 GLN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 424 GLU Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 421 SER Chi-restraints excluded: chain E residue 423 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 235 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 254 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 GLN A 968 ASN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24710 Z= 0.210 Angle : 0.541 8.339 33494 Z= 0.263 Chirality : 0.040 0.152 3930 Planarity : 0.004 0.039 4066 Dihedral : 10.001 59.557 3630 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.56 % Allowed : 11.56 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.16), residues: 2879 helix: 2.00 (0.13), residues: 1645 sheet: 0.59 (0.29), residues: 305 loop : -0.19 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 195 HIS 0.020 0.001 HIS B 654 PHE 0.014 0.001 PHE A 237 TYR 0.010 0.001 TYR B1297 ARG 0.006 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 274 time to evaluate : 3.114 Fit side-chains revert: symmetry clash REVERT: A 475 GLN cc_start: 0.7627 (tt0) cc_final: 0.7414 (tm-30) REVERT: A 586 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7541 (tm-30) REVERT: B 765 LEU cc_start: 0.5710 (OUTLIER) cc_final: 0.5362 (pp) REVERT: B 1018 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7761 (mm-40) REVERT: C 39 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7807 (p0) REVERT: D 159 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8062 (mp) REVERT: D 166 ASN cc_start: 0.6997 (m-40) cc_final: 0.6742 (m110) REVERT: D 423 PHE cc_start: 0.7655 (m-80) cc_final: 0.7258 (m-80) REVERT: D 761 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7392 (ptpp) REVERT: E 14 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7865 (pttt) REVERT: E 220 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7537 (ttt90) REVERT: E 423 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.6900 (p0) outliers start: 40 outliers final: 13 residues processed: 289 average time/residue: 1.1793 time to fit residues: 397.9334 Evaluate side-chains 279 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 259 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 GLN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 761 LYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 421 SER Chi-restraints excluded: chain E residue 423 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 95 optimal weight: 1.9990 chunk 255 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A 618 GLN A 968 ASN A1127 ASN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24710 Z= 0.205 Angle : 0.540 8.690 33494 Z= 0.262 Chirality : 0.040 0.151 3930 Planarity : 0.004 0.039 4066 Dihedral : 9.858 59.793 3630 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.00 % Allowed : 11.74 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.16), residues: 2879 helix: 2.02 (0.13), residues: 1646 sheet: 0.46 (0.29), residues: 313 loop : -0.22 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 195 HIS 0.005 0.001 HIS A 458 PHE 0.014 0.001 PHE A 237 TYR 0.012 0.001 TYR B 468 ARG 0.011 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 267 time to evaluate : 2.840 Fit side-chains revert: symmetry clash REVERT: A 475 GLN cc_start: 0.7657 (tt0) cc_final: 0.7427 (tm-30) REVERT: A 586 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7531 (tm-30) REVERT: A 618 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6975 (pt0) REVERT: B 765 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5471 (pp) REVERT: B 1006 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6912 (mt0) REVERT: B 1244 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8075 (mtmm) REVERT: C 34 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7611 (mm-30) REVERT: C 39 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7799 (p0) REVERT: D 159 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8037 (mp) REVERT: D 166 ASN cc_start: 0.6920 (m110) cc_final: 0.6712 (m110) REVERT: D 423 PHE cc_start: 0.7645 (m-80) cc_final: 0.7235 (m-80) REVERT: E 14 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7868 (pttt) REVERT: E 220 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7604 (ttt90) REVERT: E 423 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.6897 (p0) REVERT: E 563 ASN cc_start: 0.6708 (m-40) cc_final: 0.6459 (t160) outliers start: 52 outliers final: 17 residues processed: 291 average time/residue: 1.2105 time to fit residues: 411.5642 Evaluate side-chains 279 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 254 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 618 GLN Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 1006 GLN Chi-restraints excluded: chain B residue 1244 LYS Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 421 SER Chi-restraints excluded: chain E residue 423 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 273 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 238 optimal weight: 4.9990 chunk 158 optimal weight: 0.3980 chunk 282 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 130 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 GLN A 757 ASN A 968 ASN A1109 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 60 ASN D 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24710 Z= 0.143 Angle : 0.513 8.912 33494 Z= 0.249 Chirality : 0.039 0.140 3930 Planarity : 0.004 0.045 4066 Dihedral : 9.720 59.703 3630 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.33 % Allowed : 12.70 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.16), residues: 2879 helix: 2.18 (0.13), residues: 1643 sheet: 0.69 (0.30), residues: 291 loop : -0.25 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 102 HIS 0.004 0.001 HIS B1344 PHE 0.014 0.001 PHE B 678 TYR 0.010 0.001 TYR D 143 ARG 0.011 0.000 ARG A 840 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 280 time to evaluate : 2.902 Fit side-chains revert: symmetry clash REVERT: A 475 GLN cc_start: 0.7640 (tt0) cc_final: 0.7404 (tm-30) REVERT: A 586 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7500 (tm-30) REVERT: A 618 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.7053 (pt0) REVERT: A 840 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7660 (mtt-85) REVERT: B 765 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5409 (pp) REVERT: B 1006 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6799 (mt0) REVERT: C 34 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7584 (mm-30) REVERT: C 39 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7856 (p0) REVERT: D 159 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8153 (mp) REVERT: D 166 ASN cc_start: 0.6866 (m110) cc_final: 0.6661 (m110) REVERT: D 423 PHE cc_start: 0.7633 (m-80) cc_final: 0.7324 (m-80) REVERT: E 14 LYS cc_start: 0.8236 (mtmm) cc_final: 0.7837 (pttt) REVERT: E 220 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7572 (ttt90) REVERT: E 423 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6831 (p0) REVERT: E 563 ASN cc_start: 0.6664 (m-40) cc_final: 0.6410 (t160) outliers start: 34 outliers final: 14 residues processed: 296 average time/residue: 1.2818 time to fit residues: 442.9100 Evaluate side-chains 281 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 260 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 618 GLN Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 1006 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 423 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 174 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 179 optimal weight: 0.0010 chunk 192 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 221 optimal weight: 0.5980 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 GLN A1109 GLN A1127 ASN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24710 Z= 0.172 Angle : 0.525 9.710 33494 Z= 0.255 Chirality : 0.039 0.145 3930 Planarity : 0.004 0.052 4066 Dihedral : 9.662 59.901 3630 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.26 % Allowed : 13.22 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.16), residues: 2879 helix: 2.19 (0.13), residues: 1644 sheet: 0.62 (0.30), residues: 297 loop : -0.22 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 102 HIS 0.015 0.001 HIS B1031 PHE 0.015 0.001 PHE B 678 TYR 0.011 0.001 TYR B 468 ARG 0.013 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 268 time to evaluate : 3.153 Fit side-chains revert: symmetry clash REVERT: A 475 GLN cc_start: 0.7642 (tt0) cc_final: 0.7407 (tm-30) REVERT: A 586 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7489 (tm-30) REVERT: A 618 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7016 (pt0) REVERT: A 840 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7665 (mtt-85) REVERT: B 584 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8825 (mt) REVERT: B 765 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.5419 (pp) REVERT: B 1006 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6705 (mt0) REVERT: C 34 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7568 (mm-30) REVERT: C 39 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7749 (p0) REVERT: D 159 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8161 (mp) REVERT: D 166 ASN cc_start: 0.6899 (m110) cc_final: 0.6686 (m110) REVERT: D 423 PHE cc_start: 0.7683 (m-80) cc_final: 0.7346 (m-80) REVERT: E 14 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7841 (pttt) REVERT: E 220 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7567 (ttt90) REVERT: E 423 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6918 (p0) REVERT: E 563 ASN cc_start: 0.6693 (m-40) cc_final: 0.6462 (p0) outliers start: 32 outliers final: 16 residues processed: 288 average time/residue: 1.2410 time to fit residues: 417.7426 Evaluate side-chains 283 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 259 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 618 GLN Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 1006 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 423 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 256 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 246 optimal weight: 0.9990 chunk 263 optimal weight: 0.1980 chunk 158 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 237 optimal weight: 0.0040 chunk 248 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A 618 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 GLN B1005 GLN C 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24710 Z= 0.155 Angle : 0.525 13.569 33494 Z= 0.253 Chirality : 0.039 0.141 3930 Planarity : 0.003 0.039 4066 Dihedral : 9.611 59.981 3630 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.30 % Allowed : 13.44 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.16), residues: 2879 helix: 2.22 (0.13), residues: 1644 sheet: 0.63 (0.30), residues: 297 loop : -0.17 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 364 HIS 0.013 0.001 HIS B1031 PHE 0.016 0.001 PHE B 678 TYR 0.010 0.001 TYR B 733 ARG 0.010 0.000 ARG A 840 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 271 time to evaluate : 2.991 Fit side-chains revert: symmetry clash REVERT: A 475 GLN cc_start: 0.7639 (tt0) cc_final: 0.7402 (tm-30) REVERT: A 586 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 840 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7645 (mtt-85) REVERT: B 584 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8810 (mt) REVERT: B 765 LEU cc_start: 0.5966 (OUTLIER) cc_final: 0.5565 (pp) REVERT: B 1006 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6643 (mt0) REVERT: C 34 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7554 (mm-30) REVERT: C 39 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7793 (p0) REVERT: D 159 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8155 (mp) REVERT: D 166 ASN cc_start: 0.6874 (m110) cc_final: 0.6665 (m110) REVERT: D 765 ASN cc_start: 0.7845 (t0) cc_final: 0.7360 (t0) REVERT: E 14 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7841 (pttt) REVERT: E 220 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7560 (ttt90) REVERT: E 423 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6843 (p0) REVERT: E 563 ASN cc_start: 0.6653 (m-40) cc_final: 0.6443 (p0) REVERT: E 646 GLN cc_start: 0.7151 (mt0) cc_final: 0.6747 (mt0) outliers start: 33 outliers final: 19 residues processed: 291 average time/residue: 1.2123 time to fit residues: 412.3464 Evaluate side-chains 290 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 264 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 618 GLN Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 706 GLN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 1006 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 421 SER Chi-restraints excluded: chain E residue 423 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 172 optimal weight: 0.8980 chunk 278 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 GLN A1150 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 GLN B1031 HIS C 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24710 Z= 0.229 Angle : 0.559 13.568 33494 Z= 0.269 Chirality : 0.040 0.151 3930 Planarity : 0.004 0.040 4066 Dihedral : 9.612 59.812 3630 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.22 % Allowed : 13.63 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.16), residues: 2879 helix: 2.11 (0.13), residues: 1648 sheet: 0.59 (0.30), residues: 294 loop : -0.18 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 364 HIS 0.012 0.001 HIS B1031 PHE 0.017 0.001 PHE B 678 TYR 0.011 0.001 TYR D 195 ARG 0.010 0.000 ARG A 840 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 261 time to evaluate : 3.073 Fit side-chains revert: symmetry clash REVERT: A 475 GLN cc_start: 0.7682 (tt0) cc_final: 0.7480 (tm-30) REVERT: A 586 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 584 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8828 (mt) REVERT: B 765 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5579 (pp) REVERT: B 1006 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6696 (mt0) REVERT: C 34 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7605 (mm-30) REVERT: C 39 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7811 (p0) REVERT: D 159 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8038 (mp) REVERT: D 166 ASN cc_start: 0.6941 (m110) cc_final: 0.6727 (m110) REVERT: D 765 ASN cc_start: 0.7831 (t0) cc_final: 0.7328 (t0) REVERT: E 14 LYS cc_start: 0.8254 (mtmm) cc_final: 0.7845 (pttt) REVERT: E 220 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7587 (ttt90) REVERT: E 423 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6903 (p0) REVERT: E 563 ASN cc_start: 0.6733 (m-40) cc_final: 0.6505 (p0) outliers start: 31 outliers final: 16 residues processed: 281 average time/residue: 1.2395 time to fit residues: 407.0061 Evaluate side-chains 281 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 258 time to evaluate : 5.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 1006 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 421 SER Chi-restraints excluded: chain E residue 423 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 184 optimal weight: 0.5980 chunk 247 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 34 optimal weight: 0.0010 chunk 64 optimal weight: 0.9980 chunk 232 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A1127 ASN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 GLN B1005 GLN C 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.178610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123788 restraints weight = 35053.808| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.10 r_work: 0.3091 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 24710 Z= 0.154 Angle : 0.524 12.839 33494 Z= 0.252 Chirality : 0.039 0.138 3930 Planarity : 0.003 0.039 4066 Dihedral : 9.482 59.512 3630 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.04 % Allowed : 13.93 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.16), residues: 2879 helix: 2.23 (0.13), residues: 1643 sheet: 0.69 (0.30), residues: 290 loop : -0.20 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 102 HIS 0.015 0.001 HIS B1031 PHE 0.016 0.001 PHE B 678 TYR 0.010 0.001 TYR B 733 ARG 0.007 0.000 ARG D 486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8219.80 seconds wall clock time: 146 minutes 49.94 seconds (8809.94 seconds total)