Starting phenix.real_space_refine on Thu Mar 5 06:09:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7egm_31136/03_2026/7egm_31136.cif Found real_map, /net/cci-nas-00/data/ceres_data/7egm_31136/03_2026/7egm_31136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7egm_31136/03_2026/7egm_31136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7egm_31136/03_2026/7egm_31136.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7egm_31136/03_2026/7egm_31136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7egm_31136/03_2026/7egm_31136.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 12656 2.51 5 N 3382 2.21 5 O 3718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19819 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 877 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "B" Number of atoms: 4098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4098 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain breaks: 8 Chain: "C" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2747 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Chain: "D" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3250 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 4 Chain: "H" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3145 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 16, 'TRANS': 371} Chain breaks: 5 Chain: "I" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "J" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1360 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 12, 'TRANS': 154} Chain breaks: 3 Chain: "E" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3454 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 24, 'TRANS': 397} Chain breaks: 3 Time building chain proxies: 4.29, per 1000 atoms: 0.22 Number of scatterers: 19819 At special positions: 0 Unit cell: (148.24, 226.656, 108.494, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 3718 8.00 N 3382 7.00 C 12656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.65 Conformation dependent library (CDL) restraints added in 787.4 milliseconds 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4714 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 9 sheets defined 55.4% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 494 through 518 removed outlier: 3.665A pdb=" N LEU A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 516 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 538 Processing helix chain 'A' and resid 538 through 557 removed outlier: 3.884A pdb=" N ASN A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 588 removed outlier: 3.982A pdb=" N ALA A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 692 removed outlier: 3.931A pdb=" N LYS B 688 " --> pdb=" O LYS B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 719 through 734 removed outlier: 3.541A pdb=" N ALA B 725 " --> pdb=" O GLU B 721 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 732 " --> pdb=" O THR B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 765 removed outlier: 3.576A pdb=" N ASN B 762 " --> pdb=" O ASN B 758 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 764 " --> pdb=" O LEU B 760 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 765 " --> pdb=" O SER B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 800 Processing helix chain 'B' and resid 883 through 896 Processing helix chain 'B' and resid 909 through 929 removed outlier: 3.560A pdb=" N THR B 920 " --> pdb=" O ASP B 916 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 929 " --> pdb=" O LEU B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 938 Processing helix chain 'B' and resid 942 through 957 removed outlier: 3.982A pdb=" N TRP B 953 " --> pdb=" O SER B 949 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 954 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 983 removed outlier: 3.806A pdb=" N LEU B 969 " --> pdb=" O ASN B 965 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 972 " --> pdb=" O ILE B 968 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE B 977 " --> pdb=" O LYS B 973 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 982 " --> pdb=" O VAL B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1003 removed outlier: 3.703A pdb=" N LEU B 998 " --> pdb=" O CYS B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1037 removed outlier: 4.417A pdb=" N GLN B1036 " --> pdb=" O GLY B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1046 removed outlier: 3.587A pdb=" N ALA B1044 " --> pdb=" O VAL B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1063 removed outlier: 3.620A pdb=" N PHE B1057 " --> pdb=" O ASN B1053 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN B1063 " --> pdb=" O SER B1059 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1091 removed outlier: 4.092A pdb=" N ASN B1090 " --> pdb=" O ARG B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1115 removed outlier: 3.578A pdb=" N ASN B1107 " --> pdb=" O HIS B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1125 removed outlier: 3.739A pdb=" N GLN B1125 " --> pdb=" O GLN B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1154 Proline residue: B1138 - end of helix Processing helix chain 'B' and resid 1188 through 1195 Processing helix chain 'B' and resid 1199 through 1213 Processing helix chain 'B' and resid 1233 through 1260 removed outlier: 3.713A pdb=" N ILE B1239 " --> pdb=" O PRO B1235 " (cutoff:3.500A) Processing helix chain 'B' and resid 1265 through 1271 Processing helix chain 'B' and resid 1278 through 1286 removed outlier: 3.537A pdb=" N ILE B1282 " --> pdb=" O THR B1278 " (cutoff:3.500A) Processing helix chain 'B' and resid 1292 through 1314 removed outlier: 4.090A pdb=" N ILE B1296 " --> pdb=" O ASP B1292 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU B1314 " --> pdb=" O LEU B1310 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 400 removed outlier: 3.817A pdb=" N SER C 375 " --> pdb=" O LYS C 371 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 377 " --> pdb=" O TYR C 373 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TYR C 383 " --> pdb=" O HIS C 379 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 450 Processing helix chain 'C' and resid 487 through 499 Processing helix chain 'C' and resid 509 through 523 removed outlier: 4.078A pdb=" N ILE C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C 522 " --> pdb=" O GLN C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 584 Processing helix chain 'C' and resid 589 through 610 removed outlier: 3.724A pdb=" N ALA C 594 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS C 595 " --> pdb=" O THR C 591 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.623A pdb=" N VAL C 638 " --> pdb=" O LEU C 635 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 639 " --> pdb=" O ASP C 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 635 through 639' Processing helix chain 'C' and resid 641 through 646 Processing helix chain 'C' and resid 656 through 663 Processing helix chain 'D' and resid 308 through 312 removed outlier: 3.789A pdb=" N LYS D 312 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 327 removed outlier: 3.801A pdb=" N VAL D 324 " --> pdb=" O HIS D 320 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 331 removed outlier: 3.702A pdb=" N PHE D 331 " --> pdb=" O PRO D 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 328 through 331' Processing helix chain 'D' and resid 343 through 355 removed outlier: 3.642A pdb=" N PHE D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN D 352 " --> pdb=" O ASN D 348 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER D 353 " --> pdb=" O PHE D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 388 removed outlier: 3.567A pdb=" N TRP D 388 " --> pdb=" O PHE D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 444 Processing helix chain 'D' and resid 451 through 468 removed outlier: 3.746A pdb=" N LYS D 455 " --> pdb=" O SER D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 522 removed outlier: 3.534A pdb=" N GLU D 521 " --> pdb=" O LYS D 518 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN D 522 " --> pdb=" O ILE D 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 518 through 522' Processing helix chain 'D' and resid 528 through 542 Processing helix chain 'D' and resid 545 through 554 Processing helix chain 'D' and resid 557 through 567 Processing helix chain 'D' and resid 589 through 594 removed outlier: 3.751A pdb=" N LEU D 592 " --> pdb=" O LEU D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 615 removed outlier: 3.638A pdb=" N SER D 609 " --> pdb=" O ASN D 605 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR D 610 " --> pdb=" O PRO D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 640 removed outlier: 3.564A pdb=" N GLN D 640 " --> pdb=" O SER D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 741 removed outlier: 3.511A pdb=" N ARG D 677 " --> pdb=" O THR D 673 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER D 741 " --> pdb=" O VAL D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 776 removed outlier: 3.703A pdb=" N LYS D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 removed outlier: 3.856A pdb=" N MET H 59 " --> pdb=" O PRO H 56 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL H 60 " --> pdb=" O SER H 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 56 through 60' Processing helix chain 'H' and resid 70 through 106 removed outlier: 4.050A pdb=" N SER H 74 " --> pdb=" O PRO H 70 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU H 78 " --> pdb=" O SER H 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU H 85 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS H 87 " --> pdb=" O LYS H 83 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL H 100 " --> pdb=" O MET H 96 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 319 removed outlier: 3.636A pdb=" N ILE H 317 " --> pdb=" O GLN H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 338 removed outlier: 4.557A pdb=" N ILE H 332 " --> pdb=" O ALA H 328 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR H 333 " --> pdb=" O ILE H 329 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS H 337 " --> pdb=" O TYR H 333 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU H 338 " --> pdb=" O LYS H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 387 removed outlier: 4.262A pdb=" N THR H 387 " --> pdb=" O THR H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 408 Processing helix chain 'H' and resid 457 through 510 removed outlier: 4.120A pdb=" N ALA H 463 " --> pdb=" O SER H 459 " (cutoff:3.500A) Proline residue: H 478 - end of helix removed outlier: 3.623A pdb=" N GLU H 486 " --> pdb=" O LEU H 482 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN H 493 " --> pdb=" O SER H 489 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE H 507 " --> pdb=" O PHE H 503 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER H 508 " --> pdb=" O PHE H 504 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP H 510 " --> pdb=" O LYS H 506 " (cutoff:3.500A) Processing helix chain 'H' and resid 513 through 521 removed outlier: 4.452A pdb=" N ILE H 519 " --> pdb=" O LEU H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 522 through 531 removed outlier: 3.757A pdb=" N LEU H 529 " --> pdb=" O ALA H 525 " (cutoff:3.500A) Processing helix chain 'H' and resid 544 through 549 Processing helix chain 'H' and resid 549 through 564 removed outlier: 3.904A pdb=" N LEU H 553 " --> pdb=" O ASN H 549 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG H 554 " --> pdb=" O GLU H 550 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU H 555 " --> pdb=" O ALA H 551 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU H 558 " --> pdb=" O ARG H 554 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 81 removed outlier: 3.884A pdb=" N LYS I 75 " --> pdb=" O GLN I 71 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN I 76 " --> pdb=" O GLN I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 122 removed outlier: 3.607A pdb=" N ALA I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 151 removed outlier: 3.621A pdb=" N MET I 146 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN I 149 " --> pdb=" O LEU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 154 No H-bonds generated for 'chain 'I' and resid 152 through 154' Processing helix chain 'J' and resid 230 through 241 removed outlier: 3.787A pdb=" N SER J 235 " --> pdb=" O THR J 231 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS J 236 " --> pdb=" O ASN J 232 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER J 238 " --> pdb=" O ILE J 234 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU J 239 " --> pdb=" O SER J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 294 Processing helix chain 'J' and resid 329 through 335 Processing helix chain 'J' and resid 450 through 458 removed outlier: 3.555A pdb=" N LEU J 454 " --> pdb=" O GLU J 450 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU J 455 " --> pdb=" O LYS J 451 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU J 456 " --> pdb=" O ASN J 452 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG J 457 " --> pdb=" O THR J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 465 through 500 removed outlier: 3.657A pdb=" N HIS J 471 " --> pdb=" O LYS J 467 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL J 485 " --> pdb=" O GLY J 481 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS J 495 " --> pdb=" O LYS J 491 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN J 498 " --> pdb=" O LYS J 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 312 No H-bonds generated for 'chain 'E' and resid 310 through 312' Processing helix chain 'E' and resid 320 through 327 Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 339 through 355 Processing helix chain 'E' and resid 363 through 371 removed outlier: 3.800A pdb=" N ALA E 367 " --> pdb=" O SER E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 388 Processing helix chain 'E' and resid 433 through 444 Processing helix chain 'E' and resid 447 through 468 Processing helix chain 'E' and resid 514 through 524 removed outlier: 3.926A pdb=" N ASP E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 542 Processing helix chain 'E' and resid 545 through 554 removed outlier: 3.640A pdb=" N VAL E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.566A pdb=" N ALA E 595 " --> pdb=" O LEU E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 616 Processing helix chain 'E' and resid 619 through 627 removed outlier: 3.510A pdb=" N VAL E 623 " --> pdb=" O ASN E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 644 Processing helix chain 'E' and resid 648 through 747 removed outlier: 3.697A pdb=" N HIS E 652 " --> pdb=" O LYS E 648 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE E 653 " --> pdb=" O PRO E 649 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA E 696 " --> pdb=" O GLU E 692 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS E 697 " --> pdb=" O LYS E 693 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LYS E 702 " --> pdb=" O LEU E 698 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LYS E 703 " --> pdb=" O ASN E 699 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 704 " --> pdb=" O HIS E 700 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET E 708 " --> pdb=" O LEU E 704 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU E 709 " --> pdb=" O GLU E 705 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN E 732 " --> pdb=" O ASN E 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 763 through 776 removed outlier: 4.737A pdb=" N LYS E 776 " --> pdb=" O SER E 772 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 705 through 706 removed outlier: 5.953A pdb=" N ILE B 705 " --> pdb=" O ILE C 427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 1006 through 1007 removed outlier: 4.740A pdb=" N GLN B1006 " --> pdb=" O ASN B1026 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 457 through 461 Processing sheet with id=AA4, first strand: chain 'C' and resid 543 through 552 Processing sheet with id=AA5, first strand: chain 'D' and resid 414 through 417 Processing sheet with id=AA6, first strand: chain 'H' and resid 281 through 283 removed outlier: 3.595A pdb=" N ILE H 442 " --> pdb=" O LEU H 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 184 through 189 removed outlier: 3.816A pdb=" N SER H 184 " --> pdb=" O LEU H 298 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER H 296 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL H 291 " --> pdb=" O VAL H 427 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR H 425 " --> pdb=" O CYS H 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 308 through 309 Processing sheet with id=AA9, first strand: chain 'H' and resid 378 through 379 909 hydrogen bonds defined for protein. 2691 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: 3.32 Time building geometry restraints manager: 2.24 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: 5814 1.34 - 1.45: 3112 1.45 - 1.57: 11168 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 20202 Sorted by residual: bond pdb=" N ARG C 435 " pdb=" CA ARG C 435 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.21e-02 6.83e+03 8.08e+00 bond pdb=" N VAL A 545 " pdb=" CA VAL A 545 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.76e+00 bond pdb=" N ARG B 905 " pdb=" CA ARG B 905 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.58e+00 bond pdb=" N ASN C 434 " pdb=" CA ASN C 434 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.14e-02 7.69e+03 7.53e+00 bond pdb=" N VAL D 432 " pdb=" CA VAL D 432 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.52e+00 ... (remaining 20197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 26613 2.19 - 4.39: 567 4.39 - 6.58: 64 6.58 - 8.77: 28 8.77 - 10.97: 7 Bond angle restraints: 27279 Sorted by residual: angle pdb=" C SER D 397 " pdb=" N LYS D 398 " pdb=" CA LYS D 398 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ILE I 94 " pdb=" N HIS I 95 " pdb=" CA HIS I 95 " ideal model delta sigma weight residual 121.54 131.79 -10.25 1.91e+00 2.74e-01 2.88e+01 angle pdb=" C ILE C 625 " pdb=" N ARG C 626 " pdb=" CA ARG C 626 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C GLN C 508 " pdb=" N HIS C 509 " pdb=" CA HIS C 509 " ideal model delta sigma weight residual 121.31 128.21 -6.90 1.49e+00 4.50e-01 2.14e+01 angle pdb=" C ASP D 524 " pdb=" N GLU D 525 " pdb=" CA GLU D 525 " ideal model delta sigma weight residual 120.38 126.90 -6.52 1.46e+00 4.69e-01 2.00e+01 ... (remaining 27274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 11146 17.79 - 35.58: 915 35.58 - 53.37: 296 53.37 - 71.16: 78 71.16 - 88.95: 15 Dihedral angle restraints: 12450 sinusoidal: 5252 harmonic: 7198 Sorted by residual: dihedral pdb=" CA GLN C 508 " pdb=" C GLN C 508 " pdb=" N HIS C 509 " pdb=" CA HIS C 509 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA LEU H 418 " pdb=" C LEU H 418 " pdb=" N GLN H 419 " pdb=" CA GLN H 419 " ideal model delta harmonic sigma weight residual -180.00 -151.27 -28.73 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ILE I 38 " pdb=" C ILE I 38 " pdb=" N PRO I 39 " pdb=" CA PRO I 39 " ideal model delta harmonic sigma weight residual -180.00 -151.62 -28.38 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 12447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2571 0.063 - 0.126: 443 0.126 - 0.190: 50 0.190 - 0.253: 6 0.253 - 0.316: 1 Chirality restraints: 3071 Sorted by residual: chirality pdb=" CA VAL C 432 " pdb=" N VAL C 432 " pdb=" C VAL C 432 " pdb=" CB VAL C 432 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA LEU H 388 " pdb=" N LEU H 388 " pdb=" C LEU H 388 " pdb=" CB LEU H 388 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE B 868 " pdb=" CA ILE B 868 " pdb=" CG1 ILE B 868 " pdb=" CG2 ILE B 868 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 3068 not shown) Planarity restraints: 3491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 430 " 0.020 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C VAL C 430 " -0.071 2.00e-02 2.50e+03 pdb=" O VAL C 430 " 0.027 2.00e-02 2.50e+03 pdb=" N GLU C 431 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR J 462 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO J 463 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO J 463 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 463 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B1155 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO B1156 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B1156 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B1156 " 0.033 5.00e-02 4.00e+02 ... (remaining 3488 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 11 2.13 - 2.82: 6078 2.82 - 3.52: 25956 3.52 - 4.21: 44583 4.21 - 4.90: 78305 Nonbonded interactions: 154933 Sorted by model distance: nonbonded pdb=" NH1 ARG C 435 " pdb=" OH TYR E 361 " model vdw 1.440 3.120 nonbonded pdb=" NH1 ARG C 435 " pdb=" CZ TYR E 361 " model vdw 1.486 3.340 nonbonded pdb=" NH2 ARG C 435 " pdb=" CE2 TYR E 361 " model vdw 1.539 3.420 nonbonded pdb=" O ASN B 941 " pdb=" N TYR B 943 " model vdw 1.891 3.120 nonbonded pdb=" O PRO B 867 " pdb=" OD2 ASP B 950 " model vdw 1.957 3.040 ... (remaining 154928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 299 through 742 or resid 762 through 781)) selection = (chain 'E' and (resid 299 through 468 or resid 514 through 640 or resid 666 thro \ ugh 742 or resid 762 through 781)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 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: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.120 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20202 Z= 0.235 Angle : 0.813 10.968 27279 Z= 0.480 Chirality : 0.048 0.316 3071 Planarity : 0.006 0.059 3491 Dihedral : 15.456 88.952 7736 Min Nonbonded Distance : 1.440 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.30 % Favored : 93.40 % Rotamer: Outliers : 8.61 % Allowed : 10.02 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.13), residues: 2365 helix: -2.23 (0.11), residues: 1298 sheet: -1.57 (0.59), residues: 68 loop : -3.00 (0.16), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 728 TYR 0.031 0.002 TYR E 576 PHE 0.013 0.001 PHE H 278 TRP 0.011 0.001 TRP D 546 HIS 0.007 0.001 HIS I 95 Details of bonding type rmsd covalent geometry : bond 0.00458 (20202) covalent geometry : angle 0.81323 (27279) hydrogen bonds : bond 0.15895 ( 909) hydrogen bonds : angle 6.70761 ( 2691) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 323 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 TYR cc_start: 0.9132 (t80) cc_final: 0.8839 (t80) REVERT: A 543 LYS cc_start: 0.9152 (mttt) cc_final: 0.8946 (mttm) REVERT: A 553 GLU cc_start: 0.8422 (tp30) cc_final: 0.7652 (tp30) REVERT: B 719 LEU cc_start: 0.9089 (tp) cc_final: 0.8858 (tp) REVERT: B 747 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: B 792 HIS cc_start: 0.6231 (OUTLIER) cc_final: 0.5675 (t-90) REVERT: B 975 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.8900 (tp) REVERT: C 368 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.8092 (t80) REVERT: C 392 MET cc_start: 0.7981 (mmm) cc_final: 0.7749 (mmp) REVERT: C 465 ASP cc_start: 0.7848 (m-30) cc_final: 0.7626 (m-30) REVERT: C 473 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8049 (tm) REVERT: C 495 MET cc_start: 0.8767 (ttp) cc_final: 0.8534 (ttm) REVERT: C 505 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8282 (t) REVERT: C 635 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7865 (tp) REVERT: C 640 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7773 (mtm110) REVERT: C 750 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8529 (pm20) REVERT: D 417 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8442 (m-30) REVERT: D 444 MET cc_start: 0.8441 (mtm) cc_final: 0.7246 (mtm) REVERT: D 450 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.4755 (tm-30) REVERT: D 525 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: D 720 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8020 (tm-30) REVERT: D 778 GLU cc_start: 0.6280 (mt-10) cc_final: 0.5960 (tp30) REVERT: H 99 MET cc_start: 0.8573 (mmm) cc_final: 0.8250 (mmm) REVERT: H 118 ASN cc_start: 0.6004 (OUTLIER) cc_final: 0.5488 (p0) REVERT: H 332 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7822 (mm) REVERT: H 383 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7508 (p) REVERT: I 75 LYS cc_start: 0.8572 (mttt) cc_final: 0.8150 (tppt) REVERT: I 81 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7791 (mt-10) REVERT: I 97 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: I 109 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8484 (ttpp) REVERT: I 112 ILE cc_start: 0.9405 (mm) cc_final: 0.9010 (mm) REVERT: I 129 ASP cc_start: 0.6486 (m-30) cc_final: 0.6141 (t0) REVERT: I 132 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6448 (pm20) REVERT: I 140 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8357 (mtpt) REVERT: J 276 ILE cc_start: 0.7997 (tp) cc_final: 0.7180 (tt) REVERT: J 287 GLU cc_start: 0.8510 (mp0) cc_final: 0.8142 (mp0) REVERT: J 295 LYS cc_start: 0.8240 (mmtp) cc_final: 0.8003 (mmtm) REVERT: J 491 LYS cc_start: 0.7865 (mttt) cc_final: 0.7076 (tttt) REVERT: E 516 LYS cc_start: 0.1534 (OUTLIER) cc_final: 0.1303 (mtpp) REVERT: E 518 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.5425 (mtpt) REVERT: E 691 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8253 (mtt) REVERT: E 718 GLN cc_start: 0.8958 (mt0) cc_final: 0.8678 (mt0) outliers start: 195 outliers final: 49 residues processed: 489 average time/residue: 0.1502 time to fit residues: 113.1964 Evaluate side-chains 275 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 205 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 792 HIS Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1258 CYS Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 408 TRP Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 581 GLN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 640 ARG Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 140 LYS Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 458 LEU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 445 ASN Chi-restraints excluded: chain E residue 516 LYS Chi-restraints excluded: chain E residue 518 LYS Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 593 LYS Chi-restraints excluded: chain E residue 691 MET Chi-restraints excluded: chain E residue 703 LYS Chi-restraints excluded: chain E residue 716 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS A 564 HIS A 584 GLN B 706 ASN B 708 HIS B 718 ASN B 765 GLN B 792 HIS ** B 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1107 ASN B1120 GLN B1135 GLN B1142 GLN B1213 ASN B1294 GLN B1307 ASN C 509 HIS ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN D 416 HIS D 533 GLN D 560 GLN D 567 GLN D 766 GLN H 326 HIS H 460 GLN H 563 ASN I 48 ASN I 89 GLN I 110 ASN I 119 ASN J 280 GLN E 359 ASN E 394 GLN E 567 GLN E 587 ASN E 597 HIS ** E 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 ASN E 690 GLN E 730 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.104462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.081918 restraints weight = 57659.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.084672 restraints weight = 29074.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.084811 restraints weight = 18429.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.084999 restraints weight = 16160.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.085180 restraints weight = 15292.872| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20202 Z= 0.161 Angle : 0.611 9.935 27279 Z= 0.313 Chirality : 0.042 0.182 3071 Planarity : 0.005 0.048 3491 Dihedral : 9.112 67.734 2749 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.00 % Favored : 93.78 % Rotamer: Outliers : 5.08 % Allowed : 14.70 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.16), residues: 2365 helix: -0.26 (0.14), residues: 1333 sheet: -1.41 (0.54), residues: 79 loop : -2.76 (0.18), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 143 TYR 0.022 0.001 TYR H 546 PHE 0.011 0.001 PHE I 111 TRP 0.012 0.001 TRP D 546 HIS 0.010 0.001 HIS C 509 Details of bonding type rmsd covalent geometry : bond 0.00366 (20202) covalent geometry : angle 0.61139 (27279) hydrogen bonds : bond 0.04366 ( 909) hydrogen bonds : angle 4.32039 ( 2691) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 222 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 LYS cc_start: 0.9231 (mttt) cc_final: 0.8990 (mttm) REVERT: B 712 MET cc_start: 0.8925 (mmm) cc_final: 0.8665 (mmm) REVERT: B 747 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: B 975 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8915 (tt) REVERT: B 978 VAL cc_start: 0.9689 (OUTLIER) cc_final: 0.9465 (p) REVERT: B 1134 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: C 392 MET cc_start: 0.8090 (mmm) cc_final: 0.7867 (mmt) REVERT: C 518 GLN cc_start: 0.8472 (tp-100) cc_final: 0.8147 (tp-100) REVERT: C 640 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7996 (mtm110) REVERT: C 744 ASP cc_start: 0.7977 (t0) cc_final: 0.7531 (t0) REVERT: C 750 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8599 (pm20) REVERT: D 350 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8167 (mtt) REVERT: D 444 MET cc_start: 0.8327 (mtm) cc_final: 0.7677 (mtm) REVERT: D 525 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: D 635 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: H 118 ASN cc_start: 0.6123 (OUTLIER) cc_final: 0.5417 (t0) REVERT: I 75 LYS cc_start: 0.8428 (mttt) cc_final: 0.8126 (tppt) REVERT: I 86 ARG cc_start: 0.8519 (ptm-80) cc_final: 0.8315 (ttp80) REVERT: I 97 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: I 109 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8660 (ttpp) REVERT: I 112 ILE cc_start: 0.9395 (mm) cc_final: 0.8805 (mt) REVERT: I 129 ASP cc_start: 0.6450 (m-30) cc_final: 0.6023 (t0) REVERT: I 140 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8446 (mtpt) REVERT: J 295 LYS cc_start: 0.8196 (mmtp) cc_final: 0.7968 (mmtm) REVERT: J 491 LYS cc_start: 0.7876 (mttt) cc_final: 0.7233 (tttp) REVERT: E 445 ASN cc_start: 0.5825 (OUTLIER) cc_final: 0.4472 (t0) REVERT: E 691 MET cc_start: 0.8838 (mtm) cc_final: 0.8539 (mtt) outliers start: 115 outliers final: 55 residues processed: 316 average time/residue: 0.1510 time to fit residues: 73.8936 Evaluate side-chains 248 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 179 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 978 VAL Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1134 ASP Chi-restraints excluded: chain B residue 1275 LEU Chi-restraints excluded: chain B residue 1283 PHE Chi-restraints excluded: chain C residue 408 TRP Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 640 ARG Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 140 LYS Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain J residue 455 LEU Chi-restraints excluded: chain J residue 458 LEU Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 445 ASN Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain E residue 587 ASN Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain E residue 703 LYS Chi-restraints excluded: chain E residue 769 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 108 optimal weight: 0.0980 chunk 142 optimal weight: 0.0470 chunk 51 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 224 optimal weight: 0.0670 chunk 156 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 GLN B 941 ASN C 533 ASN ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN D 680 ASN H 77 GLN H 95 HIS I 49 ASN I 110 ASN E 522 GLN E 628 GLN E 700 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.105845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.083531 restraints weight = 57967.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.086272 restraints weight = 29890.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.086738 restraints weight = 18293.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.086587 restraints weight = 15426.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.086874 restraints weight = 15831.998| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20202 Z= 0.111 Angle : 0.553 8.276 27279 Z= 0.279 Chirality : 0.040 0.222 3071 Planarity : 0.004 0.042 3491 Dihedral : 7.340 59.388 2682 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.91 % Rotamer: Outliers : 3.80 % Allowed : 15.89 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.17), residues: 2365 helix: 0.55 (0.14), residues: 1337 sheet: -0.88 (0.59), residues: 79 loop : -2.51 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 728 TYR 0.018 0.001 TYR H 546 PHE 0.011 0.001 PHE D 379 TRP 0.010 0.001 TRP D 546 HIS 0.007 0.001 HIS I 95 Details of bonding type rmsd covalent geometry : bond 0.00244 (20202) covalent geometry : angle 0.55270 (27279) hydrogen bonds : bond 0.03834 ( 909) hydrogen bonds : angle 3.91183 ( 2691) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 207 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 LYS cc_start: 0.9208 (mttt) cc_final: 0.9001 (mttm) REVERT: B 712 MET cc_start: 0.8833 (mmm) cc_final: 0.8553 (mmm) REVERT: B 747 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: B 1134 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7826 (m-30) REVERT: C 368 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8110 (t80) REVERT: C 392 MET cc_start: 0.8077 (mmm) cc_final: 0.7814 (mmt) REVERT: C 521 ILE cc_start: 0.9323 (pt) cc_final: 0.9121 (mt) REVERT: C 640 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7913 (mtm110) REVERT: C 744 ASP cc_start: 0.7899 (t0) cc_final: 0.7503 (t0) REVERT: C 754 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6675 (tp) REVERT: D 525 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: D 635 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: D 720 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8170 (tm-30) REVERT: H 118 ASN cc_start: 0.6082 (OUTLIER) cc_final: 0.5470 (t0) REVERT: H 283 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7696 (tt) REVERT: I 75 LYS cc_start: 0.8422 (mttt) cc_final: 0.8168 (tppt) REVERT: I 97 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: I 109 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8663 (ttpp) REVERT: I 112 ILE cc_start: 0.9403 (mm) cc_final: 0.8887 (mt) REVERT: I 129 ASP cc_start: 0.6424 (m-30) cc_final: 0.6041 (t0) REVERT: I 140 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8481 (mtpt) REVERT: J 491 LYS cc_start: 0.7827 (mttt) cc_final: 0.7221 (tttt) REVERT: E 429 LYS cc_start: 0.8119 (tttt) cc_final: 0.7378 (mttp) REVERT: E 523 ILE cc_start: 0.7094 (mm) cc_final: 0.6800 (mm) REVERT: E 691 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8444 (mtt) outliers start: 86 outliers final: 49 residues processed: 276 average time/residue: 0.1512 time to fit residues: 64.8203 Evaluate side-chains 237 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 1134 ASP Chi-restraints excluded: chain B residue 1283 PHE Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 408 TRP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 509 HIS Chi-restraints excluded: chain C residue 581 GLN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ARG Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 624 GLN Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 140 LYS Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain J residue 455 LEU Chi-restraints excluded: chain J residue 458 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 628 GLN Chi-restraints excluded: chain E residue 691 MET Chi-restraints excluded: chain E residue 699 ASN Chi-restraints excluded: chain E residue 769 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 86 optimal weight: 0.0070 chunk 221 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 HIS C 370 ASN ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN I 119 ASN J 292 ASN J 473 HIS E 628 GLN E 718 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.105104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.082306 restraints weight = 58261.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.085117 restraints weight = 33936.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.085693 restraints weight = 19670.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.085819 restraints weight = 16037.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.086066 restraints weight = 15855.859| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20202 Z= 0.126 Angle : 0.545 8.590 27279 Z= 0.274 Chirality : 0.040 0.171 3071 Planarity : 0.004 0.046 3491 Dihedral : 6.622 59.714 2656 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.26 % Favored : 93.70 % Rotamer: Outliers : 4.37 % Allowed : 15.45 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.18), residues: 2365 helix: 0.99 (0.15), residues: 1335 sheet: -1.34 (0.57), residues: 88 loop : -2.24 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 299 TYR 0.017 0.001 TYR E 576 PHE 0.024 0.001 PHE B1286 TRP 0.010 0.001 TRP D 546 HIS 0.006 0.001 HIS I 95 Details of bonding type rmsd covalent geometry : bond 0.00286 (20202) covalent geometry : angle 0.54537 (27279) hydrogen bonds : bond 0.03741 ( 909) hydrogen bonds : angle 3.81113 ( 2691) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 191 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8209 (mp10) REVERT: A 543 LYS cc_start: 0.9237 (mttt) cc_final: 0.9007 (mttm) REVERT: B 747 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: B 1133 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.8956 (pp) REVERT: B 1134 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: C 368 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8132 (t80) REVERT: C 392 MET cc_start: 0.8094 (mmm) cc_final: 0.7830 (mmt) REVERT: C 521 ILE cc_start: 0.9354 (pt) cc_final: 0.9110 (mt) REVERT: C 640 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7880 (mtm110) REVERT: C 754 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6644 (tp) REVERT: D 450 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.4911 (tm-30) REVERT: D 720 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8164 (tm-30) REVERT: D 787 PHE cc_start: 0.1641 (OUTLIER) cc_final: 0.0902 (m-80) REVERT: H 118 ASN cc_start: 0.6069 (OUTLIER) cc_final: 0.5530 (t0) REVERT: H 182 ILE cc_start: 0.6042 (OUTLIER) cc_final: 0.5666 (mm) REVERT: I 75 LYS cc_start: 0.8530 (mttt) cc_final: 0.8284 (tppt) REVERT: I 97 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: I 112 ILE cc_start: 0.9421 (mm) cc_final: 0.9011 (mt) REVERT: I 129 ASP cc_start: 0.6552 (m-30) cc_final: 0.6163 (t0) REVERT: I 140 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8496 (mtpt) REVERT: I 152 MET cc_start: 0.6436 (ptt) cc_final: 0.6174 (ptp) REVERT: J 287 GLU cc_start: 0.8753 (mp0) cc_final: 0.8232 (mp0) REVERT: J 491 LYS cc_start: 0.7827 (mttt) cc_final: 0.7214 (tttp) REVERT: E 429 LYS cc_start: 0.8099 (tttt) cc_final: 0.7327 (mttp) REVERT: E 437 MET cc_start: 0.8535 (mmm) cc_final: 0.8067 (mmm) REVERT: E 523 ILE cc_start: 0.7061 (mm) cc_final: 0.6845 (mm) REVERT: E 691 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8491 (mtt) outliers start: 99 outliers final: 54 residues processed: 273 average time/residue: 0.1505 time to fit residues: 64.0688 Evaluate side-chains 245 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 177 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1134 ASP Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1283 PHE Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 408 TRP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 509 HIS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ARG Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 624 GLN Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 339 ASN Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 140 LYS Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain J residue 458 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 691 MET Chi-restraints excluded: chain E residue 699 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 70 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 155 optimal weight: 0.3980 chunk 39 optimal weight: 0.4980 chunk 57 optimal weight: 0.0040 chunk 81 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1238 ASN ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN D 567 GLN D 690 GLN ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN E 628 GLN E 718 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.106045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083678 restraints weight = 57609.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.085934 restraints weight = 31124.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.086781 restraints weight = 19141.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.086945 restraints weight = 15757.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.087089 restraints weight = 15321.970| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20202 Z= 0.105 Angle : 0.531 8.445 27279 Z= 0.267 Chirality : 0.040 0.224 3071 Planarity : 0.004 0.045 3491 Dihedral : 6.163 58.358 2646 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.13 % Favored : 93.83 % Rotamer: Outliers : 3.75 % Allowed : 16.25 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.18), residues: 2365 helix: 1.28 (0.15), residues: 1345 sheet: -0.66 (0.61), residues: 79 loop : -2.17 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 299 TYR 0.026 0.001 TYR E 576 PHE 0.012 0.001 PHE E 707 TRP 0.009 0.001 TRP E 388 HIS 0.006 0.001 HIS I 95 Details of bonding type rmsd covalent geometry : bond 0.00234 (20202) covalent geometry : angle 0.53083 (27279) hydrogen bonds : bond 0.03506 ( 909) hydrogen bonds : angle 3.67250 ( 2691) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 200 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: A 553 GLU cc_start: 0.8582 (tp30) cc_final: 0.8208 (tp30) REVERT: B 747 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: B 1133 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.8944 (pp) REVERT: B 1134 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7885 (m-30) REVERT: C 368 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8116 (t80) REVERT: C 392 MET cc_start: 0.8065 (mmm) cc_final: 0.7810 (mmt) REVERT: C 521 ILE cc_start: 0.9341 (pt) cc_final: 0.9130 (mt) REVERT: C 581 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8261 (mm110) REVERT: C 744 ASP cc_start: 0.7874 (t0) cc_final: 0.7415 (t0) REVERT: C 754 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6623 (tp) REVERT: D 450 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.4955 (tm-30) REVERT: D 787 PHE cc_start: 0.1722 (OUTLIER) cc_final: 0.0936 (m-80) REVERT: H 118 ASN cc_start: 0.6039 (OUTLIER) cc_final: 0.5551 (t0) REVERT: H 182 ILE cc_start: 0.5929 (OUTLIER) cc_final: 0.5574 (mm) REVERT: H 283 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7539 (tt) REVERT: H 327 ASP cc_start: 0.8884 (t0) cc_final: 0.8669 (t0) REVERT: H 401 MET cc_start: 0.6747 (pmm) cc_final: 0.6352 (pmm) REVERT: H 416 LEU cc_start: 0.8110 (mp) cc_final: 0.7877 (tp) REVERT: I 75 LYS cc_start: 0.8504 (mttt) cc_final: 0.8251 (tppt) REVERT: I 97 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8266 (tt0) REVERT: I 112 ILE cc_start: 0.9361 (mm) cc_final: 0.9121 (mm) REVERT: I 129 ASP cc_start: 0.6528 (m-30) cc_final: 0.6187 (t0) REVERT: J 491 LYS cc_start: 0.7791 (mttt) cc_final: 0.7240 (tttt) REVERT: E 429 LYS cc_start: 0.8045 (tttt) cc_final: 0.7272 (mttp) REVERT: E 444 MET cc_start: 0.5703 (OUTLIER) cc_final: 0.4971 (mtm) REVERT: E 691 MET cc_start: 0.8832 (mtm) cc_final: 0.8402 (mtt) outliers start: 85 outliers final: 54 residues processed: 271 average time/residue: 0.1408 time to fit residues: 60.8198 Evaluate side-chains 245 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 178 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1134 ASP Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1283 PHE Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 509 HIS Chi-restraints excluded: chain C residue 581 GLN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 624 GLN Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 339 ASN Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain I residue 71 GLN Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain J residue 458 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 628 GLN Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 699 ASN Chi-restraints excluded: chain E residue 716 GLU Chi-restraints excluded: chain E residue 769 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 189 optimal weight: 0.0170 chunk 42 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 235 optimal weight: 0.7980 chunk 216 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 GLN B 941 ASN ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN D 769 HIS ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN E 628 GLN E 718 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.105822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.083609 restraints weight = 58139.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.085885 restraints weight = 29624.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.086478 restraints weight = 18988.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.086588 restraints weight = 16438.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.086879 restraints weight = 15751.434| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20202 Z= 0.117 Angle : 0.546 8.529 27279 Z= 0.275 Chirality : 0.040 0.196 3071 Planarity : 0.004 0.042 3491 Dihedral : 5.746 58.608 2629 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.05 % Favored : 93.91 % Rotamer: Outliers : 3.53 % Allowed : 16.95 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.18), residues: 2365 helix: 1.48 (0.15), residues: 1335 sheet: -1.02 (0.59), residues: 84 loop : -2.03 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 640 TYR 0.026 0.001 TYR B 770 PHE 0.015 0.001 PHE D 770 TRP 0.008 0.001 TRP D 546 HIS 0.006 0.001 HIS J 473 Details of bonding type rmsd covalent geometry : bond 0.00268 (20202) covalent geometry : angle 0.54631 (27279) hydrogen bonds : bond 0.03515 ( 909) hydrogen bonds : angle 3.67313 ( 2691) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 183 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8287 (mp10) REVERT: B 747 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: B 1133 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.8966 (pp) REVERT: B 1134 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: C 368 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8130 (t80) REVERT: C 392 MET cc_start: 0.8066 (mmm) cc_final: 0.7817 (mmt) REVERT: C 754 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6605 (tp) REVERT: D 450 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.4948 (tm-30) REVERT: D 559 GLU cc_start: 0.8095 (mp0) cc_final: 0.7874 (mp0) REVERT: D 720 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8169 (tm-30) REVERT: D 787 PHE cc_start: 0.1727 (OUTLIER) cc_final: 0.0905 (m-80) REVERT: H 118 ASN cc_start: 0.5958 (OUTLIER) cc_final: 0.5471 (t0) REVERT: H 182 ILE cc_start: 0.5992 (OUTLIER) cc_final: 0.5638 (mm) REVERT: H 401 MET cc_start: 0.6604 (pmm) cc_final: 0.6203 (pmm) REVERT: H 416 LEU cc_start: 0.8135 (mp) cc_final: 0.7876 (tp) REVERT: I 97 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8332 (tt0) REVERT: I 112 ILE cc_start: 0.9379 (mm) cc_final: 0.9177 (mm) REVERT: I 129 ASP cc_start: 0.6541 (m-30) cc_final: 0.6279 (t0) REVERT: J 287 GLU cc_start: 0.8690 (mp0) cc_final: 0.8272 (mp0) REVERT: J 491 LYS cc_start: 0.7827 (mttt) cc_final: 0.7296 (tttt) REVERT: E 429 LYS cc_start: 0.7902 (tttt) cc_final: 0.7237 (mttp) REVERT: E 437 MET cc_start: 0.8543 (mmm) cc_final: 0.8167 (tpt) REVERT: E 444 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.4943 (mtm) REVERT: E 691 MET cc_start: 0.8835 (mtm) cc_final: 0.8410 (mtt) outliers start: 80 outliers final: 56 residues processed: 249 average time/residue: 0.1425 time to fit residues: 56.1960 Evaluate side-chains 241 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 174 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1134 ASP Chi-restraints excluded: chain B residue 1283 PHE Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 408 TRP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 509 HIS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 624 GLN Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 339 ASN Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain I residue 71 GLN Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain J residue 455 LEU Chi-restraints excluded: chain J residue 458 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 380 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 628 GLN Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 699 ASN Chi-restraints excluded: chain E residue 716 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 193 optimal weight: 0.7980 chunk 174 optimal weight: 10.0000 chunk 111 optimal weight: 0.3980 chunk 226 optimal weight: 0.4980 chunk 116 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 159 optimal weight: 8.9990 chunk 232 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 22 optimal weight: 0.0070 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 GLN ** B 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 730 ASN D 769 HIS ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN J 558 ASN E 628 GLN E 718 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.106893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.084617 restraints weight = 58051.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.087630 restraints weight = 30136.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.087996 restraints weight = 18126.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.087980 restraints weight = 15077.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088310 restraints weight = 15608.307| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20202 Z= 0.100 Angle : 0.530 9.240 27279 Z= 0.266 Chirality : 0.040 0.182 3071 Planarity : 0.004 0.045 3491 Dihedral : 5.525 58.670 2625 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.67 % Favored : 94.29 % Rotamer: Outliers : 3.13 % Allowed : 17.26 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.18), residues: 2365 helix: 1.68 (0.15), residues: 1332 sheet: -1.13 (0.58), residues: 90 loop : -1.91 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 640 TYR 0.024 0.001 TYR B 770 PHE 0.010 0.001 PHE D 707 TRP 0.008 0.001 TRP D 546 HIS 0.006 0.001 HIS I 95 Details of bonding type rmsd covalent geometry : bond 0.00220 (20202) covalent geometry : angle 0.52964 (27279) hydrogen bonds : bond 0.03363 ( 909) hydrogen bonds : angle 3.52852 ( 2691) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 194 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: B 747 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: B 1133 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.8959 (pp) REVERT: B 1134 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: C 368 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8094 (t80) REVERT: C 392 MET cc_start: 0.8053 (mmm) cc_final: 0.7798 (mmt) REVERT: C 744 ASP cc_start: 0.7823 (t0) cc_final: 0.7398 (t0) REVERT: C 750 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8519 (pm20) REVERT: C 754 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6493 (tp) REVERT: D 450 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.5162 (tm-30) REVERT: D 787 PHE cc_start: 0.1701 (OUTLIER) cc_final: 0.0890 (m-80) REVERT: H 108 LEU cc_start: 0.7187 (tp) cc_final: 0.6749 (mt) REVERT: H 118 ASN cc_start: 0.5822 (OUTLIER) cc_final: 0.5389 (t0) REVERT: H 182 ILE cc_start: 0.5926 (OUTLIER) cc_final: 0.5528 (mm) REVERT: H 283 ILE cc_start: 0.7696 (mp) cc_final: 0.7264 (tt) REVERT: H 300 LYS cc_start: 0.6223 (mppt) cc_final: 0.5509 (tppt) REVERT: H 401 MET cc_start: 0.6679 (pmm) cc_final: 0.6248 (pmm) REVERT: I 112 ILE cc_start: 0.9370 (mm) cc_final: 0.9164 (mm) REVERT: I 129 ASP cc_start: 0.6544 (m-30) cc_final: 0.6320 (t0) REVERT: J 287 GLU cc_start: 0.8718 (mp0) cc_final: 0.8294 (mp0) REVERT: J 491 LYS cc_start: 0.7851 (mttt) cc_final: 0.7330 (tttp) REVERT: E 429 LYS cc_start: 0.7842 (tttt) cc_final: 0.7193 (mttp) REVERT: E 444 MET cc_start: 0.5573 (OUTLIER) cc_final: 0.4560 (mtm) REVERT: E 691 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8416 (mtt) outliers start: 71 outliers final: 47 residues processed: 250 average time/residue: 0.1384 time to fit residues: 55.7138 Evaluate side-chains 234 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 174 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1134 ASP Chi-restraints excluded: chain B residue 1283 PHE Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 509 HIS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 624 GLN Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 339 ASN Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 458 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 380 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 628 GLN Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 691 MET Chi-restraints excluded: chain E residue 699 ASN Chi-restraints excluded: chain E residue 769 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 GLN B 941 ASN C 429 GLN ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 HIS ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN J 292 ASN J 558 ASN E 315 ASN E 628 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.104426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.081851 restraints weight = 58256.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.084569 restraints weight = 31049.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.085182 restraints weight = 19039.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.085272 restraints weight = 15688.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.085531 restraints weight = 15661.022| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20202 Z= 0.165 Angle : 0.588 9.456 27279 Z= 0.294 Chirality : 0.042 0.171 3071 Planarity : 0.004 0.046 3491 Dihedral : 5.686 59.477 2623 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.34 % Favored : 93.62 % Rotamer: Outliers : 3.27 % Allowed : 17.44 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 2365 helix: 1.60 (0.15), residues: 1352 sheet: -1.34 (0.56), residues: 94 loop : -1.96 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 640 TYR 0.025 0.001 TYR B 770 PHE 0.019 0.001 PHE D 770 TRP 0.009 0.001 TRP D 546 HIS 0.004 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00383 (20202) covalent geometry : angle 0.58773 (27279) hydrogen bonds : bond 0.03668 ( 909) hydrogen bonds : angle 3.75686 ( 2691) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 181 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8226 (mp10) REVERT: A 553 GLU cc_start: 0.8414 (tp30) cc_final: 0.8173 (tp30) REVERT: B 1133 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9003 (pp) REVERT: B 1134 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7825 (m-30) REVERT: C 368 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8141 (t80) REVERT: C 392 MET cc_start: 0.8066 (mmm) cc_final: 0.7821 (mmt) REVERT: C 744 ASP cc_start: 0.7916 (t0) cc_final: 0.7459 (t0) REVERT: C 750 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8536 (pm20) REVERT: D 450 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.4984 (tm-30) REVERT: D 720 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8222 (tm-30) REVERT: D 787 PHE cc_start: 0.1430 (OUTLIER) cc_final: 0.0590 (m-80) REVERT: H 118 ASN cc_start: 0.5985 (OUTLIER) cc_final: 0.5604 (t0) REVERT: H 300 LYS cc_start: 0.5858 (mppt) cc_final: 0.5390 (tppt) REVERT: H 401 MET cc_start: 0.6685 (pmm) cc_final: 0.6239 (pmm) REVERT: I 129 ASP cc_start: 0.6630 (m-30) cc_final: 0.6395 (t0) REVERT: J 287 GLU cc_start: 0.8755 (mp0) cc_final: 0.8277 (mp0) REVERT: J 295 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7947 (mtmm) REVERT: J 491 LYS cc_start: 0.7829 (mttt) cc_final: 0.7282 (tttt) REVERT: E 429 LYS cc_start: 0.7885 (tttt) cc_final: 0.7235 (mttp) REVERT: E 691 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8496 (mtt) outliers start: 74 outliers final: 55 residues processed: 241 average time/residue: 0.1372 time to fit residues: 53.3541 Evaluate side-chains 238 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 174 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1134 ASP Chi-restraints excluded: chain B residue 1283 PHE Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 408 TRP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 509 HIS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 624 GLN Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 339 ASN Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 458 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 628 GLN Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 691 MET Chi-restraints excluded: chain E residue 699 ASN Chi-restraints excluded: chain E residue 769 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 136 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 81 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 HIS ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 558 ASN E 392 ASN E 628 GLN E 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.105636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.083132 restraints weight = 57767.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.085714 restraints weight = 31358.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.086175 restraints weight = 19025.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.086485 restraints weight = 16532.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.086535 restraints weight = 15319.165| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20202 Z= 0.118 Angle : 0.559 9.288 27279 Z= 0.279 Chirality : 0.041 0.165 3071 Planarity : 0.004 0.047 3491 Dihedral : 5.475 59.458 2620 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.09 % Favored : 93.87 % Rotamer: Outliers : 2.96 % Allowed : 18.28 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.18), residues: 2365 helix: 1.67 (0.15), residues: 1348 sheet: -1.08 (0.59), residues: 90 loop : -1.94 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 640 TYR 0.025 0.001 TYR B 770 PHE 0.024 0.001 PHE D 707 TRP 0.009 0.001 TRP D 546 HIS 0.005 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00269 (20202) covalent geometry : angle 0.55866 (27279) hydrogen bonds : bond 0.03549 ( 909) hydrogen bonds : angle 3.66053 ( 2691) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8219 (mp10) REVERT: B 747 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: B 1133 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.8990 (pp) REVERT: B 1134 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: C 368 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8114 (t80) REVERT: C 392 MET cc_start: 0.8055 (mmm) cc_final: 0.7819 (mmt) REVERT: C 744 ASP cc_start: 0.7952 (t0) cc_final: 0.7517 (t0) REVERT: C 750 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8514 (pm20) REVERT: D 450 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.5129 (tm-30) REVERT: D 787 PHE cc_start: 0.1480 (OUTLIER) cc_final: 0.0645 (m-80) REVERT: H 108 LEU cc_start: 0.7079 (tp) cc_final: 0.6550 (mt) REVERT: H 118 ASN cc_start: 0.5927 (OUTLIER) cc_final: 0.5624 (t0) REVERT: H 300 LYS cc_start: 0.5836 (mppt) cc_final: 0.5353 (tppt) REVERT: H 401 MET cc_start: 0.6851 (pmm) cc_final: 0.6441 (pmm) REVERT: I 129 ASP cc_start: 0.6768 (m-30) cc_final: 0.6467 (t0) REVERT: I 140 LYS cc_start: 0.9142 (mtmp) cc_final: 0.8619 (mtpt) REVERT: J 287 GLU cc_start: 0.8763 (mp0) cc_final: 0.8266 (mp0) REVERT: J 295 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7891 (mtmm) REVERT: J 491 LYS cc_start: 0.7857 (mttt) cc_final: 0.7344 (tttt) REVERT: E 429 LYS cc_start: 0.7843 (tttt) cc_final: 0.7209 (mttp) REVERT: E 691 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8448 (mtt) outliers start: 67 outliers final: 51 residues processed: 238 average time/residue: 0.1437 time to fit residues: 54.3436 Evaluate side-chains 236 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1134 ASP Chi-restraints excluded: chain B residue 1202 SER Chi-restraints excluded: chain B residue 1283 PHE Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 408 TRP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 509 HIS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 624 GLN Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 339 ASN Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 458 LEU Chi-restraints excluded: chain J residue 505 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 628 GLN Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 691 MET Chi-restraints excluded: chain E residue 699 ASN Chi-restraints excluded: chain E residue 769 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 145 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 235 optimal weight: 0.0970 chunk 56 optimal weight: 0.6980 chunk 210 optimal weight: 0.4980 chunk 214 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 184 optimal weight: 0.0980 chunk 186 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 HIS ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 628 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.106420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.084141 restraints weight = 58069.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.086257 restraints weight = 33787.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.086900 restraints weight = 20970.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.087013 restraints weight = 17694.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.087418 restraints weight = 15972.815| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20202 Z= 0.105 Angle : 0.560 9.440 27279 Z= 0.278 Chirality : 0.040 0.168 3071 Planarity : 0.004 0.046 3491 Dihedral : 5.200 59.587 2617 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.09 % Favored : 93.87 % Rotamer: Outliers : 2.78 % Allowed : 18.23 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.18), residues: 2365 helix: 1.76 (0.15), residues: 1348 sheet: -0.99 (0.59), residues: 88 loop : -1.90 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 640 TYR 0.023 0.001 TYR B 770 PHE 0.031 0.001 PHE D 707 TRP 0.008 0.001 TRP D 546 HIS 0.004 0.001 HIS J 473 Details of bonding type rmsd covalent geometry : bond 0.00234 (20202) covalent geometry : angle 0.55963 (27279) hydrogen bonds : bond 0.03422 ( 909) hydrogen bonds : angle 3.61840 ( 2691) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 186 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8233 (mp10) REVERT: B 1133 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.8987 (pp) REVERT: B 1134 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7826 (m-30) REVERT: C 368 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8080 (t80) REVERT: C 392 MET cc_start: 0.8049 (mmm) cc_final: 0.7804 (mmt) REVERT: C 744 ASP cc_start: 0.7919 (t0) cc_final: 0.7408 (t0) REVERT: C 750 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8516 (pm20) REVERT: C 754 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6526 (tp) REVERT: D 450 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.5102 (tm-30) REVERT: D 720 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8165 (tm-30) REVERT: D 787 PHE cc_start: 0.1411 (OUTLIER) cc_final: 0.0662 (m-80) REVERT: H 108 LEU cc_start: 0.6975 (tp) cc_final: 0.6520 (mt) REVERT: H 118 ASN cc_start: 0.5806 (OUTLIER) cc_final: 0.5484 (t0) REVERT: H 181 PHE cc_start: 0.7054 (t80) cc_final: 0.6587 (t80) REVERT: H 283 ILE cc_start: 0.7583 (mp) cc_final: 0.7036 (tt) REVERT: H 300 LYS cc_start: 0.5886 (mppt) cc_final: 0.5446 (tppt) REVERT: H 401 MET cc_start: 0.6841 (pmm) cc_final: 0.6422 (pmm) REVERT: I 129 ASP cc_start: 0.6765 (m-30) cc_final: 0.6485 (t0) REVERT: I 140 LYS cc_start: 0.9139 (mtmp) cc_final: 0.8616 (mtpt) REVERT: J 287 GLU cc_start: 0.8757 (mp0) cc_final: 0.8391 (mp0) REVERT: J 491 LYS cc_start: 0.7863 (mttt) cc_final: 0.7321 (tttp) REVERT: E 429 LYS cc_start: 0.7796 (tttt) cc_final: 0.7416 (ptpp) REVERT: E 444 MET cc_start: 0.5530 (OUTLIER) cc_final: 0.4546 (mtm) REVERT: E 691 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8384 (mtt) outliers start: 63 outliers final: 50 residues processed: 235 average time/residue: 0.1368 time to fit residues: 51.9405 Evaluate side-chains 235 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 174 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1134 ASP Chi-restraints excluded: chain B residue 1202 SER Chi-restraints excluded: chain B residue 1283 PHE Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 408 TRP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 509 HIS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 624 GLN Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 339 ASN Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 458 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 628 GLN Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 691 MET Chi-restraints excluded: chain E residue 699 ASN Chi-restraints excluded: chain E residue 769 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 98 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 133 optimal weight: 0.0970 chunk 230 optimal weight: 2.9990 chunk 205 optimal weight: 0.3980 chunk 103 optimal weight: 0.0870 chunk 128 optimal weight: 0.8980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 HIS ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 628 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.107387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.085194 restraints weight = 58321.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.087898 restraints weight = 31564.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.088470 restraints weight = 19441.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.088646 restraints weight = 15419.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.088711 restraints weight = 15179.199| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20202 Z= 0.101 Angle : 0.551 9.421 27279 Z= 0.275 Chirality : 0.040 0.166 3071 Planarity : 0.004 0.046 3491 Dihedral : 5.133 59.514 2617 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.84 % Favored : 94.12 % Rotamer: Outliers : 2.87 % Allowed : 18.32 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 2365 helix: 1.84 (0.15), residues: 1347 sheet: -0.90 (0.60), residues: 88 loop : -1.91 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 640 TYR 0.020 0.001 TYR E 576 PHE 0.033 0.001 PHE D 707 TRP 0.008 0.001 TRP D 546 HIS 0.005 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00222 (20202) covalent geometry : angle 0.55084 (27279) hydrogen bonds : bond 0.03314 ( 909) hydrogen bonds : angle 3.55972 ( 2691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3519.37 seconds wall clock time: 62 minutes 11.51 seconds (3731.51 seconds total)