Starting phenix.real_space_refine (version: dev) on Sat May 14 13:44:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjl_10218/05_2022/6sjl_10218.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjl_10218/05_2022/6sjl_10218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjl_10218/05_2022/6sjl_10218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjl_10218/05_2022/6sjl_10218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjl_10218/05_2022/6sjl_10218.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjl_10218/05_2022/6sjl_10218.pdb" } resolution = 2.6 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 ------------------------------------------------------------------------------- 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= 1.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 19459 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2376 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 10, 'TRANS': 313} Chain breaks: 1 Chain: "B" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2376 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 10, 'TRANS': 313} Chain breaks: 1 Chain: "C" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2376 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 10, 'TRANS': 313} Chain breaks: 1 Chain: "D" Number of atoms: 4105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4105 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 22, 'TRANS': 498} Chain breaks: 2 Chain: "E" Number of atoms: 4113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4113 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 22, 'TRANS': 499} Chain breaks: 2 Chain: "F" Number of atoms: 4113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4113 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 22, 'TRANS': 499} Chain breaks: 2 Time building chain proxies: 11.26, per 1000 atoms: 0.58 Number of scatterers: 19459 At special positions: 0 Unit cell: (149.504, 154.624, 136.192, 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 96 16.00 O 3734 8.00 N 3455 7.00 C 12174 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.69 Conformation dependent library (CDL) restraints added in 3.2 seconds 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4594 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 28 sheets defined 28.9% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 567 through 571 Processing helix chain 'A' and resid 577 through 601 Processing helix chain 'A' and resid 607 through 619 removed outlier: 3.718A pdb=" N GLN A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'B' and resid 567 through 571 Processing helix chain 'B' and resid 577 through 601 Processing helix chain 'B' and resid 607 through 619 removed outlier: 3.821A pdb=" N GLN B 611 " --> pdb=" O ASP B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 622 No H-bonds generated for 'chain 'B' and resid 620 through 622' Processing helix chain 'C' and resid 567 through 571 Processing helix chain 'C' and resid 577 through 601 Processing helix chain 'C' and resid 607 through 619 removed outlier: 3.711A pdb=" N GLN C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 622 No H-bonds generated for 'chain 'C' and resid 620 through 622' Processing helix chain 'D' and resid 52 through 58 Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 71 through 84 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.544A pdb=" N SER D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 179 Processing helix chain 'D' and resid 198 through 212 Processing helix chain 'D' and resid 214 through 226 removed outlier: 3.601A pdb=" N ALA D 218 " --> pdb=" O ASP D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 315 removed outlier: 3.509A pdb=" N ILE D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 348 Processing helix chain 'D' and resid 349 through 365 Processing helix chain 'D' and resid 366 through 369 Processing helix chain 'D' and resid 371 through 375 removed outlier: 3.534A pdb=" N HIS D 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 394 removed outlier: 3.513A pdb=" N ALA D 394 " --> pdb=" O ASN D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 431 Processing helix chain 'D' and resid 442 through 446 removed outlier: 3.818A pdb=" N GLN D 446 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 450 No H-bonds generated for 'chain 'D' and resid 448 through 450' Processing helix chain 'D' and resid 451 through 467 Processing helix chain 'D' and resid 475 through 483 Processing helix chain 'D' and resid 529 through 533 removed outlier: 3.539A pdb=" N ILE D 533 " --> pdb=" O ASP D 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 59 removed outlier: 3.817A pdb=" N LYS E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.535A pdb=" N ILE E 85 " --> pdb=" O PHE E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 109 Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 145 through 155 Processing helix chain 'E' and resid 155 through 178 Processing helix chain 'E' and resid 198 through 212 Processing helix chain 'E' and resid 214 through 226 removed outlier: 3.546A pdb=" N ALA E 218 " --> pdb=" O ASP E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 315 Processing helix chain 'E' and resid 345 through 348 Processing helix chain 'E' and resid 349 through 365 Processing helix chain 'E' and resid 366 through 369 Processing helix chain 'E' and resid 371 through 375 Processing helix chain 'E' and resid 388 through 394 Processing helix chain 'E' and resid 416 through 431 Processing helix chain 'E' and resid 442 through 446 removed outlier: 3.998A pdb=" N GLN E 446 " --> pdb=" O THR E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 451 through 467 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.559A pdb=" N LYS E 484 " --> pdb=" O TYR E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 533 removed outlier: 3.743A pdb=" N ILE E 533 " --> pdb=" O ASP E 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 59 removed outlier: 3.822A pdb=" N LYS F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 86 removed outlier: 3.510A pdb=" N ILE F 85 " --> pdb=" O PHE F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 109 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 155 through 179 Processing helix chain 'F' and resid 198 through 212 Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.502A pdb=" N ALA F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 315 Processing helix chain 'F' and resid 345 through 348 Processing helix chain 'F' and resid 349 through 365 Processing helix chain 'F' and resid 366 through 369 Processing helix chain 'F' and resid 371 through 375 Processing helix chain 'F' and resid 388 through 394 Processing helix chain 'F' and resid 416 through 431 Processing helix chain 'F' and resid 442 through 446 removed outlier: 3.693A pdb=" N GLN F 446 " --> pdb=" O THR F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 451 through 467 Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.778A pdb=" N LYS F 484 " --> pdb=" O TYR F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 533 removed outlier: 3.523A pdb=" N ILE F 533 " --> pdb=" O ASP F 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 493 through 497 removed outlier: 9.898A pdb=" N TRP B 551 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLU A 542 " --> pdb=" O TRP B 551 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER B 553 " --> pdb=" O GLU A 542 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA A 544 " --> pdb=" O SER B 553 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ARG B 555 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 546 " --> pdb=" O ARG B 555 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 552 " --> pdb=" O PHE C 561 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N SER C 563 " --> pdb=" O ILE B 552 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE B 554 " --> pdb=" O SER C 563 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 560 " --> pdb=" O LEU C 627 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N HIS C 629 " --> pdb=" O ILE C 560 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE C 562 " --> pdb=" O HIS C 629 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY A 635 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 642 " --> pdb=" O GLY C 652 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N MET C 654 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 644 " --> pdb=" O MET C 654 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN A 685 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N SER C 679 " --> pdb=" O GLN A 685 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 687 " --> pdb=" O SER C 679 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N MET A 684 " --> pdb=" O ASN B 694 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLN B 696 " --> pdb=" O MET A 684 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 686 " --> pdb=" O GLN B 696 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP A 711 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N SER C 706 " --> pdb=" O ASP A 711 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN A 713 " --> pdb=" O SER C 706 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 710 " --> pdb=" O THR B 720 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N SER B 722 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 712 " --> pdb=" O SER B 722 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 493 through 497 removed outlier: 6.712A pdb=" N GLN C 526 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU C 546 " --> pdb=" O GLN C 526 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN C 528 " --> pdb=" O ALA C 544 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA C 544 " --> pdb=" O ASN C 528 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY C 530 " --> pdb=" O GLU C 542 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU C 542 " --> pdb=" O GLY C 530 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN C 532 " --> pdb=" O ARG C 540 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 552 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER B 563 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE A 554 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE B 560 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N HIS B 629 " --> pdb=" O ILE B 560 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE B 562 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG A 643 " --> pdb=" O MET C 636 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N SER C 638 " --> pdb=" O ARG A 643 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA A 645 " --> pdb=" O SER C 638 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE A 667 " --> pdb=" O SER B 676 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU B 678 " --> pdb=" O PHE A 667 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A 669 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL B 675 " --> pdb=" O GLN C 685 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU C 687 " --> pdb=" O VAL B 675 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU B 677 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 693 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N SER B 705 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 695 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR A 720 " --> pdb=" O ILE C 712 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N SER C 714 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER A 722 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 719 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ALA B 730 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 721 " --> pdb=" O ALA B 730 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 743 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS C 754 " --> pdb=" O ILE B 743 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 745 " --> pdb=" O LYS C 754 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 493 through 497 removed outlier: 6.791A pdb=" N GLN B 526 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 546 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN B 528 " --> pdb=" O ALA B 544 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA B 544 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY B 530 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU B 542 " --> pdb=" O GLY B 530 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN B 532 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N TRP C 551 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU B 542 " --> pdb=" O TRP C 551 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER C 553 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA B 544 " --> pdb=" O SER C 553 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ARG C 555 " --> pdb=" O ALA B 544 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 546 " --> pdb=" O ARG C 555 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY A 559 " --> pdb=" O ILE C 552 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE C 554 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE A 561 " --> pdb=" O ILE C 554 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLY C 556 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER A 563 " --> pdb=" O GLY C 556 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 560 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N HIS A 629 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 562 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 651 " --> pdb=" O ASP B 660 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THR B 662 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 653 " --> pdb=" O THR B 662 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET B 684 " --> pdb=" O ASN C 694 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLN C 696 " --> pdb=" O MET B 684 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 686 " --> pdb=" O GLN C 696 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU A 726 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL C 721 " --> pdb=" O GLU A 726 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 728 " --> pdb=" O VAL C 721 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA C 723 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 730 " --> pdb=" O ALA C 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 783 through 784 Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 9 removed outlier: 4.322A pdb=" N TYR D 4 " --> pdb=" O ALA D 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP D 8 " --> pdb=" O LYS D 28 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS D 28 " --> pdb=" O ASP D 8 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N CYS D 185 " --> pdb=" O PRO D 31 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG D 33 " --> pdb=" O CYS D 185 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA D 187 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL D 35 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE D 189 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D 37 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N PHE D 191 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE D 39 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL D 193 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE D 41 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLY D 195 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE D 43 " --> pdb=" O GLY D 195 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N GLU D 237 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE D 189 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG D 239 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE D 191 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU D 241 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL D 193 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU D 243 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY D 195 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N LEU D 304 " --> pdb=" O VAL D 279 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN D 281 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU D 306 " --> pdb=" O GLN D 281 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N THR D 283 " --> pdb=" O LEU D 306 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 805 through 809 removed outlier: 3.501A pdb=" N VAL A 829 " --> pdb=" O ARG A 797 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 799 " --> pdb=" O VAL A 827 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 783 through 784 removed outlier: 3.807A pdb=" N ALA E 27 " --> pdb=" O THR B 784 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 4 through 9 removed outlier: 4.307A pdb=" N TYR E 4 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE E 184 " --> pdb=" O PRO E 31 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG E 33 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE E 186 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL E 35 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS E 188 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N GLU E 237 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE E 189 " --> pdb=" O GLU E 237 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ARG E 239 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE E 191 " --> pdb=" O ARG E 239 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU E 241 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL E 193 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU E 243 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY E 195 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU E 304 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN E 281 " --> pdb=" O LEU E 304 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU E 306 " --> pdb=" O GLN E 281 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N THR E 283 " --> pdb=" O LEU E 306 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 805 through 809 removed outlier: 3.620A pdb=" N VAL B 829 " --> pdb=" O ARG B 797 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 783 through 785 removed outlier: 3.673A pdb=" N ALA F 27 " --> pdb=" O THR C 784 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 9 removed outlier: 4.252A pdb=" N TYR F 4 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS F 28 " --> pdb=" O ASP F 8 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N CYS F 185 " --> pdb=" O PRO F 31 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARG F 33 " --> pdb=" O CYS F 185 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ALA F 187 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL F 35 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE F 189 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU F 37 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE F 191 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE F 39 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL F 193 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE F 41 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLY F 195 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE F 43 " --> pdb=" O GLY F 195 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N GLU F 237 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE F 189 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG F 239 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE F 191 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU F 241 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL F 193 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU F 243 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY F 195 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N LYS F 278 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG F 239 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE F 280 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU F 241 " --> pdb=" O PHE F 280 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE F 282 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU F 243 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ALA F 284 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LEU F 304 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN F 281 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU F 306 " --> pdb=" O GLN F 281 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR F 283 " --> pdb=" O LEU F 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 795 through 799 Processing sheet with id=AB4, first strand: chain 'C' and resid 826 through 827 removed outlier: 3.545A pdb=" N HIS F 14 " --> pdb=" O VAL C 826 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 294 through 295 removed outlier: 6.345A pdb=" N LEU D 294 " --> pdb=" O TRP D 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 328 through 331 Processing sheet with id=AB7, first strand: chain 'D' and resid 328 through 331 removed outlier: 4.419A pdb=" N GLN D 398 " --> pdb=" O VAL D 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 495 through 497 Processing sheet with id=AB9, first strand: chain 'D' and resid 500 through 502 Processing sheet with id=AC1, first strand: chain 'E' and resid 294 through 295 removed outlier: 6.431A pdb=" N LEU E 294 " --> pdb=" O TRP E 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 328 through 331 removed outlier: 3.595A pdb=" N GLU E 336 " --> pdb=" O ALA E 403 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 328 through 331 removed outlier: 4.421A pdb=" N GLN E 398 " --> pdb=" O VAL E 386 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 495 through 497 Processing sheet with id=AC5, first strand: chain 'E' and resid 500 through 502 Processing sheet with id=AC6, first strand: chain 'F' and resid 294 through 295 removed outlier: 6.310A pdb=" N LEU F 294 " --> pdb=" O TRP F 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 328 through 331 Processing sheet with id=AC8, first strand: chain 'F' and resid 328 through 331 removed outlier: 4.599A pdb=" N GLN F 398 " --> pdb=" O VAL F 386 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 495 through 497 Processing sheet with id=AD1, first strand: chain 'F' and resid 500 through 502 810 hydrogen bonds defined for protein. 2250 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.68 Time building geometry restraints manager: 8.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4813 1.32 - 1.44: 3715 1.44 - 1.57: 11096 1.57 - 1.69: 0 1.69 - 1.81: 165 Bond restraints: 19789 Sorted by residual: bond pdb=" CB ARG B 547 " pdb=" CG ARG B 547 " ideal model delta sigma weight residual 1.520 1.440 0.080 3.00e-02 1.11e+03 7.09e+00 bond pdb=" CB ARG A 547 " pdb=" CG ARG A 547 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.12e+00 bond pdb=" C SER D 197 " pdb=" N ARG D 198 " ideal model delta sigma weight residual 1.333 1.299 0.034 1.41e-02 5.03e+03 5.93e+00 bond pdb=" CG ARG B 547 " pdb=" CD ARG B 547 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.84e+00 bond pdb=" C SER E 197 " pdb=" N ARG E 198 " ideal model delta sigma weight residual 1.333 1.299 0.034 1.41e-02 5.03e+03 5.77e+00 ... (remaining 19784 not shown) Histogram of bond angle deviations from ideal: 95.40 - 103.58: 261 103.58 - 111.77: 9273 111.77 - 119.95: 7924 119.95 - 128.13: 9112 128.13 - 136.32: 143 Bond angle restraints: 26713 Sorted by residual: angle pdb=" C ALA F 411 " pdb=" N VAL F 412 " pdb=" CA VAL F 412 " ideal model delta sigma weight residual 122.59 119.08 3.51 7.20e-01 1.93e+00 2.38e+01 angle pdb=" C GLU B 812 " pdb=" N ASN B 813 " pdb=" CA ASN B 813 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.07e+01 angle pdb=" N ARG D 198 " pdb=" CA ARG D 198 " pdb=" C ARG D 198 " ideal model delta sigma weight residual 114.75 109.19 5.56 1.26e+00 6.30e-01 1.95e+01 angle pdb=" N ARG E 198 " pdb=" CA ARG E 198 " pdb=" C ARG E 198 " ideal model delta sigma weight residual 114.75 109.35 5.40 1.26e+00 6.30e-01 1.83e+01 angle pdb=" C LYS E 29 " pdb=" N LYS E 30 " pdb=" CA LYS E 30 " ideal model delta sigma weight residual 121.59 136.32 -14.73 3.54e+00 7.98e-02 1.73e+01 ... (remaining 26708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10764 17.96 - 35.93: 943 35.93 - 53.89: 182 53.89 - 71.85: 46 71.85 - 89.81: 12 Dihedral angle restraints: 11947 sinusoidal: 4777 harmonic: 7170 Sorted by residual: dihedral pdb=" CA ASP A 811 " pdb=" C ASP A 811 " pdb=" N GLU A 812 " pdb=" CA GLU A 812 " ideal model delta harmonic sigma weight residual 180.00 147.36 32.64 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA VAL D 24 " pdb=" C VAL D 24 " pdb=" N VAL D 25 " pdb=" CA VAL D 25 " ideal model delta harmonic sigma weight residual 180.00 150.91 29.09 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ARG D 198 " pdb=" C ARG D 198 " pdb=" N GLY D 199 " pdb=" CA GLY D 199 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 11944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2276 0.064 - 0.128: 625 0.128 - 0.193: 59 0.193 - 0.257: 0 0.257 - 0.321: 2 Chirality restraints: 2962 Sorted by residual: chirality pdb=" CG LEU A 783 " pdb=" CB LEU A 783 " pdb=" CD1 LEU A 783 " pdb=" CD2 LEU A 783 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE C 823 " pdb=" CA ILE C 823 " pdb=" CG1 ILE C 823 " pdb=" CG2 ILE C 823 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU A 642 " pdb=" CB LEU A 642 " pdb=" CD1 LEU A 642 " pdb=" CD2 LEU A 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 2959 not shown) Planarity restraints: 3524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 81 " 0.029 2.00e-02 2.50e+03 2.99e-02 1.56e+01 pdb=" CG PHE E 81 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE E 81 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE E 81 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE E 81 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE E 81 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE E 81 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 81 " 0.032 2.00e-02 2.50e+03 2.95e-02 1.53e+01 pdb=" CG PHE F 81 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE F 81 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE F 81 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 81 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 81 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE F 81 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 81 " -0.026 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE D 81 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE D 81 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE D 81 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 81 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE D 81 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 81 " -0.002 2.00e-02 2.50e+03 ... (remaining 3521 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 216 2.57 - 3.15: 16243 3.15 - 3.73: 31551 3.73 - 4.32: 49900 4.32 - 4.90: 79453 Nonbonded interactions: 177363 Sorted by model distance: nonbonded pdb=" NH2 ARG D 422 " pdb=" O LEU D 445 " model vdw 1.985 2.520 nonbonded pdb=" NH2 ARG E 422 " pdb=" O LEU E 445 " model vdw 2.050 2.520 nonbonded pdb=" NH2 ARG F 422 " pdb=" O LEU F 445 " model vdw 2.050 2.520 nonbonded pdb=" O ARG A 640 " pdb=" OG SER B 646 " model vdw 2.088 2.440 nonbonded pdb=" O ARG B 640 " pdb=" OG SER C 646 " model vdw 2.110 2.440 ... (remaining 177358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 3 through 133 or resid 143 through 539)) selection = (chain 'F' and (resid 3 through 133 or resid 143 through 539)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 12174 2.51 5 N 3455 2.21 5 O 3734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.720 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.160 Process input model: 54.090 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.013 0.124 19789 Z= 0.865 Angle : 0.866 14.729 26713 Z= 0.481 Chirality : 0.055 0.321 2962 Planarity : 0.005 0.045 3524 Dihedral : 14.603 89.815 7353 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.74 % Favored : 94.06 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.14), residues: 2507 helix: -1.54 (0.17), residues: 621 sheet: -1.80 (0.22), residues: 418 loop : -2.08 (0.14), residues: 1468 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 2.423 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 1.5847 time to fit residues: 467.3109 Evaluate side-chains 186 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.305 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN A 583 GLN A 605 GLN A 694 ASN A 696 GLN B 502 ASN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 HIS B 583 GLN B 615 ASN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 GLN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 ASN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 GLN C 571 GLN C 583 GLN C 615 ASN C 813 ASN D 49 ASN D 76 GLN D 179 ASN D 208 ASN D 213 GLN D 281 GLN D 295 ASN D 370 HIS D 487 HIS D 493 ASN D 512 HIS E 14 HIS E 76 GLN E 179 ASN E 190 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN E 213 GLN E 281 GLN E 286 ASN E 370 HIS E 429 GLN E 442 ASN E 446 GLN E 472 GLN E 487 HIS E 493 ASN E 512 HIS F 20 ASN F 76 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 GLN ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN F 213 GLN F 281 GLN F 286 ASN F 487 HIS F 493 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 19789 Z= 0.228 Angle : 0.587 11.723 26713 Z= 0.317 Chirality : 0.045 0.229 2962 Planarity : 0.004 0.045 3524 Dihedral : 6.100 30.729 2711 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.16), residues: 2507 helix: 0.17 (0.19), residues: 633 sheet: -1.38 (0.22), residues: 432 loop : -1.59 (0.16), residues: 1442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 233 time to evaluate : 2.411 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 17 residues processed: 260 average time/residue: 1.4593 time to fit residues: 424.0850 Evaluate side-chains 210 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 2.288 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.7463 time to fit residues: 6.8094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 0.0000 chunk 190 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 chunk 247 optimal weight: 0.0040 chunk 204 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN A 707 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 49 ASN D 123 GLN E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 19789 Z= 0.355 Angle : 0.603 7.455 26713 Z= 0.325 Chirality : 0.045 0.222 2962 Planarity : 0.004 0.106 3524 Dihedral : 6.069 29.621 2711 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2507 helix: 0.74 (0.20), residues: 633 sheet: -1.14 (0.22), residues: 452 loop : -1.42 (0.16), residues: 1422 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 198 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 30 residues processed: 238 average time/residue: 1.3774 time to fit residues: 370.2186 Evaluate side-chains 212 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 182 time to evaluate : 2.317 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 22 residues processed: 8 average time/residue: 0.7027 time to fit residues: 10.0519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 6.9990 chunk 172 optimal weight: 0.4980 chunk 118 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 230 optimal weight: 0.9990 chunk 243 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 218 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN B 725 GLN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 49 ASN D 123 GLN E 170 GLN E 429 GLN E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 19789 Z= 0.197 Angle : 0.547 12.795 26713 Z= 0.293 Chirality : 0.044 0.214 2962 Planarity : 0.003 0.039 3524 Dihedral : 5.661 31.810 2711 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.16), residues: 2507 helix: 1.25 (0.20), residues: 633 sheet: -0.86 (0.23), residues: 432 loop : -1.35 (0.16), residues: 1442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 207 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 27 residues processed: 248 average time/residue: 1.3831 time to fit residues: 386.2174 Evaluate side-chains 213 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 2.478 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 6 average time/residue: 0.9820 time to fit residues: 10.2343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 61 optimal weight: 0.0470 overall best weight: 1.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN B 725 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 791 GLN D 49 ASN E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN E 469 GLN E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 19789 Z= 0.407 Angle : 0.617 7.125 26713 Z= 0.329 Chirality : 0.046 0.236 2962 Planarity : 0.004 0.107 3524 Dihedral : 5.936 29.056 2711 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.23 % Favored : 94.73 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 2507 helix: 1.23 (0.20), residues: 633 sheet: -0.84 (0.23), residues: 437 loop : -1.31 (0.16), residues: 1437 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 194 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 39 residues processed: 237 average time/residue: 1.3453 time to fit residues: 361.1941 Evaluate side-chains 224 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 185 time to evaluate : 2.311 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 31 residues processed: 8 average time/residue: 0.6522 time to fit residues: 9.6797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 243 optimal weight: 0.6980 chunk 202 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN B 750 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 49 ASN E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.132 19789 Z= 0.267 Angle : 0.584 13.716 26713 Z= 0.313 Chirality : 0.044 0.212 2962 Planarity : 0.004 0.045 3524 Dihedral : 5.737 30.317 2711 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.16), residues: 2507 helix: 1.42 (0.20), residues: 633 sheet: -0.71 (0.23), residues: 431 loop : -1.28 (0.16), residues: 1443 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 194 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 37 residues processed: 239 average time/residue: 1.3307 time to fit residues: 360.2255 Evaluate side-chains 225 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 2.498 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 31 residues processed: 6 average time/residue: 0.7163 time to fit residues: 8.5357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 242 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 49 ASN D 106 ASN E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN E 469 GLN E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.114 19789 Z= 0.206 Angle : 0.539 9.129 26713 Z= 0.289 Chirality : 0.043 0.210 2962 Planarity : 0.004 0.121 3524 Dihedral : 5.512 29.945 2711 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2507 helix: 1.72 (0.20), residues: 627 sheet: -0.57 (0.23), residues: 431 loop : -1.27 (0.16), residues: 1449 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 204 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 36 residues processed: 249 average time/residue: 1.3407 time to fit residues: 377.2506 Evaluate side-chains 227 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 2.535 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 30 residues processed: 6 average time/residue: 0.7376 time to fit residues: 8.8669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN B 750 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 49 ASN D 286 ASN E 5 GLN E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 HIS E 429 GLN E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 19789 Z= 0.316 Angle : 0.583 6.990 26713 Z= 0.310 Chirality : 0.044 0.213 2962 Planarity : 0.004 0.056 3524 Dihedral : 5.686 28.674 2711 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2507 helix: 1.57 (0.20), residues: 632 sheet: -0.57 (0.23), residues: 431 loop : -1.23 (0.16), residues: 1444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 194 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 36 residues processed: 232 average time/residue: 1.4677 time to fit residues: 384.8916 Evaluate side-chains 225 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 189 time to evaluate : 2.320 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 28 residues processed: 8 average time/residue: 0.7427 time to fit residues: 10.4312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.5980 chunk 212 optimal weight: 6.9990 chunk 226 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 49 ASN E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN F 170 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.451 19789 Z= 0.392 Angle : 0.791 73.891 26713 Z= 0.379 Chirality : 0.045 0.252 2962 Planarity : 0.004 0.068 3524 Dihedral : 5.689 28.664 2711 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2507 helix: 1.54 (0.20), residues: 632 sheet: -0.55 (0.24), residues: 431 loop : -1.23 (0.16), residues: 1444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 190 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 39 residues processed: 226 average time/residue: 1.3952 time to fit residues: 355.6480 Evaluate side-chains 229 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 190 time to evaluate : 2.274 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 31 residues processed: 8 average time/residue: 0.6729 time to fit residues: 9.7641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 49 ASN E 5 GLN E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.451 19789 Z= 0.393 Angle : 0.796 73.891 26713 Z= 0.385 Chirality : 0.045 0.252 2962 Planarity : 0.004 0.126 3524 Dihedral : 5.689 28.664 2711 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2507 helix: 1.54 (0.20), residues: 632 sheet: -0.55 (0.24), residues: 431 loop : -1.23 (0.16), residues: 1444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 31 residues processed: 222 average time/residue: 1.4282 time to fit residues: 359.2284 Evaluate side-chains 220 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 2.493 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 31 residues processed: 0 time to fit residues: 3.3673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 49 ASN E 5 GLN E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.156083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.098083 restraints weight = 19464.688| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.65 r_work: 0.3184 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work: 0.3146 rms_B_bonded: 1.51 restraints_weight: 0.1250 r_work: 0.3125 rms_B_bonded: 1.64 restraints_weight: 0.0625 r_work: 0.3101 rms_B_bonded: 1.84 restraints_weight: 0.0312 r_work: 0.3073 rms_B_bonded: 2.10 restraints_weight: 0.0156 r_work: 0.3041 rms_B_bonded: 2.46 restraints_weight: 0.0078 r_work: 0.3004 rms_B_bonded: 2.91 restraints_weight: 0.0039 r_work: 0.2959 rms_B_bonded: 3.51 restraints_weight: 0.0020 r_work: 0.2907 rms_B_bonded: 4.28 restraints_weight: 0.0010 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.451 19789 Z= 0.393 Angle : 0.796 73.786 26713 Z= 0.385 Chirality : 0.045 0.251 2962 Planarity : 0.004 0.125 3524 Dihedral : 5.689 28.664 2711 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2507 helix: 1.54 (0.20), residues: 632 sheet: -0.55 (0.24), residues: 431 loop : -1.23 (0.16), residues: 1444 =============================================================================== Job complete usr+sys time: 6286.75 seconds wall clock time: 113 minutes 2.87 seconds (6782.87 seconds total)