Starting phenix.real_space_refine on Sat Mar 16 02:03:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s59_10099/03_2024/6s59_10099_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s59_10099/03_2024/6s59_10099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s59_10099/03_2024/6s59_10099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s59_10099/03_2024/6s59_10099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s59_10099/03_2024/6s59_10099_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s59_10099/03_2024/6s59_10099_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 66 5.16 5 C 8429 2.51 5 N 2312 2.21 5 O 2582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "B ARG 734": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13397 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 6545 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 318} Link IDs: {'PTRANS': 51, 'TRANS': 981} Chain breaks: 1 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1098 Unresolved non-hydrogen angles: 1393 Unresolved non-hydrogen dihedrals: 903 Unresolved non-hydrogen chiralities: 113 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 6, 'TYR:plan': 10, 'ASN:plan1': 14, 'ASP:plan': 18, 'PHE:plan': 18, 'GLU:plan': 23, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 514 Chain: "B" Number of atoms: 6543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 6543 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 318} Link IDs: {'PTRANS': 51, 'TRANS': 981} Chain breaks: 1 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1103 Unresolved non-hydrogen angles: 1404 Unresolved non-hydrogen dihedrals: 909 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 6, 'TYR:plan': 10, 'ASN:plan1': 14, 'ASP:plan': 18, 'PHE:plan': 18, 'GLU:plan': 23, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 515 Chain: "A" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 149 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 67 Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 160 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 56 Time building chain proxies: 7.67, per 1000 atoms: 0.57 Number of scatterers: 13397 At special positions: 0 Unit cell: (141.12, 125.16, 127.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 8 15.00 O 2582 8.00 N 2312 7.00 C 8429 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: 4.98 Conformation dependent library (CDL) restraints added in 2.7 seconds 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3674 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 8 sheets defined 49.5% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 11 through 13 No H-bonds generated for 'chain 'A' and resid 11 through 13' Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.683A pdb=" N GLN A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 33 through 37' Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 74 through 77 No H-bonds generated for 'chain 'A' and resid 74 through 77' Processing helix chain 'A' and resid 98 through 101 No H-bonds generated for 'chain 'A' and resid 98 through 101' Processing helix chain 'A' and resid 118 through 124 Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 251 through 266 removed outlier: 4.134A pdb=" N LYS A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 291 No H-bonds generated for 'chain 'A' and resid 288 through 291' Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 412 through 421 removed outlier: 4.236A pdb=" N GLU A 416 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 420 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 421 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 448 removed outlier: 3.886A pdb=" N VAL A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 473 removed outlier: 3.704A pdb=" N VAL A 473 " --> pdb=" O GLY A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 500 removed outlier: 3.746A pdb=" N SER A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY A 493 " --> pdb=" O ASN A 489 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR A 495 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ALA A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 540 removed outlier: 3.611A pdb=" N ALA A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 519 " --> pdb=" O GLY A 515 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N THR A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 571 removed outlier: 3.574A pdb=" N TYR A 555 " --> pdb=" O ASN A 552 " (cutoff:3.500A) Proline residue: A 558 - end of helix removed outlier: 3.574A pdb=" N VAL A 563 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 564 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 568 " --> pdb=" O GLY A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 594 removed outlier: 4.136A pdb=" N LEU A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 592 " --> pdb=" O CYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 623 removed outlier: 4.438A pdb=" N GLY A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU A 623 " --> pdb=" O THR A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 646 removed outlier: 3.534A pdb=" N ALA A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 681 Proline residue: A 657 - end of helix removed outlier: 4.071A pdb=" N LEU A 666 " --> pdb=" O PHE A 663 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 671 " --> pdb=" O GLY A 668 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS A 675 " --> pdb=" O VAL A 672 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE A 676 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 677 " --> pdb=" O THR A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 691 through 720 removed outlier: 3.704A pdb=" N THR A 695 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LYS A 696 " --> pdb=" O ASN A 693 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 706 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE A 710 " --> pdb=" O GLY A 707 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY A 712 " --> pdb=" O THR A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 752 removed outlier: 4.361A pdb=" N ILE A 749 " --> pdb=" O SER A 745 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ILE A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Proline residue: A 751 - end of helix Processing helix chain 'A' and resid 758 through 781 removed outlier: 3.932A pdb=" N ILE A 762 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS A 764 " --> pdb=" O THR A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 810 removed outlier: 3.755A pdb=" N ILE A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR A 793 " --> pdb=" O PRO A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 836 removed outlier: 4.128A pdb=" N ILE A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET A 833 " --> pdb=" O LEU A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 845 No H-bonds generated for 'chain 'A' and resid 842 through 845' Processing helix chain 'A' and resid 871 through 879 removed outlier: 3.690A pdb=" N ASP A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 895 removed outlier: 3.522A pdb=" N ALA A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 911 removed outlier: 3.541A pdb=" N ALA A 902 " --> pdb=" O GLN A 898 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP A 903 " --> pdb=" O TYR A 899 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 904 " --> pdb=" O PRO A 900 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN A 911 " --> pdb=" O MET A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 937 removed outlier: 3.732A pdb=" N LEU A 933 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 950 No H-bonds generated for 'chain 'A' and resid 947 through 950' Processing helix chain 'A' and resid 972 through 975 No H-bonds generated for 'chain 'A' and resid 972 through 975' Processing helix chain 'A' and resid 1026 through 1038 removed outlier: 3.802A pdb=" N ALA A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 60 through 66 Processing helix chain 'B' and resid 74 through 77 No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 142 through 145 removed outlier: 4.312A pdb=" N GLY B 145 " --> pdb=" O ILE B 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 145' Processing helix chain 'B' and resid 148 through 164 Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 251 through 266 removed outlier: 3.673A pdb=" N LYS B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 292 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 338 through 356 removed outlier: 4.070A pdb=" N ALA B 355 " --> pdb=" O LYS B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 Processing helix chain 'B' and resid 412 through 421 Processing helix chain 'B' and resid 425 through 448 removed outlier: 4.127A pdb=" N THR B 429 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 472 Processing helix chain 'B' and resid 478 through 480 No H-bonds generated for 'chain 'B' and resid 478 through 480' Processing helix chain 'B' and resid 482 through 500 removed outlier: 4.111A pdb=" N SER B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 493 " --> pdb=" O ASN B 489 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR B 495 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA B 496 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL B 497 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 541 removed outlier: 4.174A pdb=" N VAL B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET B 541 " --> pdb=" O ARG B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 572 removed outlier: 3.559A pdb=" N LEU B 556 " --> pdb=" O TYR B 553 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 557 " --> pdb=" O LEU B 554 " (cutoff:3.500A) Proline residue: B 558 - end of helix removed outlier: 3.559A pdb=" N THR B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 563 " --> pdb=" O GLY B 560 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY B 564 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 568 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 572 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 593 removed outlier: 3.890A pdb=" N LEU B 582 " --> pdb=" O GLN B 578 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 592 " --> pdb=" O CYS B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 623 removed outlier: 4.341A pdb=" N GLY B 608 " --> pdb=" O GLY B 604 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 623 " --> pdb=" O THR B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 647 removed outlier: 3.689A pdb=" N MET B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 681 Proline residue: B 657 - end of helix removed outlier: 3.501A pdb=" N ALA B 661 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 664 " --> pdb=" O ALA B 661 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 677 " --> pdb=" O THR B 674 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 681 " --> pdb=" O GLU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 721 Processing helix chain 'B' and resid 735 through 749 removed outlier: 4.255A pdb=" N ILE B 749 " --> pdb=" O SER B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 765 removed outlier: 3.626A pdb=" N THR B 763 " --> pdb=" O THR B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 781 Processing helix chain 'B' and resid 790 through 810 removed outlier: 3.725A pdb=" N LEU B 795 " --> pdb=" O VAL B 791 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN B 796 " --> pdb=" O ILE B 792 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 809 " --> pdb=" O ALA B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 836 removed outlier: 3.653A pdb=" N SER B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 871 through 878 Processing helix chain 'B' and resid 890 through 895 removed outlier: 3.997A pdb=" N ALA B 895 " --> pdb=" O GLY B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 911 removed outlier: 4.052A pdb=" N GLU B 910 " --> pdb=" O LYS B 906 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN B 911 " --> pdb=" O MET B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 937 Processing helix chain 'B' and resid 947 through 950 No H-bonds generated for 'chain 'B' and resid 947 through 950' Processing helix chain 'B' and resid 972 through 975 No H-bonds generated for 'chain 'B' and resid 972 through 975' Processing helix chain 'B' and resid 1026 through 1041 removed outlier: 3.568A pdb=" N TYR B1041 " --> pdb=" O VAL B1037 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 15 through 18 removed outlier: 6.758A pdb=" N ASN A 45 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL A 18 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL A 47 " --> pdb=" O VAL A 18 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.274A pdb=" N THR A 130 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N SER A 110 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU A 132 " --> pdb=" O SER A 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 187 through 190 removed outlier: 6.356A pdb=" N ILE A 270 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL A 190 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 272 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL A 299 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N SER A 273 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL A 301 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 916 through 918 removed outlier: 7.112A pdb=" N LEU A 959 " --> pdb=" O ILE A 885 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N THR A 887 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU A 961 " --> pdb=" O THR A 887 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLN A 994 " --> pdb=" O VAL A 960 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL A 962 " --> pdb=" O GLN A 994 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 996 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 15 through 18 removed outlier: 6.148A pdb=" N ASN B 45 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 18 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 47 " --> pdb=" O VAL B 18 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.887A pdb=" N THR B 130 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N SER B 110 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 132 " --> pdb=" O SER B 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 187 through 190 removed outlier: 6.336A pdb=" N ILE B 270 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 190 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE B 272 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 299 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N SER B 273 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B 301 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR B 326 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASP B 302 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE B 328 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 320 " --> pdb=" O HIS B 327 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 915 through 917 removed outlier: 6.320A pdb=" N ILE B 884 " --> pdb=" O ARG B 916 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU B 959 " --> pdb=" O ILE B 885 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N THR B 887 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU B 961 " --> pdb=" O THR B 887 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN B 994 " --> pdb=" O VAL B 960 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL B 962 " --> pdb=" O GLN B 994 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE B 996 " --> pdb=" O VAL B 962 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 625 hydrogen bonds defined for protein. 1629 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: 4.37 Time building geometry restraints manager: 5.41 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: 2356 1.32 - 1.44: 3062 1.44 - 1.57: 8001 1.57 - 1.69: 16 1.69 - 1.81: 113 Bond restraints: 13548 Sorted by residual: bond pdb=" O13 PC1 B1101 " pdb=" P PC1 B1101 " ideal model delta sigma weight residual 1.652 1.590 0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" O13 PC1 A1103 " pdb=" P PC1 A1103 " ideal model delta sigma weight residual 1.652 1.593 0.059 2.00e-02 2.50e+03 8.64e+00 bond pdb=" O13 PC1 B1102 " pdb=" P PC1 B1102 " ideal model delta sigma weight residual 1.652 1.593 0.059 2.00e-02 2.50e+03 8.59e+00 bond pdb=" O13 PC1 A1101 " pdb=" P PC1 A1101 " ideal model delta sigma weight residual 1.652 1.594 0.058 2.00e-02 2.50e+03 8.50e+00 bond pdb=" O13 PC1 A1102 " pdb=" P PC1 A1102 " ideal model delta sigma weight residual 1.652 1.597 0.055 2.00e-02 2.50e+03 7.57e+00 ... (remaining 13543 not shown) Histogram of bond angle deviations from ideal: 96.47 - 104.08: 241 104.08 - 111.68: 6212 111.68 - 119.29: 5089 119.29 - 126.90: 6862 126.90 - 134.50: 96 Bond angle restraints: 18500 Sorted by residual: angle pdb=" N LEU A 730 " pdb=" CA LEU A 730 " pdb=" C LEU A 730 " ideal model delta sigma weight residual 109.54 116.41 -6.87 1.37e+00 5.33e-01 2.52e+01 angle pdb=" C ILE A 392 " pdb=" N PHE A 393 " pdb=" CA PHE A 393 " ideal model delta sigma weight residual 120.09 126.24 -6.15 1.25e+00 6.40e-01 2.42e+01 angle pdb=" C THR B 597 " pdb=" N GLN B 598 " pdb=" CA GLN B 598 " ideal model delta sigma weight residual 121.54 130.32 -8.78 1.91e+00 2.74e-01 2.11e+01 angle pdb=" N PHE B 954 " pdb=" CA PHE B 954 " pdb=" C PHE B 954 " ideal model delta sigma weight residual 109.81 119.15 -9.34 2.21e+00 2.05e-01 1.78e+01 angle pdb=" C ALA B 38 " pdb=" N LEU B 39 " pdb=" CA LEU B 39 " ideal model delta sigma weight residual 121.54 129.48 -7.94 1.91e+00 2.74e-01 1.73e+01 ... (remaining 18495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 7575 17.12 - 34.25: 333 34.25 - 51.37: 75 51.37 - 68.49: 22 68.49 - 85.62: 11 Dihedral angle restraints: 8016 sinusoidal: 2234 harmonic: 5782 Sorted by residual: dihedral pdb=" CA MET B 788 " pdb=" C MET B 788 " pdb=" N PRO B 789 " pdb=" CA PRO B 789 " ideal model delta harmonic sigma weight residual -180.00 -153.69 -26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA VAL B 473 " pdb=" C VAL B 473 " pdb=" N TRP B 474 " pdb=" CA TRP B 474 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA PHE B 752 " pdb=" C PHE B 752 " pdb=" N MET B 753 " pdb=" CA MET B 753 " ideal model delta harmonic sigma weight residual 180.00 155.51 24.49 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 8013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1613 0.059 - 0.118: 535 0.118 - 0.177: 120 0.177 - 0.236: 6 0.236 - 0.295: 1 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CB VAL A 922 " pdb=" CA VAL A 922 " pdb=" CG1 VAL A 922 " pdb=" CG2 VAL A 922 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA PHE B 954 " pdb=" N PHE B 954 " pdb=" C PHE B 954 " pdb=" CB PHE B 954 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL B 791 " pdb=" CA VAL B 791 " pdb=" CG1 VAL B 791 " pdb=" CG2 VAL B 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2272 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 482 " 0.049 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO B 483 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 483 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 483 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B1011 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO B1012 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B1012 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B1012 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1011 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO A1012 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A1012 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1012 " -0.032 5.00e-02 4.00e+02 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3552 2.79 - 3.32: 12301 3.32 - 3.84: 21616 3.84 - 4.37: 22800 4.37 - 4.90: 39878 Nonbonded interactions: 100147 Sorted by model distance: nonbonded pdb=" O ASN A 838 " pdb=" OG1 THR A 851 " model vdw 2.262 2.440 nonbonded pdb=" O ALA B 662 " pdb=" OG SER B 665 " model vdw 2.295 2.440 nonbonded pdb=" OH TYR B 683 " pdb=" O PRO B 756 " model vdw 2.297 2.440 nonbonded pdb=" O LYS B1036 " pdb=" OG SER B1040 " model vdw 2.303 2.440 nonbonded pdb=" OH TYR A 683 " pdb=" O PRO A 756 " model vdw 2.325 2.440 ... (remaining 100142 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' and (resid 5 through 470 or (resid 471 and (name N or name CA or name \ C or name O or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or res \ id 472 through 594 or (resid 595 and (name N or name CA or name C or name O or n \ ame CG or name CD1 or name CD2)) or resid 596 through 803 or (resid 804 and (nam \ e N or name CA or name C or name O or name SG )) or resid 805 through 1042 or re \ sid 1101 or (resid 1102 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ O31 or name O32 or name P )) or resid 1103 or (resid 1104 and (name N or name C \ 1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name \ C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or \ name C28 or name C29 or name C2A or name C2B or name C3 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C3A or name C3B or name C3C or name O11 or name O12 or name O13 or n \ ame O14 or name O21 or name O22 or name O31 or name O32 or name P )))) selection = (chain 'B' and (resid 5 through 466 or (resid 467 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CD1)) or resid 468 through 1042 or r \ esid 1101 through 1102 or (resid 1103 and (name N or name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C3 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name O11 or name O \ 12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or na \ me P )) or (resid 1104 and (name N or name C1 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C2A or \ name C2B or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 \ or name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name \ C3C or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or n \ ame O31 or name O32 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 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: 0.010 Extract box with map and model: 1.680 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 38.600 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.008 0.082 13548 Z= 0.555 Angle : 1.023 10.252 18500 Z= 0.527 Chirality : 0.059 0.295 2275 Planarity : 0.007 0.073 2420 Dihedral : 11.928 85.616 4342 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.63 % Allowed : 5.42 % Favored : 93.95 % 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: -4.12 (0.14), residues: 2058 helix: -2.30 (0.12), residues: 1024 sheet: -2.44 (0.35), residues: 163 loop : -3.26 (0.17), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP A 801 HIS 0.015 0.003 HIS A 664 PHE 0.032 0.003 PHE A 562 TYR 0.027 0.003 TYR A1015 ARG 0.008 0.001 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 238 time to evaluate : 1.548 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 416 GLU cc_start: 0.7424 (mp0) cc_final: 0.7117 (tt0) REVERT: A 552 ASN cc_start: 0.8908 (p0) cc_final: 0.8529 (p0) REVERT: A 595 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9109 (pp) REVERT: A 693 ASN cc_start: 0.8173 (t0) cc_final: 0.7968 (m-40) REVERT: A 754 MET cc_start: 0.7312 (tmt) cc_final: 0.7111 (tmt) REVERT: A 926 MET cc_start: 0.8630 (ttp) cc_final: 0.8363 (ttt) REVERT: B 441 THR cc_start: 0.8309 (t) cc_final: 0.8088 (p) REVERT: B 709 THR cc_start: 0.9421 (m) cc_final: 0.9056 (t) REVERT: B 756 PRO cc_start: 0.8257 (Cg_endo) cc_final: 0.7994 (Cg_exo) REVERT: B 913 LYS cc_start: 0.8116 (mttm) cc_final: 0.7893 (mttp) REVERT: B 947 MET cc_start: 0.9252 (ttp) cc_final: 0.8960 (ttp) REVERT: B 981 ILE cc_start: 0.9401 (mm) cc_final: 0.9150 (mm) REVERT: B 994 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8694 (mp10) outliers start: 6 outliers final: 0 residues processed: 242 average time/residue: 0.2049 time to fit residues: 76.9478 Evaluate side-chains 176 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 40.0000 chunk 83 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 120 optimal weight: 40.0000 chunk 187 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN B 552 ASN B 658 GLN B 721 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13548 Z= 0.184 Angle : 0.579 11.175 18500 Z= 0.296 Chirality : 0.044 0.174 2275 Planarity : 0.005 0.047 2420 Dihedral : 9.573 89.159 2395 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.23 % Allowed : 11.89 % Favored : 84.88 % 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: -2.14 (0.17), residues: 2058 helix: -0.28 (0.16), residues: 1020 sheet: -1.94 (0.38), residues: 161 loop : -2.73 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 801 HIS 0.005 0.001 HIS B 481 PHE 0.014 0.001 PHE A 752 TYR 0.026 0.001 TYR B 683 ARG 0.002 0.000 ARG B1038 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 212 time to evaluate : 1.511 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 416 GLU cc_start: 0.7253 (mp0) cc_final: 0.6869 (tt0) REVERT: A 550 GLU cc_start: 0.8403 (pp20) cc_final: 0.7991 (mp0) REVERT: A 693 ASN cc_start: 0.8123 (t0) cc_final: 0.7842 (m-40) REVERT: A 754 MET cc_start: 0.7351 (tmt) cc_final: 0.7149 (tmt) REVERT: B 503 MET cc_start: 0.7776 (ttm) cc_final: 0.7446 (ttp) REVERT: B 890 TYR cc_start: 0.8133 (t80) cc_final: 0.7434 (t80) REVERT: B 903 ASP cc_start: 0.7973 (p0) cc_final: 0.7716 (p0) REVERT: B 913 LYS cc_start: 0.7987 (mttm) cc_final: 0.7622 (mttm) REVERT: B 925 ARG cc_start: 0.8552 (mtm180) cc_final: 0.8000 (mtm180) outliers start: 31 outliers final: 17 residues processed: 231 average time/residue: 0.2007 time to fit residues: 72.7430 Evaluate side-chains 197 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 978 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 50.0000 chunk 58 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 127 optimal weight: 50.0000 chunk 51 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 185 optimal weight: 6.9990 chunk 63 optimal weight: 30.0000 chunk 150 optimal weight: 4.9990 overall best weight: 10.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13548 Z= 0.428 Angle : 0.717 9.434 18500 Z= 0.363 Chirality : 0.048 0.183 2275 Planarity : 0.005 0.059 2420 Dihedral : 9.924 83.983 2393 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.69 % Allowed : 16.68 % Favored : 78.62 % 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: -1.54 (0.18), residues: 2058 helix: 0.10 (0.16), residues: 1037 sheet: -1.57 (0.40), residues: 153 loop : -2.31 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 801 HIS 0.006 0.002 HIS B 920 PHE 0.019 0.002 PHE B 562 TYR 0.025 0.002 TYR B 704 ARG 0.005 0.001 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 181 time to evaluate : 1.430 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 519 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9131 (pt) REVERT: A 552 ASN cc_start: 0.8936 (p0) cc_final: 0.8478 (p0) REVERT: A 589 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8850 (p) REVERT: A 693 ASN cc_start: 0.8283 (t0) cc_final: 0.7965 (m-40) REVERT: A 724 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8512 (tt) REVERT: A 754 MET cc_start: 0.7341 (tmt) cc_final: 0.6876 (tmt) REVERT: A 1041 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7351 (m-10) REVERT: B 903 ASP cc_start: 0.7995 (p0) cc_final: 0.7703 (p0) REVERT: B 913 LYS cc_start: 0.8022 (mttm) cc_final: 0.7704 (mttm) outliers start: 45 outliers final: 27 residues processed: 208 average time/residue: 0.2073 time to fit residues: 68.8799 Evaluate side-chains 199 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 168 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 978 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 1.9990 chunk 140 optimal weight: 50.0000 chunk 97 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 125 optimal weight: 50.0000 chunk 188 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 178 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13548 Z= 0.311 Angle : 0.628 9.420 18500 Z= 0.315 Chirality : 0.045 0.181 2275 Planarity : 0.004 0.063 2420 Dihedral : 9.734 86.821 2393 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.53 % Allowed : 16.79 % Favored : 77.69 % 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: -1.11 (0.19), residues: 2058 helix: 0.47 (0.17), residues: 1036 sheet: -1.52 (0.40), residues: 161 loop : -2.10 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 801 HIS 0.004 0.001 HIS B 664 PHE 0.017 0.002 PHE B 562 TYR 0.020 0.002 TYR B 704 ARG 0.003 0.001 ARG B1038 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 180 time to evaluate : 1.465 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 550 GLU cc_start: 0.8565 (pp20) cc_final: 0.8084 (mp0) REVERT: A 589 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8843 (p) REVERT: A 693 ASN cc_start: 0.8303 (t0) cc_final: 0.7916 (m-40) REVERT: A 754 MET cc_start: 0.7342 (tmt) cc_final: 0.6876 (tmt) REVERT: A 1041 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7275 (m-10) REVERT: B 647 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8604 (tp) REVERT: B 745 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8207 (p) REVERT: B 925 ARG cc_start: 0.8633 (mtm180) cc_final: 0.7968 (mtm180) REVERT: B 981 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9293 (mt) REVERT: B 1014 PHE cc_start: 0.9305 (t80) cc_final: 0.9065 (m-80) outliers start: 53 outliers final: 34 residues processed: 211 average time/residue: 0.1920 time to fit residues: 64.6041 Evaluate side-chains 210 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 171 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 745 SER Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 956 ASP Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 984 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 1.9990 chunk 113 optimal weight: 50.0000 chunk 2 optimal weight: 50.0000 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 chunk 137 optimal weight: 50.0000 chunk 0 optimal weight: 90.0000 chunk 101 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 489 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13548 Z= 0.182 Angle : 0.563 11.081 18500 Z= 0.276 Chirality : 0.043 0.181 2275 Planarity : 0.004 0.062 2420 Dihedral : 9.286 89.530 2393 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.11 % Allowed : 18.46 % Favored : 76.43 % 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: -0.62 (0.20), residues: 2058 helix: 0.94 (0.17), residues: 1025 sheet: -1.19 (0.42), residues: 161 loop : -1.94 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 990 HIS 0.003 0.001 HIS B 481 PHE 0.012 0.001 PHE B 562 TYR 0.020 0.001 TYR B 704 ARG 0.002 0.000 ARG B1038 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 188 time to evaluate : 1.650 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 589 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8820 (p) REVERT: A 651 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8672 (tt) REVERT: A 693 ASN cc_start: 0.8318 (t0) cc_final: 0.7906 (m-40) REVERT: A 754 MET cc_start: 0.7360 (tmt) cc_final: 0.6994 (tmt) REVERT: A 1041 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7268 (m-10) REVERT: B 458 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8591 (mpp) REVERT: B 538 MET cc_start: 0.8777 (ttm) cc_final: 0.8401 (mtp) REVERT: B 745 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8177 (p) REVERT: B 903 ASP cc_start: 0.7845 (p0) cc_final: 0.7610 (p0) REVERT: B 925 ARG cc_start: 0.8557 (mtm180) cc_final: 0.7870 (mtm180) REVERT: B 946 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: B 981 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9267 (mt) outliers start: 49 outliers final: 27 residues processed: 221 average time/residue: 0.1940 time to fit residues: 68.7985 Evaluate side-chains 213 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 745 SER Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain B residue 877 MET Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 956 ASP Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 981 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 39 optimal weight: 30.0000 chunk 116 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 199 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 40.0000 chunk 65 optimal weight: 10.0000 chunk 104 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13548 Z= 0.265 Angle : 0.606 15.530 18500 Z= 0.297 Chirality : 0.044 0.175 2275 Planarity : 0.004 0.059 2420 Dihedral : 9.366 89.978 2393 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.21 % Allowed : 19.29 % Favored : 75.50 % 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: -0.42 (0.20), residues: 2058 helix: 1.08 (0.17), residues: 1025 sheet: -1.05 (0.42), residues: 161 loop : -1.82 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 801 HIS 0.004 0.001 HIS B 920 PHE 0.012 0.001 PHE B 710 TYR 0.019 0.001 TYR B 704 ARG 0.002 0.000 ARG B1038 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 181 time to evaluate : 1.460 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 589 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8813 (p) REVERT: A 651 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8713 (tt) REVERT: A 693 ASN cc_start: 0.8295 (t0) cc_final: 0.7885 (m-40) REVERT: A 754 MET cc_start: 0.7339 (tmt) cc_final: 0.6883 (tmt) REVERT: A 1041 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7323 (m-10) REVERT: B 458 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8655 (mpp) REVERT: B 903 ASP cc_start: 0.7893 (p0) cc_final: 0.7578 (p0) REVERT: B 946 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8234 (tt0) outliers start: 50 outliers final: 38 residues processed: 217 average time/residue: 0.1917 time to fit residues: 67.1850 Evaluate side-chains 217 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 174 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 877 MET Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 956 ASP Chi-restraints excluded: chain B residue 978 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 1.9990 chunk 22 optimal weight: 50.0000 chunk 113 optimal weight: 50.0000 chunk 145 optimal weight: 6.9990 chunk 112 optimal weight: 50.0000 chunk 167 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 121 optimal weight: 50.0000 chunk 91 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13548 Z= 0.194 Angle : 0.574 14.097 18500 Z= 0.277 Chirality : 0.043 0.165 2275 Planarity : 0.004 0.059 2420 Dihedral : 9.078 87.518 2393 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.90 % Allowed : 19.60 % Favored : 75.50 % 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: -0.19 (0.20), residues: 2058 helix: 1.24 (0.17), residues: 1024 sheet: -0.50 (0.44), residues: 151 loop : -1.76 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 990 HIS 0.003 0.001 HIS B 481 PHE 0.010 0.001 PHE B 562 TYR 0.020 0.001 TYR B 704 ARG 0.002 0.000 ARG B1038 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 187 time to evaluate : 1.505 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 589 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8796 (p) REVERT: A 693 ASN cc_start: 0.8324 (t0) cc_final: 0.7903 (m-40) REVERT: A 754 MET cc_start: 0.7396 (tmt) cc_final: 0.6967 (tmt) REVERT: A 1041 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7354 (m-10) REVERT: B 458 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8600 (mpp) REVERT: B 538 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8436 (mtp) REVERT: B 913 LYS cc_start: 0.7853 (mttp) cc_final: 0.7578 (mttm) REVERT: B 946 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8140 (tt0) outliers start: 47 outliers final: 36 residues processed: 217 average time/residue: 0.1989 time to fit residues: 69.0453 Evaluate side-chains 220 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 179 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain B residue 877 MET Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 956 ASP Chi-restraints excluded: chain B residue 978 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 50.0000 chunk 79 optimal weight: 7.9990 chunk 118 optimal weight: 40.0000 chunk 59 optimal weight: 9.9990 chunk 39 optimal weight: 40.0000 chunk 38 optimal weight: 50.0000 chunk 126 optimal weight: 50.0000 chunk 135 optimal weight: 50.0000 chunk 98 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13548 Z= 0.393 Angle : 0.686 13.746 18500 Z= 0.340 Chirality : 0.047 0.201 2275 Planarity : 0.004 0.063 2420 Dihedral : 9.554 89.025 2393 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 6.26 % Allowed : 19.92 % Favored : 73.83 % 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: -0.37 (0.20), residues: 2058 helix: 1.04 (0.17), residues: 1014 sheet: -0.75 (0.44), residues: 152 loop : -1.71 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 990 HIS 0.005 0.001 HIS B 920 PHE 0.018 0.002 PHE B 710 TYR 0.019 0.002 TYR B 704 ARG 0.003 0.001 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 175 time to evaluate : 1.531 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 552 ASN cc_start: 0.8924 (p0) cc_final: 0.8332 (p0) REVERT: A 589 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8813 (p) REVERT: A 693 ASN cc_start: 0.8321 (t0) cc_final: 0.7899 (m-40) REVERT: A 1041 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7362 (m-10) REVERT: B 538 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8532 (mtp) REVERT: B 566 TYR cc_start: 0.8299 (t80) cc_final: 0.8053 (t80) REVERT: B 946 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8315 (tt0) outliers start: 60 outliers final: 40 residues processed: 217 average time/residue: 0.1904 time to fit residues: 66.2812 Evaluate side-chains 213 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 169 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 877 MET Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 956 ASP Chi-restraints excluded: chain B residue 978 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 80 optimal weight: 0.0010 chunk 145 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 167 optimal weight: 0.5980 chunk 174 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 overall best weight: 2.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13548 Z= 0.162 Angle : 0.577 12.475 18500 Z= 0.278 Chirality : 0.043 0.214 2275 Planarity : 0.004 0.065 2420 Dihedral : 9.001 85.147 2393 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.80 % Allowed : 21.38 % Favored : 73.83 % 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: -0.06 (0.20), residues: 2058 helix: 1.31 (0.17), residues: 1019 sheet: -0.69 (0.44), residues: 160 loop : -1.57 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 990 HIS 0.003 0.001 HIS B 481 PHE 0.009 0.001 PHE A 562 TYR 0.021 0.001 TYR B 849 ARG 0.007 0.000 ARG A1038 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 188 time to evaluate : 1.448 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 550 GLU cc_start: 0.8577 (pp20) cc_final: 0.8248 (mp0) REVERT: A 589 VAL cc_start: 0.9085 (OUTLIER) cc_final: 0.8781 (p) REVERT: A 693 ASN cc_start: 0.8312 (t0) cc_final: 0.7865 (m-40) REVERT: A 754 MET cc_start: 0.7401 (tmt) cc_final: 0.6990 (tmt) REVERT: A 988 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7925 (mt-10) REVERT: A 1041 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7325 (m-10) REVERT: B 458 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8572 (mpp) REVERT: B 538 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8387 (mtp) REVERT: B 903 ASP cc_start: 0.8000 (p0) cc_final: 0.7726 (p0) REVERT: B 925 ARG cc_start: 0.8509 (mtm180) cc_final: 0.7906 (mtm180) REVERT: B 946 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8112 (tt0) outliers start: 46 outliers final: 35 residues processed: 218 average time/residue: 0.1894 time to fit residues: 66.9442 Evaluate side-chains 219 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 179 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain B residue 877 MET Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 956 ASP Chi-restraints excluded: chain B residue 978 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 50.0000 chunk 195 optimal weight: 4.9990 chunk 119 optimal weight: 30.0000 chunk 92 optimal weight: 8.9990 chunk 136 optimal weight: 50.0000 chunk 205 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 16 optimal weight: 50.0000 chunk 126 optimal weight: 40.0000 chunk 100 optimal weight: 7.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13548 Z= 0.332 Angle : 0.660 12.693 18500 Z= 0.324 Chirality : 0.046 0.193 2275 Planarity : 0.004 0.064 2420 Dihedral : 9.291 88.268 2393 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.01 % Allowed : 21.38 % Favored : 73.62 % 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: -0.16 (0.20), residues: 2058 helix: 1.23 (0.17), residues: 1011 sheet: -0.68 (0.44), residues: 157 loop : -1.60 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 990 HIS 0.005 0.001 HIS B 920 PHE 0.017 0.002 PHE B 710 TYR 0.019 0.002 TYR B 704 ARG 0.006 0.001 ARG A1038 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 172 time to evaluate : 1.475 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 589 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8820 (p) REVERT: A 693 ASN cc_start: 0.8302 (t0) cc_final: 0.7879 (m-40) REVERT: A 988 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8103 (mt-10) REVERT: A 1041 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7341 (m-10) REVERT: B 458 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8657 (mpp) REVERT: B 538 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8680 (mtp) REVERT: B 566 TYR cc_start: 0.8190 (t80) cc_final: 0.7977 (t80) REVERT: B 903 ASP cc_start: 0.8082 (p0) cc_final: 0.7811 (p0) REVERT: B 925 ARG cc_start: 0.8541 (mtm180) cc_final: 0.7908 (mtm180) REVERT: B 946 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8224 (tt0) outliers start: 48 outliers final: 41 residues processed: 203 average time/residue: 0.2056 time to fit residues: 67.5758 Evaluate side-chains 216 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 170 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 877 MET Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 956 ASP Chi-restraints excluded: chain B residue 978 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 30.0000 chunk 174 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 20 optimal weight: 50.0000 chunk 30 optimal weight: 40.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.144751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121172 restraints weight = 34044.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.122336 restraints weight = 22205.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122493 restraints weight = 15967.647| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13548 Z= 0.180 Angle : 0.586 12.287 18500 Z= 0.283 Chirality : 0.044 0.200 2275 Planarity : 0.004 0.066 2420 Dihedral : 8.923 84.174 2393 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.80 % Allowed : 21.79 % Favored : 73.41 % 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: 0.01 (0.20), residues: 2058 helix: 1.34 (0.17), residues: 1024 sheet: -0.56 (0.44), residues: 158 loop : -1.52 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 990 HIS 0.003 0.001 HIS B 481 PHE 0.011 0.001 PHE A 562 TYR 0.020 0.001 TYR B 704 ARG 0.007 0.000 ARG A1038 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2359.41 seconds wall clock time: 44 minutes 49.02 seconds (2689.02 seconds total)