Starting phenix.real_space_refine on Thu Jul 31 09:53:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s59_10099/07_2025/6s59_10099.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s59_10099/07_2025/6s59_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/cci-nas-00/data/ceres_data/6s59_10099/07_2025/6s59_10099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s59_10099/07_2025/6s59_10099.map" model { file = "/net/cci-nas-00/data/ceres_data/6s59_10099/07_2025/6s59_10099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s59_10099/07_2025/6s59_10099.cif" } 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. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.29, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 2.0 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... Secondary structure from input PDB file: 86 helices and 12 sheets defined 55.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 10 through 13 Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.683A pdb=" N GLN A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 59 through 66 Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'A' and resid 147 through 165 removed outlier: 4.197A pdb=" N ALA A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 207 Processing helix chain 'A' and resid 216 through 226 Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 337 through 357 removed outlier: 3.924A pdb=" N SER A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 424 through 449 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 452 through 474 removed outlier: 4.027A pdb=" N SER A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 473 " --> pdb=" O GLY A 469 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP A 474 " --> pdb=" O TYR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 492 removed outlier: 3.625A pdb=" N LEU A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 496 through 501 removed outlier: 3.580A pdb=" N VAL A 501 " --> pdb=" O VAL A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 539 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 551 through 554 Processing helix chain 'A' and resid 555 through 572 removed outlier: 3.663A pdb=" N ALA A 559 " --> pdb=" O TYR A 555 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 595 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) removed outlier: 3.871A pdb=" N LEU A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 622 removed outlier: 4.438A pdb=" N GLY A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 647 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 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 655 through 682 removed outlier: 4.247A pdb=" N LEU A 659 " --> pdb=" O ASP A 655 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 667 " --> pdb=" O PHE A 663 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 676 " --> pdb=" O VAL A 672 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 686 removed outlier: 3.628A pdb=" N PHE A 686 " --> pdb=" O TYR A 683 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 683 through 686' Processing helix chain 'A' and resid 691 through 721 removed outlier: 3.852A pdb=" N LYS A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 711 " --> pdb=" O GLY A 707 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 713 " --> pdb=" O THR A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.574A pdb=" N PHE A 752 " --> pdb=" O GLY A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 3.557A pdb=" N GLY A 761 " --> pdb=" O SER A 757 " (cutoff:3.500A) 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) removed outlier: 3.876A pdb=" N ALA A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 811 removed outlier: 4.265A pdb=" N VAL A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) 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 812 through 837 removed outlier: 4.263A pdb=" N THR A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) 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 841 through 846 Processing helix chain 'A' and resid 870 through 880 removed outlier: 3.835A pdb=" N ALA A 874 " --> pdb=" O ASN A 870 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 894 removed outlier: 4.098A pdb=" N CYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 4.002A pdb=" N ILE A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 928 through 938 removed outlier: 4.121A pdb=" N VAL A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) 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 946 through 951 Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'A' and resid 1025 through 1039 removed outlier: 3.802A pdb=" N ALA A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 38 removed outlier: 3.969A pdb=" N ALA B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 removed outlier: 3.621A pdb=" N TYR B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.665A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 78' Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 141 through 146 removed outlier: 4.312A pdb=" N GLY B 145 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 removed outlier: 4.023A pdb=" N ALA B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 207 Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 250 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 287 through 293 Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 337 through 357 removed outlier: 4.070A pdb=" N ALA B 355 " --> pdb=" O LYS B 351 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 383 Processing helix chain 'B' and resid 411 through 422 Processing helix chain 'B' and resid 424 through 449 removed outlier: 3.828A pdb=" N LYS B 428 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR B 429 " --> pdb=" O PRO B 425 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 473 removed outlier: 3.783A pdb=" N SER B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 473 " --> pdb=" O GLY B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 479 No H-bonds generated for 'chain 'B' and resid 477 through 479' Processing helix chain 'B' and resid 480 through 492 removed outlier: 3.709A pdb=" N LEU B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 501 removed outlier: 3.689A pdb=" N VAL B 501 " --> pdb=" O VAL B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 540 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) Processing helix chain 'B' and resid 552 through 554 No H-bonds generated for 'chain 'B' and resid 552 through 554' Processing helix chain 'B' and resid 555 through 571 removed outlier: 3.588A pdb=" N ALA B 559 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 594 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 602 through 622 removed outlier: 4.341A pdb=" N GLY B 608 " --> pdb=" O GLY B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 648 removed outlier: 4.086A pdb=" N GLN B 632 " --> pdb=" O GLU B 628 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 654 No H-bonds generated for 'chain 'B' and resid 652 through 654' Processing helix chain 'B' and resid 655 through 682 removed outlier: 4.090A pdb=" N LEU B 659 " --> pdb=" O ASP B 655 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 665 " --> pdb=" O ALA B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 722 removed outlier: 3.540A pdb=" N GLY B 722 " --> pdb=" O GLY B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 748 Processing helix chain 'B' and resid 757 through 766 removed outlier: 3.626A pdb=" N THR B 763 " --> pdb=" O THR B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 782 removed outlier: 4.164A pdb=" N ALA B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 811 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 812 through 835 removed outlier: 3.699A pdb=" N THR B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 846 removed outlier: 3.729A pdb=" N LEU B 846 " --> pdb=" O ALA B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 879 removed outlier: 3.558A pdb=" N ALA B 874 " --> pdb=" O ASN B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 894 Processing helix chain 'B' and resid 898 through 910 removed outlier: 4.052A pdb=" N GLU B 910 " --> pdb=" O LYS B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 938 removed outlier: 3.855A pdb=" N VAL B 932 " --> pdb=" O GLY B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 951 Processing helix chain 'B' and resid 966 through 970 removed outlier: 3.924A pdb=" N ASN B 970 " --> pdb=" O ASP B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 976 removed outlier: 3.814A pdb=" N GLU B 975 " --> pdb=" O SER B 971 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 976 " --> pdb=" O ALA B 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 971 through 976' Processing helix chain 'B' and resid 1025 through 1042 removed outlier: 3.568A pdb=" N TYR B1041 " --> pdb=" O VAL B1037 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.513A pdb=" N VAL A 47 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 46 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.662A pdb=" N LEU A 108 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.957A pdb=" N ILE A 96 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 210 removed outlier: 6.871A pdb=" N SER A 298 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE A 328 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 300 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 387 Processing sheet with id=AA6, first strand: chain 'A' and resid 944 through 945 removed outlier: 5.797A pdb=" N PHE A 917 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE A 885 " --> pdb=" O LEU A 961 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE A 963 " --> pdb=" O ILE A 885 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR A 887 " --> pdb=" O ILE A 963 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 960 " --> pdb=" O ILE A 996 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N MET A 998 " --> pdb=" O VAL A 960 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL A 962 " --> pdb=" O MET A 998 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 18 Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 110 removed outlier: 5.814A pdb=" N LEU B 108 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA B 133 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL B 384 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 177 removed outlier: 4.118A pdb=" N THR B 177 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 180 " --> pdb=" O THR B 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 209 through 210 removed outlier: 6.077A pdb=" N LEU B 271 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 300 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP B 302 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 944 through 945 removed outlier: 8.363A pdb=" N LEU B 945 " --> pdb=" O VAL B 915 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE B 917 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE B 885 " --> pdb=" O LEU B 961 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE B 963 " --> pdb=" O ILE B 885 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR B 887 " --> pdb=" O ILE B 963 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B1022 " --> pdb=" O VAL B 995 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL B 997 " --> pdb=" O LEU B1022 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 2187 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: 5.14 Time building geometry restraints manager: 4.15 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: 0.00 - 2.05: 17589 2.05 - 4.10: 715 4.10 - 6.15: 136 6.15 - 8.20: 47 8.20 - 10.25: 13 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: 3530 2.79 - 3.32: 12176 3.32 - 3.84: 21506 3.84 - 4.37: 22604 4.37 - 4.90: 39843 Nonbonded interactions: 99659 Sorted by model distance: nonbonded pdb=" O ASN A 838 " pdb=" OG1 THR A 851 " model vdw 2.262 3.040 nonbonded pdb=" O ALA B 662 " pdb=" OG SER B 665 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR B 683 " pdb=" O PRO B 756 " model vdw 2.297 3.040 nonbonded pdb=" O LYS B1036 " pdb=" OG SER B1040 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR A 683 " pdb=" O PRO A 756 " model vdw 2.325 3.040 ... (remaining 99654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '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: 0.280 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: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.490 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.410 ------------------------------------------------------------------------------- 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= 0.354 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 Details of bonding type rmsd hydrogen bonds : bond 0.15046 ( 747) hydrogen bonds : angle 6.31036 ( 2187) covalent geometry : bond 0.00827 (13548) covalent geometry : angle 1.02286 (18500) *********************** 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 to be fit. rotamer outliers: 6 poor density : 238 time to evaluate : 1.358 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: 0.2081 time to fit residues: 77.9674 Evaluate side-chains 176 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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: 0.9990 chunk 156 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 50.0000 chunk 83 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 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 721 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.146264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.123291 restraints weight = 33984.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123983 restraints weight = 24125.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124016 restraints weight = 19703.995| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13548 Z= 0.131 Angle : 0.600 9.444 18500 Z= 0.307 Chirality : 0.044 0.196 2275 Planarity : 0.005 0.048 2420 Dihedral : 9.651 88.241 2395 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.40 % Allowed : 11.78 % Favored : 85.82 % 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: -2.06 (0.18), residues: 2058 helix: -0.31 (0.15), residues: 1052 sheet: -2.16 (0.36), residues: 166 loop : -2.57 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 801 HIS 0.005 0.001 HIS B 664 PHE 0.017 0.002 PHE B 562 TYR 0.027 0.002 TYR B 683 ARG 0.003 0.001 ARG B1038 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 747) hydrogen bonds : angle 4.37093 ( 2187) covalent geometry : bond 0.00285 (13548) covalent geometry : angle 0.59973 (18500) *********************** 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 236 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 2.361 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. REVERT: A 552 ASN cc_start: 0.8628 (p0) cc_final: 0.8000 (p0) REVERT: A 595 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9110 (pp) REVERT: B 701 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9021 (tp) REVERT: B 745 SER cc_start: 0.8289 (t) cc_final: 0.7453 (p) REVERT: B 890 TYR cc_start: 0.7801 (t80) cc_final: 0.6858 (t80) REVERT: B 1019 THR cc_start: 0.8763 (m) cc_final: 0.8553 (p) outliers start: 23 outliers final: 11 residues processed: 226 average time/residue: 0.2152 time to fit residues: 76.3615 Evaluate side-chains 193 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 701 LEU 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 A residue 1019 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 791 VAL 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 183 optimal weight: 7.9990 chunk 13 optimal weight: 50.0000 chunk 159 optimal weight: 8.9990 chunk 142 optimal weight: 0.0070 chunk 105 optimal weight: 50.0000 chunk 157 optimal weight: 0.0980 chunk 112 optimal weight: 0.0570 chunk 30 optimal weight: 50.0000 chunk 60 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 overall best weight: 2.4320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 489 ASN B 552 ASN B 952 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.147517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.125200 restraints weight = 34150.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125713 restraints weight = 25305.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126052 restraints weight = 18816.580| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13548 Z= 0.112 Angle : 0.556 9.639 18500 Z= 0.278 Chirality : 0.043 0.194 2275 Planarity : 0.004 0.062 2420 Dihedral : 9.184 89.275 2395 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.44 % Allowed : 15.02 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 2058 helix: 0.60 (0.16), residues: 1061 sheet: -1.71 (0.37), residues: 169 loop : -2.21 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 801 HIS 0.006 0.001 HIS B 952 PHE 0.025 0.001 PHE B 562 TYR 0.024 0.001 TYR B 704 ARG 0.003 0.000 ARG B1038 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 747) hydrogen bonds : angle 3.92430 ( 2187) covalent geometry : bond 0.00245 (13548) covalent geometry : angle 0.55592 (18500) *********************** 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 235 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 1.679 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: 0.8633 (p0) cc_final: 0.8104 (m-40) REVERT: A 595 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9090 (pp) REVERT: A 1041 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.7066 (m-10) REVERT: B 745 SER cc_start: 0.8413 (t) cc_final: 0.7587 (p) outliers start: 33 outliers final: 18 residues processed: 223 average time/residue: 0.2154 time to fit residues: 76.4207 Evaluate side-chains 205 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 595 LEU 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 754 MET Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain B residue 952 HIS 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 189 optimal weight: 20.0000 chunk 122 optimal weight: 50.0000 chunk 162 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 141 optimal weight: 50.0000 chunk 181 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 175 optimal weight: 30.0000 chunk 179 optimal weight: 20.0000 chunk 160 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN B 952 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.144729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122300 restraints weight = 34062.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122094 restraints weight = 24874.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122423 restraints weight = 19857.255| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13548 Z= 0.184 Angle : 0.608 8.716 18500 Z= 0.305 Chirality : 0.045 0.145 2275 Planarity : 0.004 0.059 2420 Dihedral : 9.305 87.776 2395 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.28 % Allowed : 16.37 % Favored : 79.35 % 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: -0.61 (0.19), residues: 2058 helix: 0.95 (0.16), residues: 1064 sheet: -1.63 (0.38), residues: 168 loop : -1.98 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 801 HIS 0.019 0.002 HIS B 952 PHE 0.021 0.002 PHE B 562 TYR 0.023 0.002 TYR B 704 ARG 0.003 0.001 ARG B1038 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 747) hydrogen bonds : angle 3.94317 ( 2187) covalent geometry : bond 0.00426 (13548) covalent geometry : angle 0.60786 (18500) *********************** 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 224 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 1.424 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 446 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8895 (tt) REVERT: A 595 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9151 (pp) REVERT: A 724 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8051 (tt) REVERT: A 731 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8368 (tp) REVERT: A 1041 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.7034 (m-10) REVERT: B 745 SER cc_start: 0.8584 (t) cc_final: 0.7686 (p) REVERT: B 1014 PHE cc_start: 0.8442 (t80) cc_final: 0.7985 (m-80) outliers start: 41 outliers final: 24 residues processed: 208 average time/residue: 0.1962 time to fit residues: 65.1911 Evaluate side-chains 204 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 620 LEU 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 731 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 854 THR 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 526 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 978 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 59 optimal weight: 10.0000 chunk 188 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 98 optimal weight: 0.0980 chunk 124 optimal weight: 50.0000 chunk 70 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 134 optimal weight: 0.9980 chunk 197 optimal weight: 0.0970 overall best weight: 3.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 866 HIS ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.146115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.123485 restraints weight = 34197.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123547 restraints weight = 26179.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123911 restraints weight = 19547.874| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13548 Z= 0.128 Angle : 0.570 9.081 18500 Z= 0.282 Chirality : 0.044 0.152 2275 Planarity : 0.004 0.065 2420 Dihedral : 9.192 89.612 2395 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.86 % Allowed : 17.21 % Favored : 78.94 % 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: -0.26 (0.20), residues: 2058 helix: 1.25 (0.16), residues: 1064 sheet: -1.44 (0.38), residues: 168 loop : -1.83 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 801 HIS 0.004 0.001 HIS B 664 PHE 0.019 0.001 PHE B 562 TYR 0.020 0.001 TYR B 704 ARG 0.002 0.000 ARG A 879 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 747) hydrogen bonds : angle 3.79715 ( 2187) covalent geometry : bond 0.00293 (13548) covalent geometry : angle 0.56956 (18500) *********************** 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 226 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 1.189 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. REVERT: A 446 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8854 (tt) REVERT: A 595 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9142 (pp) REVERT: A 724 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8033 (tt) REVERT: A 731 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8282 (tp) REVERT: A 1041 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.7049 (m-10) REVERT: B 458 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7202 (mpp) REVERT: B 745 SER cc_start: 0.8504 (t) cc_final: 0.7610 (p) REVERT: B 1014 PHE cc_start: 0.8379 (t80) cc_final: 0.7958 (m-80) outliers start: 37 outliers final: 21 residues processed: 211 average time/residue: 0.2369 time to fit residues: 81.7728 Evaluate side-chains 205 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 620 LEU 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 731 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain B residue 952 HIS Chi-restraints excluded: chain B residue 978 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 10 optimal weight: 50.0000 chunk 149 optimal weight: 8.9990 chunk 196 optimal weight: 0.0040 chunk 140 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 9 optimal weight: 30.0000 chunk 79 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 174 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 overall best weight: 3.7398 ------------------------------------------------------------------------------- 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** B 952 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.146234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122702 restraints weight = 35021.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.123093 restraints weight = 25757.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123650 restraints weight = 19239.232| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13548 Z= 0.127 Angle : 0.568 9.112 18500 Z= 0.281 Chirality : 0.044 0.152 2275 Planarity : 0.004 0.065 2420 Dihedral : 9.122 89.512 2395 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.59 % Allowed : 17.52 % Favored : 77.89 % 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: -0.04 (0.20), residues: 2058 helix: 1.43 (0.17), residues: 1064 sheet: -1.30 (0.39), residues: 168 loop : -1.75 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 801 HIS 0.012 0.001 HIS B 952 PHE 0.019 0.001 PHE B 562 TYR 0.020 0.001 TYR B 704 ARG 0.004 0.000 ARG B 916 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 747) hydrogen bonds : angle 3.72288 ( 2187) covalent geometry : bond 0.00294 (13548) covalent geometry : angle 0.56826 (18500) *********************** 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 232 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 1.415 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. REVERT: A 446 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8871 (tt) REVERT: A 595 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9119 (pp) REVERT: A 724 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8042 (tt) REVERT: A 731 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8256 (tp) REVERT: A 1041 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.7083 (m-10) REVERT: B 745 SER cc_start: 0.8469 (t) cc_final: 0.7602 (p) REVERT: B 946 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7039 (tt0) REVERT: B 1014 PHE cc_start: 0.8415 (t80) cc_final: 0.7944 (m-80) outliers start: 44 outliers final: 26 residues processed: 214 average time/residue: 0.1969 time to fit residues: 68.5046 Evaluate side-chains 212 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 620 LEU 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 731 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 854 THR 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 501 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 729 LEU 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 846 LEU Chi-restraints excluded: chain B residue 946 GLU 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 71 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 40.0000 chunk 154 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 17 optimal weight: 50.0000 chunk 45 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 88 optimal weight: 0.1980 overall best weight: 6.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.144285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117446 restraints weight = 35266.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119263 restraints weight = 20229.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120868 restraints weight = 15253.751| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13548 Z= 0.179 Angle : 0.613 8.919 18500 Z= 0.303 Chirality : 0.045 0.156 2275 Planarity : 0.004 0.065 2420 Dihedral : 9.271 89.930 2395 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.11 % Allowed : 18.25 % Favored : 76.64 % 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: 1.43 (0.17), residues: 1063 sheet: -1.26 (0.39), residues: 168 loop : -1.66 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 801 HIS 0.005 0.001 HIS B 664 PHE 0.019 0.002 PHE B 562 TYR 0.021 0.001 TYR B 704 ARG 0.003 0.000 ARG A 537 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 747) hydrogen bonds : angle 3.85299 ( 2187) covalent geometry : bond 0.00420 (13548) covalent geometry : angle 0.61303 (18500) *********************** 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 233 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 1.491 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. REVERT: A 595 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9151 (pp) REVERT: A 724 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8017 (tt) REVERT: A 731 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8234 (tp) REVERT: A 1041 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.7079 (m-10) REVERT: B 745 SER cc_start: 0.8524 (t) cc_final: 0.7668 (p) REVERT: B 946 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7038 (tt0) REVERT: B 1014 PHE cc_start: 0.8440 (t80) cc_final: 0.7911 (m-80) outliers start: 49 outliers final: 34 residues processed: 216 average time/residue: 0.1966 time to fit residues: 68.5193 Evaluate side-chains 219 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 667 VAL 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 731 LEU Chi-restraints excluded: chain A residue 754 MET 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 854 THR 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 441 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 729 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 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 978 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 95 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 177 optimal weight: 0.1980 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 122 optimal weight: 40.0000 chunk 56 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 ASN ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.144708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119035 restraints weight = 34508.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121083 restraints weight = 19905.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122426 restraints weight = 13740.504| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13548 Z= 0.117 Angle : 0.562 9.214 18500 Z= 0.276 Chirality : 0.043 0.152 2275 Planarity : 0.004 0.071 2420 Dihedral : 9.071 86.868 2395 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.48 % Allowed : 19.60 % Favored : 75.91 % 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: 0.24 (0.20), residues: 2058 helix: 1.64 (0.17), residues: 1068 sheet: -1.10 (0.39), residues: 168 loop : -1.61 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 990 HIS 0.004 0.001 HIS B 664 PHE 0.026 0.001 PHE B 562 TYR 0.022 0.001 TYR B 704 ARG 0.002 0.000 ARG B1038 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 747) hydrogen bonds : angle 3.61932 ( 2187) covalent geometry : bond 0.00269 (13548) covalent geometry : angle 0.56219 (18500) *********************** 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 to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 1.550 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. REVERT: A 595 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9137 (pp) REVERT: A 724 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8089 (tt) REVERT: A 731 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8155 (tp) REVERT: A 1041 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7019 (m-10) REVERT: B 745 SER cc_start: 0.8461 (t) cc_final: 0.7576 (p) REVERT: B 903 ASP cc_start: 0.7379 (p0) cc_final: 0.7075 (p0) REVERT: B 946 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6964 (tt0) REVERT: B 1014 PHE cc_start: 0.8370 (t80) cc_final: 0.7900 (m-80) outliers start: 43 outliers final: 31 residues processed: 220 average time/residue: 0.2517 time to fit residues: 90.0006 Evaluate side-chains 220 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 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 570 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 645 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 731 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 854 THR 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 501 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 763 THR 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 892 LEU Chi-restraints excluded: chain B residue 946 GLU 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 103 optimal weight: 60.0000 chunk 168 optimal weight: 9.9990 chunk 97 optimal weight: 0.1980 chunk 80 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 101 optimal weight: 30.0000 chunk 203 optimal weight: 1.9990 chunk 202 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.147477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121527 restraints weight = 35201.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.123266 restraints weight = 20016.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124831 restraints weight = 15025.596| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13548 Z= 0.105 Angle : 0.550 9.272 18500 Z= 0.269 Chirality : 0.043 0.161 2275 Planarity : 0.004 0.071 2420 Dihedral : 8.894 85.242 2395 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.96 % Allowed : 20.33 % Favored : 75.70 % 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: 1.76 (0.17), residues: 1073 sheet: -0.90 (0.40), residues: 169 loop : -1.63 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 990 HIS 0.002 0.001 HIS B 481 PHE 0.018 0.001 PHE A 562 TYR 0.022 0.001 TYR B 704 ARG 0.002 0.000 ARG B1038 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 747) hydrogen bonds : angle 3.55247 ( 2187) covalent geometry : bond 0.00235 (13548) covalent geometry : angle 0.55035 (18500) *********************** 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 225 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.432 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. REVERT: A 595 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9114 (pp) REVERT: A 907 MET cc_start: 0.7493 (tpp) cc_final: 0.7220 (tpp) REVERT: A 1041 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.7022 (m-10) REVERT: B 745 SER cc_start: 0.8489 (t) cc_final: 0.7631 (p) REVERT: B 1014 PHE cc_start: 0.8393 (t80) cc_final: 0.7928 (m-80) outliers start: 38 outliers final: 27 residues processed: 209 average time/residue: 0.1815 time to fit residues: 61.6482 Evaluate side-chains 217 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR 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 570 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 645 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 730 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 763 THR 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 892 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 90 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 131 optimal weight: 40.0000 chunk 58 optimal weight: 5.9990 chunk 125 optimal weight: 50.0000 chunk 89 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 205 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.146027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120505 restraints weight = 35368.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122295 restraints weight = 21677.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.122616 restraints weight = 14181.822| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2929 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= 0.145 Angle : 0.603 9.804 18500 Z= 0.293 Chirality : 0.045 0.276 2275 Planarity : 0.004 0.066 2420 Dihedral : 9.018 85.592 2395 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.65 % Allowed : 21.17 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.40 (0.20), residues: 2058 helix: 1.73 (0.17), residues: 1069 sheet: -0.85 (0.40), residues: 169 loop : -1.53 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 801 HIS 0.003 0.001 HIS B 920 PHE 0.029 0.002 PHE B 562 TYR 0.022 0.001 TYR B 704 ARG 0.002 0.000 ARG B1038 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 747) hydrogen bonds : angle 3.68972 ( 2187) covalent geometry : bond 0.00341 (13548) covalent geometry : angle 0.60279 (18500) ********************** 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 223 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 1.537 Fit side-chains TARDY: cannot create tardy model for: "CYS B 804 " (corrupted residue). Skipping it. REVERT: A 595 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9118 (pp) REVERT: A 988 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6855 (mt-10) REVERT: A 1041 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.7097 (m-10) REVERT: B 645 LEU cc_start: 0.8530 (mt) cc_final: 0.8207 (tp) REVERT: B 745 SER cc_start: 0.8492 (t) cc_final: 0.7603 (p) REVERT: B 1014 PHE cc_start: 0.8439 (t80) cc_final: 0.7942 (m-80) outliers start: 35 outliers final: 32 residues processed: 209 average time/residue: 0.1867 time to fit residues: 63.3765 Evaluate side-chains 216 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 467 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 645 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 730 LEU Chi-restraints excluded: chain A residue 754 MET 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 854 THR Chi-restraints excluded: chain A residue 862 ILE 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 526 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 837 MET 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 892 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 134 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 chunk 109 optimal weight: 50.0000 chunk 27 optimal weight: 0.6980 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.145604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120533 restraints weight = 35723.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121564 restraints weight = 23413.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.122056 restraints weight = 16164.054| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13548 Z= 0.152 Angle : 0.605 8.980 18500 Z= 0.296 Chirality : 0.045 0.317 2275 Planarity : 0.004 0.066 2420 Dihedral : 9.092 85.127 2395 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.07 % Allowed : 21.27 % Favored : 74.66 % 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: 0.40 (0.20), residues: 2058 helix: 1.71 (0.17), residues: 1070 sheet: -0.87 (0.40), residues: 169 loop : -1.49 (0.24), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 801 HIS 0.003 0.001 HIS B 920 PHE 0.026 0.002 PHE B 562 TYR 0.022 0.001 TYR B 704 ARG 0.002 0.000 ARG B1038 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 747) hydrogen bonds : angle 3.71011 ( 2187) covalent geometry : bond 0.00357 (13548) covalent geometry : angle 0.60452 (18500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4368.56 seconds wall clock time: 79 minutes 6.12 seconds (4746.12 seconds total)