Starting phenix.real_space_refine on Fri Mar 15 17:26:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs7_33423/03_2024/7xs7_33423_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs7_33423/03_2024/7xs7_33423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs7_33423/03_2024/7xs7_33423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs7_33423/03_2024/7xs7_33423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs7_33423/03_2024/7xs7_33423_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs7_33423/03_2024/7xs7_33423_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 2 5.49 5 S 68 5.16 5 C 8190 2.51 5 N 1908 2.21 5 O 2102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B GLU 539": "OE1" <-> "OE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "B TYR 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 716": "OE1" <-> "OE2" Residue "B PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 794": "OE1" <-> "OE2" Residue "B PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1014": "OD1" <-> "OD2" Residue "B ASP 1016": "OD1" <-> "OD2" Residue "B PHE 1098": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A ASP 458": "OD1" <-> "OD2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A TYR 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 794": "OE1" <-> "OE2" Residue "A PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A PHE 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1016": "OD1" <-> "OD2" Residue "A ASP 1029": "OD1" <-> "OD2" Residue "A PHE 1098": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1125": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12270 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5867 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 706} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 5867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5867 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 706} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 268 Unusual residues: {'0V9': 1, 'C14': 8, 'D12': 5, 'HP6': 7} Classifications: {'undetermined': 21} Link IDs: {None: 20} Chain: "A" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 268 Unusual residues: {'0V9': 1, 'C14': 8, 'D12': 5, 'HP6': 7} Classifications: {'undetermined': 21} Link IDs: {None: 20} Time building chain proxies: 6.40, per 1000 atoms: 0.52 Number of scatterers: 12270 At special positions: 0 Unit cell: (138.92, 80.04, 115.92, 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 68 16.00 P 2 15.00 O 2102 8.00 N 1908 7.00 C 8190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.84 Conformation dependent library (CDL) restraints added in 1.9 seconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2780 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 10 sheets defined 48.1% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'B' and resid 393 through 400 removed outlier: 3.584A pdb=" N ASP B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 459 through 477 removed outlier: 3.560A pdb=" N GLY B 463 " --> pdb=" O HIS B 459 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 516 removed outlier: 3.562A pdb=" N ALA B 511 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 586 removed outlier: 3.591A pdb=" N ALA B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 611 through 619 removed outlier: 4.033A pdb=" N GLU B 618 " --> pdb=" O GLN B 614 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'B' and resid 645 through 659 removed outlier: 4.062A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 668 removed outlier: 3.727A pdb=" N PHE B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 695 removed outlier: 3.556A pdb=" N TYR B 694 " --> pdb=" O PRO B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 710 No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 712 through 715 removed outlier: 3.567A pdb=" N ALA B 715 " --> pdb=" O MET B 712 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 712 through 715' Processing helix chain 'B' and resid 718 through 725 removed outlier: 3.850A pdb=" N VAL B 725 " --> pdb=" O CYS B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 773 removed outlier: 3.605A pdb=" N LEU B 755 " --> pdb=" O PRO B 751 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 757 " --> pdb=" O PHE B 753 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 762 " --> pdb=" O ARG B 758 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 766 " --> pdb=" O ASN B 762 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER B 768 " --> pdb=" O SER B 764 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 769 " --> pdb=" O PHE B 765 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 771 " --> pdb=" O ALA B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 removed outlier: 3.510A pdb=" N VAL B 778 " --> pdb=" O PHE B 775 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP B 779 " --> pdb=" O TYR B 776 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 780 " --> pdb=" O ARG B 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 775 through 780' Processing helix chain 'B' and resid 785 through 806 removed outlier: 3.690A pdb=" N PHE B 799 " --> pdb=" O PHE B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 822 removed outlier: 3.646A pdb=" N PHE B 812 " --> pdb=" O SER B 808 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'B' and resid 834 through 854 removed outlier: 4.174A pdb=" N LEU B 839 " --> pdb=" O SER B 835 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 849 " --> pdb=" O CYS B 845 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE B 850 " --> pdb=" O THR B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 895 removed outlier: 3.687A pdb=" N VAL B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 883 " --> pdb=" O MET B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 931 Processing helix chain 'B' and resid 943 through 947 Processing helix chain 'B' and resid 956 through 962 Processing helix chain 'B' and resid 998 through 1009 Processing helix chain 'B' and resid 1029 through 1036 removed outlier: 3.929A pdb=" N THR B1033 " --> pdb=" O ASP B1029 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B1034 " --> pdb=" O GLU B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1058 removed outlier: 4.058A pdb=" N VAL B1043 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B1044 " --> pdb=" O ARG B1040 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B1050 " --> pdb=" O PHE B1046 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN B1051 " --> pdb=" O TRP B1047 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B1055 " --> pdb=" O ASN B1051 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B1058 " --> pdb=" O ILE B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1072 Processing helix chain 'B' and resid 1093 through 1130 removed outlier: 3.805A pdb=" N PHE B1098 " --> pdb=" O ALA B1094 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B1099 " --> pdb=" O SER B1095 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B1105 " --> pdb=" O ILE B1101 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B1106 " --> pdb=" O LEU B1102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B1109 " --> pdb=" O VAL B1105 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B1111 " --> pdb=" O LEU B1107 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B1112 " --> pdb=" O SER B1108 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B1113 " --> pdb=" O ALA B1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 400 removed outlier: 3.552A pdb=" N ASP A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) 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 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 459 through 477 removed outlier: 3.555A pdb=" N GLY A 463 " --> pdb=" O HIS A 459 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 507 through 516 removed outlier: 3.594A pdb=" N ALA A 511 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 removed outlier: 3.590A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 611 through 619 removed outlier: 4.034A pdb=" N GLU A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 645 through 659 removed outlier: 4.060A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 655 " --> pdb=" O ASN A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 668 removed outlier: 3.729A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 695 removed outlier: 3.561A pdb=" N TYR A 694 " --> pdb=" O PRO A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 710 No H-bonds generated for 'chain 'A' and resid 707 through 710' Processing helix chain 'A' and resid 712 through 715 removed outlier: 3.567A pdb=" N ALA A 715 " --> pdb=" O MET A 712 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 712 through 715' Processing helix chain 'A' and resid 718 through 725 removed outlier: 3.821A pdb=" N VAL A 725 " --> pdb=" O CYS A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 773 removed outlier: 3.553A pdb=" N LEU A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 757 " --> pdb=" O PHE A 753 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 768 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 769 " --> pdb=" O PHE A 765 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.508A pdb=" N VAL A 778 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP A 779 " --> pdb=" O TYR A 776 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 780 " --> pdb=" O ARG A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 775 through 780' Processing helix chain 'A' and resid 785 through 806 removed outlier: 3.709A pdb=" N PHE A 799 " --> pdb=" O PHE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 822 removed outlier: 3.645A pdb=" N PHE A 812 " --> pdb=" O SER A 808 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 831 No H-bonds generated for 'chain 'A' and resid 829 through 831' Processing helix chain 'A' and resid 834 through 854 removed outlier: 4.172A pdb=" N LEU A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 849 " --> pdb=" O CYS A 845 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 850 " --> pdb=" O THR A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 895 removed outlier: 3.760A pdb=" N VAL A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 883 " --> pdb=" O MET A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 931 Processing helix chain 'A' and resid 943 through 947 Processing helix chain 'A' and resid 956 through 962 Processing helix chain 'A' and resid 998 through 1011 removed outlier: 3.833A pdb=" N VAL A1011 " --> pdb=" O LYS A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1036 removed outlier: 3.904A pdb=" N THR A1033 " --> pdb=" O ASP A1029 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY A1034 " --> pdb=" O GLU A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1058 removed outlier: 4.058A pdb=" N VAL A1043 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1044 " --> pdb=" O ARG A1040 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A1050 " --> pdb=" O PHE A1046 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A1051 " --> pdb=" O TRP A1047 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE A1054 " --> pdb=" O THR A1050 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A1055 " --> pdb=" O ASN A1051 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A1058 " --> pdb=" O ILE A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1072 Processing helix chain 'A' and resid 1093 through 1130 removed outlier: 3.799A pdb=" N PHE A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A1099 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A1105 " --> pdb=" O ILE A1101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1109 " --> pdb=" O VAL A1105 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A1111 " --> pdb=" O LEU A1107 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A1112 " --> pdb=" O SER A1108 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A1113 " --> pdb=" O ALA A1109 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 386 through 389 removed outlier: 3.558A pdb=" N SER B 389 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 493 through 499 removed outlier: 6.810A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE B 597 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL B 451 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR B 599 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N THR B 453 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU B 601 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 679 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 540 through 542 Processing sheet with id= D, first strand: chain 'B' and resid 630 through 633 Processing sheet with id= E, first strand: chain 'B' and resid 545 through 549 removed outlier: 3.636A pdb=" N ASN B 545 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 557 " --> pdb=" O ASN B 545 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER B 555 " --> pdb=" O THR B 547 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 386 through 389 removed outlier: 3.516A pdb=" N SER A 389 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 493 through 499 removed outlier: 6.795A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A 597 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL A 451 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A 599 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR A 453 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 601 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 679 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 540 through 542 Processing sheet with id= I, first strand: chain 'A' and resid 630 through 633 Processing sheet with id= J, first strand: chain 'A' and resid 545 through 549 removed outlier: 3.638A pdb=" N ASN A 545 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 557 " --> pdb=" O ASN A 545 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER A 555 " --> pdb=" O THR A 547 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 4.26 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: 1861 1.32 - 1.44: 3439 1.44 - 1.57: 7110 1.57 - 1.69: 4 1.69 - 1.81: 104 Bond restraints: 12518 Sorted by residual: bond pdb=" C1 0V9 B1221 " pdb=" O3P 0V9 B1221 " ideal model delta sigma weight residual 1.409 1.453 -0.044 2.00e-02 2.50e+03 4.87e+00 bond pdb=" C1 0V9 A2001 " pdb=" O3P 0V9 A2001 " ideal model delta sigma weight residual 1.409 1.453 -0.044 2.00e-02 2.50e+03 4.87e+00 bond pdb=" O3P 0V9 B1221 " pdb=" P 0V9 B1221 " ideal model delta sigma weight residual 1.648 1.605 0.043 2.00e-02 2.50e+03 4.53e+00 bond pdb=" C31 0V9 A2001 " pdb=" C32 0V9 A2001 " ideal model delta sigma weight residual 1.535 1.493 0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" C31 0V9 B1221 " pdb=" C32 0V9 B1221 " ideal model delta sigma weight residual 1.535 1.493 0.042 2.00e-02 2.50e+03 4.39e+00 ... (remaining 12513 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.18: 262 107.18 - 113.88: 6928 113.88 - 120.59: 5038 120.59 - 127.30: 4413 127.30 - 134.00: 113 Bond angle restraints: 16754 Sorted by residual: angle pdb=" N VAL A 996 " pdb=" CA VAL A 996 " pdb=" C VAL A 996 " ideal model delta sigma weight residual 113.20 107.53 5.67 9.60e-01 1.09e+00 3.49e+01 angle pdb=" N VAL B 996 " pdb=" CA VAL B 996 " pdb=" C VAL B 996 " ideal model delta sigma weight residual 113.20 107.56 5.64 9.60e-01 1.09e+00 3.45e+01 angle pdb=" N ILE B 914 " pdb=" CA ILE B 914 " pdb=" C ILE B 914 " ideal model delta sigma weight residual 112.90 107.85 5.05 9.60e-01 1.09e+00 2.77e+01 angle pdb=" N ILE A 914 " pdb=" CA ILE A 914 " pdb=" C ILE A 914 " ideal model delta sigma weight residual 112.90 107.86 5.04 9.60e-01 1.09e+00 2.75e+01 angle pdb=" N TYR A1028 " pdb=" CA TYR A1028 " pdb=" C TYR A1028 " ideal model delta sigma weight residual 114.56 108.68 5.88 1.27e+00 6.20e-01 2.15e+01 ... (remaining 16749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.57: 7136 27.57 - 55.14: 320 55.14 - 82.71: 24 82.71 - 110.27: 10 110.27 - 137.84: 2 Dihedral angle restraints: 7492 sinusoidal: 3190 harmonic: 4302 Sorted by residual: dihedral pdb=" C37 0V9 A2001 " pdb=" C38 0V9 A2001 " pdb=" C39 0V9 A2001 " pdb=" C40 0V9 A2001 " ideal model delta sinusoidal sigma weight residual 195.15 57.31 137.84 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C37 0V9 B1221 " pdb=" C38 0V9 B1221 " pdb=" C39 0V9 B1221 " pdb=" C40 0V9 B1221 " ideal model delta sinusoidal sigma weight residual 195.15 57.38 137.77 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C1 0V9 B1221 " pdb=" O3P 0V9 B1221 " pdb=" P 0V9 B1221 " pdb=" O4P 0V9 B1221 " ideal model delta sinusoidal sigma weight residual -67.07 -170.76 103.69 1 3.00e+01 1.11e-03 1.32e+01 ... (remaining 7489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1015 0.032 - 0.064: 657 0.064 - 0.096: 123 0.096 - 0.128: 38 0.128 - 0.160: 5 Chirality restraints: 1838 Sorted by residual: chirality pdb=" CA ASN A 456 " pdb=" N ASN A 456 " pdb=" C ASN A 456 " pdb=" CB ASN A 456 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA TYR A 538 " pdb=" N TYR A 538 " pdb=" C TYR A 538 " pdb=" CB TYR A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ASN B 456 " pdb=" N ASN B 456 " pdb=" C ASN B 456 " pdb=" CB ASN B 456 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 1835 not shown) Planarity restraints: 2018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 0V9 B1221 " 0.015 2.00e-02 2.50e+03 2.87e-02 8.22e+00 pdb=" C18 0V9 B1221 " -0.038 2.00e-02 2.50e+03 pdb=" C19 0V9 B1221 " 0.038 2.00e-02 2.50e+03 pdb=" C20 0V9 B1221 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 0V9 A2001 " -0.015 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C18 0V9 A2001 " 0.037 2.00e-02 2.50e+03 pdb=" C19 0V9 A2001 " -0.037 2.00e-02 2.50e+03 pdb=" C20 0V9 A2001 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1025 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A1026 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A1026 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1026 " -0.021 5.00e-02 4.00e+02 ... (remaining 2015 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 29 2.54 - 3.13: 8598 3.13 - 3.72: 16345 3.72 - 4.31: 23449 4.31 - 4.90: 40525 Nonbonded interactions: 88946 Sorted by model distance: nonbonded pdb=" O PRO A1026 " pdb=" O SER A1027 " model vdw 1.946 3.040 nonbonded pdb=" O PRO B1026 " pdb=" O SER B1027 " model vdw 1.980 3.040 nonbonded pdb=" OG1 THR B 547 " pdb=" OG SER B 555 " model vdw 2.342 2.440 nonbonded pdb=" OG1 THR A 547 " pdb=" OG SER A 555 " model vdw 2.348 2.440 nonbonded pdb=" O LYS B 981 " pdb=" O ILE B 982 " model vdw 2.371 3.040 ... (remaining 88941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 378 through 1131 or resid 2002 through 2008 or resid 2010 \ through 2012 or resid 2014 through 2019)) selection = (chain 'B' and (resid 378 through 1131 or resid 1202 through 1208 or resid 1210 \ through 1212 or resid 1214 through 1219)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 6.750 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 31.510 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 : 0.004 0.044 12518 Z= 0.273 Angle : 0.710 8.756 16754 Z= 0.442 Chirality : 0.040 0.160 1838 Planarity : 0.003 0.038 2018 Dihedral : 14.805 137.842 4712 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.16 % Favored : 95.56 % Rotamer: Outliers : 0.16 % Allowed : 0.31 % Favored : 99.53 % 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: -2.73 (0.21), residues: 1442 helix: -1.24 (0.19), residues: 718 sheet: -3.25 (0.32), residues: 134 loop : -2.01 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1103 HIS 0.002 0.001 HIS B 783 PHE 0.013 0.001 PHE B 678 TYR 0.016 0.001 TYR B 538 ARG 0.003 0.000 ARG B 758 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 1.334 Fit side-chains REVERT: A 1123 ARG cc_start: 0.7152 (ttt90) cc_final: 0.6945 (ttt90) outliers start: 2 outliers final: 0 residues processed: 137 average time/residue: 0.2541 time to fit residues: 50.2274 Evaluate side-chains 106 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 783 HIS B1099 ASN A 536 HIS A 560 GLN A 783 HIS A1099 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12518 Z= 0.176 Angle : 0.478 5.487 16754 Z= 0.253 Chirality : 0.040 0.148 1838 Planarity : 0.003 0.026 2018 Dihedral : 9.078 115.368 2002 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.13 % Favored : 94.73 % Rotamer: Outliers : 0.47 % Allowed : 5.68 % Favored : 93.86 % 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: -1.72 (0.22), residues: 1442 helix: -0.25 (0.20), residues: 718 sheet: -2.62 (0.36), residues: 134 loop : -1.80 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.003 0.001 HIS A 459 PHE 0.018 0.001 PHE A 387 TYR 0.012 0.001 TYR B 538 ARG 0.002 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 1.407 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 119 average time/residue: 0.2388 time to fit residues: 42.3125 Evaluate side-chains 107 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1006 ASP Chi-restraints excluded: chain A residue 1006 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 131 optimal weight: 0.0050 chunk 141 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 129 optimal weight: 0.0770 chunk 44 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 overall best weight: 0.3352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 ASN B 536 HIS A 472 ASN A 560 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12518 Z= 0.103 Angle : 0.412 10.043 16754 Z= 0.214 Chirality : 0.038 0.134 1838 Planarity : 0.003 0.026 2018 Dihedral : 7.637 82.593 2002 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.44 % Favored : 95.42 % Rotamer: Outliers : 0.93 % Allowed : 7.93 % Favored : 91.14 % 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: -1.10 (0.22), residues: 1442 helix: 0.33 (0.21), residues: 730 sheet: -2.08 (0.38), residues: 134 loop : -1.73 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1103 HIS 0.002 0.000 HIS B 937 PHE 0.007 0.001 PHE A 678 TYR 0.007 0.001 TYR B 827 ARG 0.002 0.000 ARG A1123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: B 457 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.5749 (mp0) REVERT: A 457 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.5713 (mp0) outliers start: 12 outliers final: 3 residues processed: 136 average time/residue: 0.2239 time to fit residues: 45.6867 Evaluate side-chains 113 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 1006 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 67 optimal weight: 0.0050 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 68 optimal weight: 0.2980 chunk 124 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 ASN A 472 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12518 Z= 0.111 Angle : 0.425 10.010 16754 Z= 0.213 Chirality : 0.038 0.129 1838 Planarity : 0.002 0.026 2018 Dihedral : 7.378 80.058 2002 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.58 % Favored : 95.28 % Rotamer: Outliers : 0.78 % Allowed : 9.10 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.22), residues: 1442 helix: 0.64 (0.21), residues: 732 sheet: -1.73 (0.39), residues: 134 loop : -1.65 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 806 HIS 0.002 0.000 HIS A 459 PHE 0.008 0.001 PHE A 678 TYR 0.006 0.001 TYR B 827 ARG 0.003 0.000 ARG A1123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 457 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.5802 (mp0) REVERT: A 457 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.5731 (mp0) REVERT: A 1006 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.7888 (m-30) outliers start: 10 outliers final: 4 residues processed: 114 average time/residue: 0.2354 time to fit residues: 40.3434 Evaluate side-chains 113 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 1014 ASP Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 1006 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 2 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12518 Z= 0.272 Angle : 0.490 8.352 16754 Z= 0.255 Chirality : 0.041 0.137 1838 Planarity : 0.003 0.025 2018 Dihedral : 8.585 82.943 2002 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.83 % Favored : 94.04 % Rotamer: Outliers : 1.24 % Allowed : 10.58 % Favored : 88.18 % 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: -0.74 (0.22), residues: 1442 helix: 0.70 (0.20), residues: 718 sheet: -1.46 (0.41), residues: 134 loop : -1.76 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 806 HIS 0.004 0.001 HIS A 459 PHE 0.015 0.001 PHE A 678 TYR 0.010 0.001 TYR B 538 ARG 0.002 0.000 ARG B1123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.327 Fit side-chains REVERT: B 379 LYS cc_start: 0.6778 (tppt) cc_final: 0.5796 (tptt) REVERT: B 457 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.5943 (mp0) REVERT: B 1008 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: A 379 LYS cc_start: 0.6837 (tppt) cc_final: 0.5805 (tptt) REVERT: A 457 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.5992 (mp0) REVERT: A 1006 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.7972 (m-30) outliers start: 16 outliers final: 9 residues processed: 122 average time/residue: 0.2351 time to fit residues: 42.9938 Evaluate side-chains 120 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1014 ASP Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1102 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12518 Z= 0.282 Angle : 0.492 7.890 16754 Z= 0.259 Chirality : 0.041 0.135 1838 Planarity : 0.003 0.027 2018 Dihedral : 9.220 83.181 2002 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.62 % Favored : 94.24 % Rotamer: Outliers : 2.26 % Allowed : 10.89 % Favored : 86.86 % 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: -0.67 (0.22), residues: 1442 helix: 0.71 (0.20), residues: 718 sheet: -1.05 (0.43), residues: 134 loop : -1.75 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 806 HIS 0.003 0.001 HIS B 774 PHE 0.014 0.001 PHE A 678 TYR 0.009 0.001 TYR A1119 ARG 0.004 0.000 ARG B1123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 1.311 Fit side-chains REVERT: B 379 LYS cc_start: 0.6830 (tppt) cc_final: 0.5867 (tptt) REVERT: B 457 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.5987 (mp0) REVERT: B 1008 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: B 1101 ILE cc_start: 0.8914 (tp) cc_final: 0.8485 (tp) REVERT: A 379 LYS cc_start: 0.6687 (tppt) cc_final: 0.5699 (tptt) REVERT: A 457 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.5975 (mp0) REVERT: A 1006 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8284 (m-30) REVERT: A 1101 ILE cc_start: 0.8907 (tp) cc_final: 0.8484 (tp) outliers start: 29 outliers final: 14 residues processed: 134 average time/residue: 0.2263 time to fit residues: 45.1003 Evaluate side-chains 128 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1014 ASP Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1102 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12518 Z= 0.252 Angle : 0.477 7.195 16754 Z= 0.252 Chirality : 0.041 0.134 1838 Planarity : 0.003 0.026 2018 Dihedral : 9.244 83.116 2002 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.89 % Favored : 93.97 % Rotamer: Outliers : 2.18 % Allowed : 11.82 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.51 (0.22), residues: 1442 helix: 0.84 (0.20), residues: 718 sheet: -0.81 (0.45), residues: 134 loop : -1.72 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 806 HIS 0.003 0.001 HIS A 459 PHE 0.013 0.001 PHE A 678 TYR 0.008 0.001 TYR A1119 ARG 0.004 0.000 ARG B1123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 1.255 Fit side-chains REVERT: B 379 LYS cc_start: 0.6754 (tppt) cc_final: 0.5792 (tptt) REVERT: B 457 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.5948 (mp0) REVERT: B 1008 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: B 1101 ILE cc_start: 0.8911 (tp) cc_final: 0.8455 (tp) REVERT: A 379 LYS cc_start: 0.6755 (tppt) cc_final: 0.5742 (tptt) REVERT: A 457 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.5940 (mp0) REVERT: A 1006 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: A 1008 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.8022 (m-80) outliers start: 28 outliers final: 14 residues processed: 134 average time/residue: 0.2477 time to fit residues: 48.2271 Evaluate side-chains 129 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1014 ASP Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1008 TYR Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1102 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.0980 chunk 82 optimal weight: 0.0770 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12518 Z= 0.201 Angle : 0.451 7.106 16754 Z= 0.238 Chirality : 0.040 0.133 1838 Planarity : 0.003 0.026 2018 Dihedral : 9.004 82.530 2002 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.48 % Favored : 94.38 % Rotamer: Outliers : 2.02 % Allowed : 11.98 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.22), residues: 1442 helix: 1.03 (0.20), residues: 722 sheet: -0.61 (0.45), residues: 134 loop : -1.73 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 806 HIS 0.003 0.001 HIS A 459 PHE 0.011 0.001 PHE B 678 TYR 0.007 0.001 TYR B 827 ARG 0.005 0.000 ARG B1123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.335 Fit side-chains REVERT: B 379 LYS cc_start: 0.6879 (tppt) cc_final: 0.5938 (tptt) REVERT: B 457 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.5881 (mp0) REVERT: B 1008 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: B 1101 ILE cc_start: 0.8893 (tp) cc_final: 0.8442 (tp) REVERT: A 379 LYS cc_start: 0.6820 (tppt) cc_final: 0.5818 (tptt) REVERT: A 457 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.5868 (mp0) REVERT: A 1006 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8230 (m-30) REVERT: A 1008 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7985 (m-80) outliers start: 26 outliers final: 17 residues processed: 130 average time/residue: 0.2314 time to fit residues: 43.9986 Evaluate side-chains 132 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1014 ASP Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1008 TYR Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1102 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.4980 chunk 121 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 0.0170 chunk 39 optimal weight: 0.0770 chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 0.0770 chunk 84 optimal weight: 5.9990 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12518 Z= 0.098 Angle : 0.405 7.057 16754 Z= 0.210 Chirality : 0.038 0.128 1838 Planarity : 0.003 0.027 2018 Dihedral : 7.988 82.229 2002 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.65 % Favored : 95.21 % Rotamer: Outliers : 1.40 % Allowed : 12.52 % Favored : 86.08 % 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: 0.11 (0.23), residues: 1442 helix: 1.38 (0.21), residues: 728 sheet: -0.32 (0.45), residues: 134 loop : -1.56 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1103 HIS 0.001 0.000 HIS A 459 PHE 0.006 0.001 PHE B 652 TYR 0.007 0.001 TYR A 842 ARG 0.005 0.000 ARG B1123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.384 Fit side-chains REVERT: B 379 LYS cc_start: 0.6830 (tppt) cc_final: 0.5998 (tptt) REVERT: B 457 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.5668 (mp0) REVERT: B 656 MET cc_start: 0.8463 (mmp) cc_final: 0.7982 (mmp) REVERT: B 1008 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: A 379 LYS cc_start: 0.6751 (tppt) cc_final: 0.5857 (tptt) REVERT: A 457 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.5672 (mp0) REVERT: A 656 MET cc_start: 0.8458 (mmp) cc_final: 0.7975 (mmp) outliers start: 18 outliers final: 10 residues processed: 132 average time/residue: 0.2529 time to fit residues: 48.3291 Evaluate side-chains 121 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 1102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 560 GLN B 575 ASN A 575 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12518 Z= 0.255 Angle : 0.476 7.191 16754 Z= 0.249 Chirality : 0.041 0.136 1838 Planarity : 0.003 0.026 2018 Dihedral : 8.981 82.547 2002 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.34 % Favored : 94.52 % Rotamer: Outliers : 1.48 % Allowed : 13.06 % Favored : 85.46 % 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 (0.23), residues: 1442 helix: 1.24 (0.20), residues: 728 sheet: -0.28 (0.46), residues: 134 loop : -1.65 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 806 HIS 0.003 0.001 HIS A 774 PHE 0.012 0.001 PHE B 678 TYR 0.009 0.001 TYR B 797 ARG 0.004 0.000 ARG B1123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 1.431 Fit side-chains REVERT: B 379 LYS cc_start: 0.6784 (tppt) cc_final: 0.5837 (tptt) REVERT: B 457 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6001 (mp0) REVERT: B 656 MET cc_start: 0.8606 (mmp) cc_final: 0.8177 (mmp) REVERT: B 1008 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: B 1101 ILE cc_start: 0.8914 (tp) cc_final: 0.8468 (tp) REVERT: A 379 LYS cc_start: 0.6711 (tppt) cc_final: 0.5711 (tptt) REVERT: A 457 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.5960 (mp0) REVERT: A 656 MET cc_start: 0.8602 (mmp) cc_final: 0.8177 (mmp) outliers start: 19 outliers final: 13 residues processed: 123 average time/residue: 0.2652 time to fit residues: 46.9586 Evaluate side-chains 122 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1014 ASP Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 1102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.0470 chunk 100 optimal weight: 0.8980 overall best weight: 0.7280 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.124365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.091462 restraints weight = 16799.612| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.21 r_work: 0.2767 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12518 Z= 0.129 Angle : 0.420 7.148 16754 Z= 0.219 Chirality : 0.039 0.129 1838 Planarity : 0.003 0.026 2018 Dihedral : 8.423 82.027 2002 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.85 % Favored : 95.01 % Rotamer: Outliers : 1.24 % Allowed : 12.91 % Favored : 85.85 % 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: 0.18 (0.23), residues: 1442 helix: 1.43 (0.21), residues: 730 sheet: -0.06 (0.46), residues: 134 loop : -1.59 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1103 HIS 0.003 0.000 HIS A 459 PHE 0.008 0.001 PHE A 678 TYR 0.007 0.001 TYR A 842 ARG 0.004 0.000 ARG B1123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2431.72 seconds wall clock time: 46 minutes 42.32 seconds (2802.32 seconds total)