Starting phenix.real_space_refine on Thu Aug 6 12:20:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q11_72113/08_2026/9q11_72113.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q11_72113/08_2026/9q11_72113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q11_72113/08_2026/9q11_72113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q11_72113/08_2026/9q11_72113.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q11_72113/08_2026/9q11_72113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q11_72113/08_2026/9q11_72113.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 226 5.49 5 S 43 5.16 5 C 8611 2.51 5 N 2714 2.21 5 O 3337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14931 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1171 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain: "D" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "F" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 642 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "G" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "B" Number of atoms: 4605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 4605 Classifications: {'RNA': 217} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 20, 'rna3p_pur': 82, 'rna3p_pyr': 97} Link IDs: {'rna2p': 38, 'rna3p': 178} Chain breaks: 2 Chain: "A" Number of atoms: 7633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 951, 7633 Classifications: {'peptide': 951} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 892} Chain breaks: 3 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1FZ': 1, '55C': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.15, per 1000 atoms: 0.21 Number of scatterers: 14931 At special positions: 0 Unit cell: (150.7, 126.5, 126.5, 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 43 16.00 P 226 15.00 O 3337 8.00 N 2714 7.00 C 8611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 470.9 milliseconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 10 sheets defined 55.8% alpha, 13.3% beta 61 base pairs and 123 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 158 through 165 Processing helix chain 'C' and resid 167 through 177 removed outlier: 3.857A pdb=" N GLU C 171 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N PHE C 174 " --> pdb=" O GLU C 171 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG C 175 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'F' and resid 27 through 38 Processing helix chain 'F' and resid 46 through 73 removed outlier: 4.613A pdb=" N VAL F 50 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN F 69 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 90 Processing helix chain 'F' and resid 91 through 98 Processing helix chain 'G' and resid 38 through 50 Processing helix chain 'G' and resid 56 through 85 removed outlier: 3.510A pdb=" N GLU G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 103 removed outlier: 3.518A pdb=" N ILE G 95 " --> pdb=" O THR G 91 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG G 100 " --> pdb=" O GLN G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 125 Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 24 through 31 removed outlier: 3.729A pdb=" N ARG A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.721A pdb=" N ALA A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.573A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.535A pdb=" N ALA A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.733A pdb=" N HIS A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 removed outlier: 4.026A pdb=" N LEU A 332 " --> pdb=" O LYS A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 355 through 365 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.622A pdb=" N GLN A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 403 removed outlier: 3.538A pdb=" N HIS A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.678A pdb=" N LYS A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 452 removed outlier: 3.576A pdb=" N VAL A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 473 removed outlier: 3.631A pdb=" N GLY A 463 " --> pdb=" O TRP A 459 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.666A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.594A pdb=" N ASN A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 496 " --> pdb=" O LYS A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.692A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 521 " --> pdb=" O ALA A 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 517 through 521' Processing helix chain 'A' and resid 530 through 551 removed outlier: 3.580A pdb=" N HIS A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 544 " --> pdb=" O ILE A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 559 Processing helix chain 'A' and resid 578 through 596 removed outlier: 4.124A pdb=" N LYS A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 4.246A pdb=" N ARG A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 672 removed outlier: 5.500A pdb=" N ARG A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 Processing helix chain 'A' and resid 682 through 698 removed outlier: 3.816A pdb=" N THR A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 720 removed outlier: 3.556A pdb=" N ILE A 720 " --> pdb=" O TYR A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 734 removed outlier: 3.582A pdb=" N LYS A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 769 removed outlier: 3.960A pdb=" N LEU A 769 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 removed outlier: 3.652A pdb=" N HIS A 779 " --> pdb=" O GLN A 775 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 782 " --> pdb=" O ALA A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 815 removed outlier: 3.793A pdb=" N VAL A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 811 " --> pdb=" O ASP A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 851 removed outlier: 3.559A pdb=" N MET A 849 " --> pdb=" O CYS A 845 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 851 " --> pdb=" O GLY A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 860 removed outlier: 4.342A pdb=" N ASP A 860 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 890 removed outlier: 3.587A pdb=" N ARG A 889 " --> pdb=" O ARG A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 895 Processing helix chain 'A' and resid 911 through 915 Processing helix chain 'A' and resid 946 through 950 removed outlier: 3.597A pdb=" N ALA A 950 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 982 removed outlier: 3.519A pdb=" N ARG A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 980 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 993 through 1017 removed outlier: 3.520A pdb=" N TYR A1010 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1051 removed outlier: 4.151A pdb=" N PHE A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A1035 " --> pdb=" O PHE A1031 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1083 removed outlier: 3.978A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1091 - end of helix removed outlier: 4.333A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN A1102 " --> pdb=" O THR A1098 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1119 removed outlier: 3.530A pdb=" N ALA A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1117 " --> pdb=" O THR A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1130 removed outlier: 4.027A pdb=" N THR A1129 " --> pdb=" O ASP A1126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 113 through 122 removed outlier: 5.920A pdb=" N LEU C 117 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N SER C 147 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 119 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR C 143 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N SER C 152 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N LEU C 204 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG C 154 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL C 206 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 156 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ARG C 208 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP C 186 " --> pdb=" O ASP C 207 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE C 209 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 184 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU C 211 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU C 182 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG C 180 " --> pdb=" O PRO C 213 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG C 180 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 43 through 44 removed outlier: 6.722A pdb=" N ARG F 43 " --> pdb=" O ILE G 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.855A pdb=" N GLU A 20 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU A 798 " --> pdb=" O TYR A 739 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N TYR A 739 " --> pdb=" O LEU A 798 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 744 " --> pdb=" O LYS A 760 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 565 Processing sheet with id=AA8, first strand: chain 'A' and resid 598 through 600 removed outlier: 6.345A pdb=" N GLN A 827 " --> pdb=" O HIS A 816 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS A 816 " --> pdb=" O GLN A 827 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 617 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ARG A 819 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 862 through 865 removed outlier: 3.681A pdb=" N VAL A 711 " --> pdb=" O PHE A 870 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 927 through 930 492 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 160 hydrogen bonds 302 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 123 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 1.51 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: 2008 1.32 - 1.44: 5457 1.44 - 1.56: 7736 1.56 - 1.69: 447 1.69 - 1.81: 57 Bond restraints: 15705 Sorted by residual: bond pdb=" O3B 1FZ A1202 " pdb=" PG 1FZ A1202 " ideal model delta sigma weight residual 1.703 1.627 0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" N3A 1FZ A1202 " pdb=" PB 1FZ A1202 " ideal model delta sigma weight residual 1.698 1.629 0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" O5' 1FZ A1202 " pdb=" PA 1FZ A1202 " ideal model delta sigma weight residual 1.640 1.574 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C HIS A 546 " pdb=" O HIS A 546 " ideal model delta sigma weight residual 1.237 1.199 0.037 1.19e-02 7.06e+03 9.76e+00 bond pdb=" O2A 1FZ A1202 " pdb=" PA 1FZ A1202 " ideal model delta sigma weight residual 1.497 1.558 -0.061 2.00e-02 2.50e+03 9.38e+00 ... (remaining 15700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 21849 2.03 - 4.06: 477 4.06 - 6.09: 16 6.09 - 8.11: 3 8.11 - 10.14: 2 Bond angle restraints: 22347 Sorted by residual: angle pdb=" C2 G B 309 " pdb=" N3 G B 309 " pdb=" C4 G B 309 " ideal model delta sigma weight residual 111.90 114.80 -2.90 5.00e-01 4.00e+00 3.37e+01 angle pdb=" C5 G B 309 " pdb=" C4 G B 309 " pdb=" N3 G B 309 " ideal model delta sigma weight residual 128.60 126.25 2.35 5.00e-01 4.00e+00 2.21e+01 angle pdb=" C8 G B 309 " pdb=" N9 G B 309 " pdb=" C4 G B 309 " ideal model delta sigma weight residual 106.40 104.52 1.88 4.00e-01 6.25e+00 2.21e+01 angle pdb=" C3' G B 309 " pdb=" C2' G B 309 " pdb=" C1' G B 309 " ideal model delta sigma weight residual 101.50 105.08 -3.58 8.00e-01 1.56e+00 2.00e+01 angle pdb=" C VAL A 596 " pdb=" CA VAL A 596 " pdb=" CB VAL A 596 " ideal model delta sigma weight residual 111.29 104.09 7.20 1.64e+00 3.72e-01 1.93e+01 ... (remaining 22342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.60: 9155 33.60 - 67.19: 585 67.19 - 100.79: 97 100.79 - 134.38: 7 134.38 - 167.98: 4 Dihedral angle restraints: 9848 sinusoidal: 6146 harmonic: 3702 Sorted by residual: dihedral pdb=" O4' U B 312 " pdb=" C1' U B 312 " pdb=" N1 U B 312 " pdb=" C2 U B 312 " ideal model delta sinusoidal sigma weight residual 200.00 32.44 167.56 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" O4' C B 141 " pdb=" C1' C B 141 " pdb=" N1 C B 141 " pdb=" C2 C B 141 " ideal model delta sinusoidal sigma weight residual 200.00 73.50 126.50 1 1.50e+01 4.44e-03 6.80e+01 dihedral pdb=" O4' U B 43 " pdb=" C1' U B 43 " pdb=" N1 U B 43 " pdb=" C2 U B 43 " ideal model delta sinusoidal sigma weight residual -128.00 39.98 -167.98 1 1.70e+01 3.46e-03 6.57e+01 ... (remaining 9845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2185 0.050 - 0.100: 330 0.100 - 0.151: 177 0.151 - 0.201: 3 0.201 - 0.251: 2 Chirality restraints: 2697 Sorted by residual: chirality pdb=" C3' G B 309 " pdb=" C4' G B 309 " pdb=" O3' G B 309 " pdb=" C2' G B 309 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA THR A1129 " pdb=" N THR A1129 " pdb=" C THR A1129 " pdb=" CB THR A1129 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' DA D 15 " pdb=" C4' DA D 15 " pdb=" O3' DA D 15 " pdb=" C2' DA D 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 2694 not shown) Planarity restraints: 2026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 55C A1201 " -0.055 2.00e-02 2.50e+03 6.14e-02 4.71e+01 pdb=" C11 55C A1201 " 0.019 2.00e-02 2.50e+03 pdb=" C12 55C A1201 " 0.100 2.00e-02 2.50e+03 pdb=" C13 55C A1201 " -0.073 2.00e-02 2.50e+03 pdb=" C14 55C A1201 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 55C A1201 " -0.027 2.00e-02 2.50e+03 2.95e-02 1.09e+01 pdb=" C13 55C A1201 " 0.013 2.00e-02 2.50e+03 pdb=" C15 55C A1201 " -0.035 2.00e-02 2.50e+03 pdb=" N1 55C A1201 " 0.047 2.00e-02 2.50e+03 pdb=" O21 55C A1201 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 163 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO A 164 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.019 5.00e-02 4.00e+02 ... (remaining 2023 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 235 2.64 - 3.21: 12757 3.21 - 3.77: 22318 3.77 - 4.34: 33834 4.34 - 4.90: 50409 Nonbonded interactions: 119553 Sorted by model distance: nonbonded pdb=" O2' C B 313 " pdb=" O TRP A 510 " model vdw 2.080 3.040 nonbonded pdb=" O2' A B 175 " pdb=" OP1 A B 176 " model vdw 2.092 3.040 nonbonded pdb=" O PRO C 131 " pdb=" OG SER C 132 " model vdw 2.161 3.040 nonbonded pdb=" OD1 ASP A 337 " pdb=" OG SER A 582 " model vdw 2.211 3.040 nonbonded pdb=" O2' G B 71 " pdb=" OP1 C B 72 " model vdw 2.240 3.040 ... (remaining 119548 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 15.290 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.003 0.076 15705 Z= 0.199 Angle : 0.610 10.142 22347 Z= 0.445 Chirality : 0.044 0.251 2697 Planarity : 0.004 0.061 2026 Dihedral : 19.834 167.978 7452 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.18 % Allowed : 3.38 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.47 (0.19), residues: 1261 helix: -3.90 (0.12), residues: 606 sheet: -0.85 (0.41), residues: 132 loop : -2.12 (0.24), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 979 TYR 0.007 0.001 TYR A 122 PHE 0.014 0.001 PHE A 331 TRP 0.007 0.001 TRP C 167 HIS 0.006 0.001 HIS A 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.20 (15705) covalent geometry : angle 0.61048 / 0.44 (22347) hydrogen bonds : bond 0.28732 / 19.62 ( 652) hydrogen bonds : angle 9.21799 / 6.40 ( 1688) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 44 VAL cc_start: 0.5435 (p) cc_final: 0.5196 (m) REVERT: F 85 GLN cc_start: 0.6931 (mm-40) cc_final: 0.6626 (tm-30) REVERT: G 96 GLN cc_start: 0.5910 (tt0) cc_final: 0.5688 (tp-100) REVERT: A 322 PRO cc_start: 0.5739 (Cg_endo) cc_final: 0.5536 (Cg_exo) outliers start: 2 outliers final: 1 residues processed: 139 average time/residue: 0.7167 time to fit residues: 107.2303 Evaluate side-chains 85 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1129 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 151 HIS F 32 HIS F 69 ASN A 609 HIS A 799 ASN A 816 HIS A 925 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.125192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.075231 restraints weight = 31222.822| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.15 r_work: 0.2923 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15705 Z= 0.160 Angle : 0.645 11.060 22347 Z= 0.354 Chirality : 0.041 0.432 2697 Planarity : 0.006 0.083 2026 Dihedral : 22.093 177.136 4988 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.64 % Allowed : 8.86 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.21), residues: 1261 helix: -1.60 (0.18), residues: 623 sheet: -0.40 (0.41), residues: 142 loop : -1.58 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 938 TYR 0.027 0.001 TYR C 203 PHE 0.014 0.002 PHE A 331 TRP 0.006 0.001 TRP A1026 HIS 0.005 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (15705) covalent geometry : angle 0.64515 / 0.35 (22347) hydrogen bonds : bond 0.07354 / 4.91 ( 652) hydrogen bonds : angle 4.74754 / 3.33 ( 1688) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 ARG cc_start: 0.8550 (pmm-80) cc_final: 0.7699 (mtp85) REVERT: C 113 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7427 (mpp80) REVERT: C 175 ARG cc_start: 0.8277 (tpp80) cc_final: 0.8062 (tpp80) REVERT: C 207 ASP cc_start: 0.8681 (m-30) cc_final: 0.8275 (m-30) REVERT: C 218 ARG cc_start: 0.7934 (mtm-85) cc_final: 0.7640 (mtm-85) REVERT: F 85 GLN cc_start: 0.7491 (mm-40) cc_final: 0.7233 (tm-30) REVERT: G 117 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8473 (tmtt) REVERT: A 338 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8378 (pttt) REVERT: A 512 MET cc_start: 0.9489 (mmm) cc_final: 0.9109 (mmt) REVERT: A 1054 MET cc_start: 0.8981 (ttm) cc_final: 0.8623 (ttm) outliers start: 18 outliers final: 7 residues processed: 105 average time/residue: 0.6158 time to fit residues: 71.4209 Evaluate side-chains 91 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1131 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 69 ASN G 48 GLN G 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.123346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.072648 restraints weight = 31787.892| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.20 r_work: 0.2880 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15705 Z= 0.200 Angle : 0.627 9.475 22347 Z= 0.338 Chirality : 0.042 0.254 2697 Planarity : 0.005 0.043 2026 Dihedral : 22.077 175.759 4988 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.74 % Allowed : 9.32 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.22), residues: 1261 helix: -0.35 (0.20), residues: 629 sheet: -0.32 (0.40), residues: 153 loop : -1.34 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 938 TYR 0.021 0.001 TYR C 203 PHE 0.023 0.002 PHE A 331 TRP 0.009 0.001 TRP A1026 HIS 0.006 0.001 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (15705) covalent geometry : angle 0.62722 / 0.34 (22347) hydrogen bonds : bond 0.06414 / 4.31 ( 652) hydrogen bonds : angle 4.30988 / 3.04 ( 1688) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 ARG cc_start: 0.8616 (pmm-80) cc_final: 0.7865 (mtp85) REVERT: C 113 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7414 (mpp80) REVERT: C 144 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8427 (mp) REVERT: C 227 ASP cc_start: 0.8139 (t0) cc_final: 0.7890 (t0) REVERT: C 236 ASP cc_start: 0.8152 (m-30) cc_final: 0.7798 (p0) REVERT: F 85 GLN cc_start: 0.7418 (mm-40) cc_final: 0.7213 (tm-30) REVERT: G 106 GLU cc_start: 0.8292 (tt0) cc_final: 0.8074 (tp30) REVERT: G 117 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8491 (tmtt) REVERT: A 20 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: A 83 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8674 (ptp90) REVERT: A 1054 MET cc_start: 0.9077 (ttm) cc_final: 0.8764 (ttm) REVERT: A 1129 THR cc_start: 0.9559 (OUTLIER) cc_final: 0.9298 (p) outliers start: 30 outliers final: 12 residues processed: 110 average time/residue: 0.6516 time to fit residues: 78.6419 Evaluate side-chains 98 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 1129 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 120 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 123 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 0.0970 chunk 137 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 79 optimal weight: 0.3980 chunk 15 optimal weight: 0.0980 chunk 100 optimal weight: 3.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 69 ASN G 48 GLN A 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.124072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073121 restraints weight = 31697.318| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.26 r_work: 0.2925 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15705 Z= 0.118 Angle : 0.536 8.554 22347 Z= 0.296 Chirality : 0.037 0.237 2697 Planarity : 0.005 0.047 2026 Dihedral : 22.006 177.242 4988 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.28 % Allowed : 10.14 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.23), residues: 1261 helix: 0.47 (0.21), residues: 631 sheet: 0.05 (0.41), residues: 142 loop : -1.25 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 96 TYR 0.021 0.001 TYR C 203 PHE 0.012 0.001 PHE A 331 TRP 0.008 0.001 TRP C 167 HIS 0.003 0.001 HIS F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (15705) covalent geometry : angle 0.53573 / 0.30 (22347) hydrogen bonds : bond 0.04865 / 3.24 ( 652) hydrogen bonds : angle 3.97232 / 2.81 ( 1688) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 92 ARG cc_start: 0.8429 (pmm-80) cc_final: 0.7837 (mtp85) REVERT: C 113 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7114 (mpp80) REVERT: C 154 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8130 (ptt90) REVERT: C 236 ASP cc_start: 0.8164 (m-30) cc_final: 0.7778 (p0) REVERT: F 85 GLN cc_start: 0.7318 (mm-40) cc_final: 0.7118 (tm-30) REVERT: G 96 GLN cc_start: 0.6958 (tt0) cc_final: 0.6301 (tp-100) REVERT: G 106 GLU cc_start: 0.8118 (tt0) cc_final: 0.7917 (tp30) REVERT: A 20 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: A 83 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8650 (ptp90) outliers start: 25 outliers final: 8 residues processed: 104 average time/residue: 0.6828 time to fit residues: 77.6941 Evaluate side-chains 95 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 709 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 52 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 69 ASN G 48 GLN ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.120450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.069227 restraints weight = 31647.161| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.23 r_work: 0.2823 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 15705 Z= 0.311 Angle : 0.688 9.665 22347 Z= 0.360 Chirality : 0.046 0.249 2697 Planarity : 0.006 0.042 2026 Dihedral : 22.063 177.493 4987 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.56 % Allowed : 10.68 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.23), residues: 1261 helix: 0.47 (0.21), residues: 625 sheet: -0.21 (0.40), residues: 153 loop : -1.20 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1011 TYR 0.018 0.002 TYR C 203 PHE 0.030 0.002 PHE A 331 TRP 0.010 0.002 TRP C 167 HIS 0.006 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.31 (15705) covalent geometry : angle 0.68759 / 0.36 (22347) hydrogen bonds : bond 0.06532 / 4.37 ( 652) hydrogen bonds : angle 4.20103 / 2.98 ( 1688) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 81 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 ARG cc_start: 0.8640 (pmm-80) cc_final: 0.7996 (mtp85) REVERT: C 113 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7299 (mpp80) REVERT: C 144 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8448 (mp) REVERT: C 236 ASP cc_start: 0.8297 (m-30) cc_final: 0.7941 (p0) REVERT: G 106 GLU cc_start: 0.8197 (tt0) cc_final: 0.7943 (tp30) REVERT: G 117 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8379 (tmtt) REVERT: A 20 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: A 372 MET cc_start: 0.6728 (tpp) cc_final: 0.6496 (tpt) REVERT: A 631 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7831 (ttp-170) REVERT: A 1056 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9002 (mp) REVERT: A 1129 THR cc_start: 0.9542 (OUTLIER) cc_final: 0.9290 (p) outliers start: 39 outliers final: 20 residues processed: 115 average time/residue: 0.6509 time to fit residues: 82.3459 Evaluate side-chains 106 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1131 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 chunk 32 optimal weight: 30.0000 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 69 ASN G 48 GLN ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.120721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.069629 restraints weight = 31453.932| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.21 r_work: 0.2835 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15705 Z= 0.241 Angle : 0.621 9.369 22347 Z= 0.332 Chirality : 0.042 0.248 2697 Planarity : 0.005 0.045 2026 Dihedral : 22.063 179.927 4987 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.65 % Allowed : 12.42 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.24), residues: 1261 helix: 0.62 (0.21), residues: 631 sheet: -0.23 (0.41), residues: 144 loop : -1.21 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 901 TYR 0.018 0.001 TYR C 203 PHE 0.024 0.002 PHE A 331 TRP 0.010 0.002 TRP A 387 HIS 0.004 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 (15705) covalent geometry : angle 0.62112 / 0.33 (22347) hydrogen bonds : bond 0.05894 / 3.92 ( 652) hydrogen bonds : angle 4.10936 / 2.92 ( 1688) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: C 100 ARG cc_start: 0.8762 (ptm-80) cc_final: 0.8543 (mtp-110) REVERT: C 113 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7088 (mpp80) REVERT: C 144 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8473 (mp) REVERT: C 236 ASP cc_start: 0.8295 (m-30) cc_final: 0.8010 (p0) REVERT: G 70 ILE cc_start: 0.7951 (mm) cc_final: 0.7727 (mp) REVERT: G 96 GLN cc_start: 0.7075 (tt0) cc_final: 0.6341 (tp-100) REVERT: G 106 GLU cc_start: 0.8160 (tt0) cc_final: 0.7947 (tp30) REVERT: G 117 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8412 (tmtt) REVERT: A 20 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: A 149 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7340 (tt) REVERT: A 1129 THR cc_start: 0.9528 (OUTLIER) cc_final: 0.9280 (p) outliers start: 29 outliers final: 15 residues processed: 105 average time/residue: 0.6372 time to fit residues: 73.7554 Evaluate side-chains 93 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1129 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 41 optimal weight: 20.0000 chunk 121 optimal weight: 0.7980 chunk 46 optimal weight: 10.9990 chunk 102 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 185 GLN F 69 ASN G 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.121940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.071478 restraints weight = 31231.699| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.19 r_work: 0.2872 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15705 Z= 0.147 Angle : 0.560 8.722 22347 Z= 0.305 Chirality : 0.038 0.248 2697 Planarity : 0.005 0.054 2026 Dihedral : 21.981 178.211 4987 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.19 % Allowed : 13.24 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.24), residues: 1261 helix: 0.92 (0.21), residues: 632 sheet: -0.20 (0.42), residues: 137 loop : -1.19 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 901 TYR 0.018 0.001 TYR C 203 PHE 0.017 0.001 PHE A 331 TRP 0.008 0.001 TRP A1026 HIS 0.003 0.001 HIS F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (15705) covalent geometry : angle 0.56031 / 0.30 (22347) hydrogen bonds : bond 0.05117 / 3.40 ( 652) hydrogen bonds : angle 3.95160 / 2.81 ( 1688) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 113 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7080 (mpp80) REVERT: C 144 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8470 (mp) REVERT: C 236 ASP cc_start: 0.8322 (m-30) cc_final: 0.7913 (p0) REVERT: G 44 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7225 (mmtm) REVERT: G 69 ASP cc_start: 0.7888 (t0) cc_final: 0.7676 (m-30) REVERT: G 70 ILE cc_start: 0.7934 (mm) cc_final: 0.7695 (mp) REVERT: G 106 GLU cc_start: 0.8138 (tt0) cc_final: 0.7932 (tp30) REVERT: A 20 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: A 339 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.8900 (pt0) outliers start: 24 outliers final: 13 residues processed: 93 average time/residue: 0.5528 time to fit residues: 57.6562 Evaluate side-chains 90 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 1131 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 9 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.122034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.071526 restraints weight = 31441.555| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.20 r_work: 0.2873 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15705 Z= 0.153 Angle : 0.552 8.566 22347 Z= 0.299 Chirality : 0.038 0.250 2697 Planarity : 0.005 0.055 2026 Dihedral : 21.903 178.722 4987 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.47 % Allowed : 13.15 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.24), residues: 1261 helix: 1.08 (0.21), residues: 633 sheet: -0.23 (0.43), residues: 137 loop : -1.10 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 901 TYR 0.017 0.001 TYR C 203 PHE 0.018 0.001 PHE A 331 TRP 0.008 0.001 TRP A1026 HIS 0.003 0.001 HIS F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (15705) covalent geometry : angle 0.55233 / 0.30 (22347) hydrogen bonds : bond 0.05016 / 3.34 ( 652) hydrogen bonds : angle 3.89767 / 2.78 ( 1688) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.507 Fit side-chains REVERT: C 113 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7049 (mpp80) REVERT: C 144 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8486 (mp) REVERT: C 236 ASP cc_start: 0.8428 (m-30) cc_final: 0.8045 (p0) REVERT: F 30 ARG cc_start: 0.6533 (mtt180) cc_final: 0.6138 (ttm170) REVERT: G 44 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7236 (mmtm) REVERT: G 70 ILE cc_start: 0.7910 (mm) cc_final: 0.7666 (mp) REVERT: G 117 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8430 (tmtt) REVERT: A 20 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: A 339 GLU cc_start: 0.9404 (OUTLIER) cc_final: 0.8993 (pt0) REVERT: A 372 MET cc_start: 0.6758 (tpp) cc_final: 0.6482 (tpt) REVERT: A 1056 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8916 (mp) REVERT: A 1129 THR cc_start: 0.9493 (OUTLIER) cc_final: 0.9281 (p) outliers start: 27 outliers final: 15 residues processed: 94 average time/residue: 0.5994 time to fit residues: 62.8142 Evaluate side-chains 91 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1131 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 147 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 53 optimal weight: 0.0060 chunk 107 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 69 ASN G 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.122712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.072036 restraints weight = 31449.973| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.21 r_work: 0.2882 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15705 Z= 0.130 Angle : 0.546 8.364 22347 Z= 0.295 Chirality : 0.037 0.249 2697 Planarity : 0.004 0.059 2026 Dihedral : 21.890 178.277 4987 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.47 % Allowed : 13.33 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1261 helix: 1.20 (0.22), residues: 633 sheet: -0.24 (0.42), residues: 137 loop : -1.06 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 901 TYR 0.016 0.001 TYR C 203 PHE 0.016 0.001 PHE A 331 TRP 0.008 0.001 TRP A1026 HIS 0.003 0.001 HIS F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (15705) covalent geometry : angle 0.54560 / 0.30 (22347) hydrogen bonds : bond 0.04791 / 3.19 ( 652) hydrogen bonds : angle 3.84277 / 2.75 ( 1688) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: C 113 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6801 (mpp80) REVERT: C 144 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8420 (mp) REVERT: C 236 ASP cc_start: 0.8454 (m-30) cc_final: 0.8166 (p0) REVERT: F 30 ARG cc_start: 0.6513 (mtt180) cc_final: 0.6129 (ttm170) REVERT: G 44 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.7107 (mmtm) REVERT: G 70 ILE cc_start: 0.7861 (mm) cc_final: 0.7644 (mp) REVERT: G 96 GLN cc_start: 0.6791 (tt0) cc_final: 0.6257 (tp-100) REVERT: G 117 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8439 (tmtt) REVERT: A 20 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: A 1129 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.9229 (p) outliers start: 27 outliers final: 16 residues processed: 95 average time/residue: 0.5538 time to fit residues: 58.6298 Evaluate side-chains 89 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1131 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 68 optimal weight: 0.2980 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.121946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071324 restraints weight = 31387.276| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.26 r_work: 0.2853 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15705 Z= 0.127 Angle : 0.530 8.855 22347 Z= 0.287 Chirality : 0.037 0.251 2697 Planarity : 0.004 0.059 2026 Dihedral : 21.851 178.250 4987 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.65 % Favored : 96.27 % Rotamer: Outliers : 2.01 % Allowed : 13.88 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1261 helix: 1.36 (0.22), residues: 633 sheet: -0.25 (0.42), residues: 136 loop : -1.00 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 901 TYR 0.017 0.001 TYR C 203 PHE 0.017 0.001 PHE C 209 TRP 0.008 0.001 TRP A 581 HIS 0.004 0.001 HIS G 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (15705) covalent geometry : angle 0.53028 / 0.29 (22347) hydrogen bonds : bond 0.04623 / 3.08 ( 652) hydrogen bonds : angle 3.79541 / 2.71 ( 1688) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 113 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6780 (mpp80) REVERT: C 144 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8380 (mp) REVERT: C 236 ASP cc_start: 0.8460 (m-30) cc_final: 0.8182 (p0) REVERT: F 30 ARG cc_start: 0.6254 (mtt180) cc_final: 0.5875 (ttm170) REVERT: G 70 ILE cc_start: 0.8000 (mm) cc_final: 0.7786 (mp) REVERT: G 117 LYS cc_start: 0.8820 (mtpp) cc_final: 0.8395 (tmtt) REVERT: A 20 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: A 372 MET cc_start: 0.6367 (tpp) cc_final: 0.6038 (tpt) REVERT: A 787 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7772 (ptm160) REVERT: A 1129 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.9198 (p) outliers start: 22 outliers final: 14 residues processed: 91 average time/residue: 0.5651 time to fit residues: 57.2818 Evaluate side-chains 87 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1131 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 11 optimal weight: 0.0980 chunk 138 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 125 optimal weight: 0.0770 chunk 99 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.122262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.071802 restraints weight = 31215.105| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.22 r_work: 0.2870 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15705 Z= 0.119 Angle : 0.527 8.805 22347 Z= 0.284 Chirality : 0.036 0.252 2697 Planarity : 0.004 0.079 2026 Dihedral : 21.813 178.178 4987 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.49 % Favored : 96.43 % Rotamer: Outliers : 1.92 % Allowed : 14.43 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.24), residues: 1261 helix: 1.47 (0.22), residues: 632 sheet: -0.24 (0.42), residues: 136 loop : -0.90 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 901 TYR 0.016 0.001 TYR C 203 PHE 0.015 0.001 PHE A 331 TRP 0.008 0.001 TRP A 478 HIS 0.005 0.001 HIS G 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (15705) covalent geometry : angle 0.52737 / 0.28 (22347) hydrogen bonds : bond 0.04455 / 2.97 ( 652) hydrogen bonds : angle 3.74236 / 2.68 ( 1688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5218.76 seconds wall clock time: 89 minutes 34.71 seconds (5374.71 seconds total)