Starting phenix.real_space_refine on Thu Aug 6 10:34:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q19_72120/08_2026/9q19_72120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q19_72120/08_2026/9q19_72120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q19_72120/08_2026/9q19_72120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q19_72120/08_2026/9q19_72120.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q19_72120/08_2026/9q19_72120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q19_72120/08_2026/9q19_72120.map" } resolution = 3.4 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= 0.013 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 216 5.49 5 S 42 5.16 5 C 8409 2.51 5 N 2649 2.21 5 O 3235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 14551 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7423 Classifications: {'peptide': 926} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 870} Chain breaks: 4 Chain: "B" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 4442 Classifications: {'RNA': 209} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 16, 'rna3p_pur': 82, 'rna3p_pyr': 94} Link IDs: {'rna2p': 33, 'rna3p': 175} Chain breaks: 3 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: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "F" 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: "G" 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: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'55C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.97, per 1000 atoms: 0.20 Number of scatterers: 14551 At special positions: 0 Unit cell: (150.7, 122.1, 123.2, 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 42 16.00 P 216 15.00 O 3235 8.00 N 2649 7.00 C 8409 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: 1.25 Conformation dependent library (CDL) restraints added in 559.9 milliseconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2348 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 10 sheets defined 57.6% alpha, 13.1% beta 65 base pairs and 121 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.635A pdb=" N ARG A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.807A pdb=" N ALA A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 329 through 332 removed outlier: 3.751A 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 353 through 366 removed outlier: 3.821A pdb=" N ARG A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.633A pdb=" N GLN A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 403 removed outlier: 3.684A pdb=" N GLN A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 4.250A pdb=" N LYS A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 452 removed outlier: 4.143A pdb=" N GLN A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.919A pdb=" N GLY A 463 " --> pdb=" O TRP A 459 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.771A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 479' Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.924A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 551 removed outlier: 3.742A pdb=" N HIS A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 544 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.527A pdb=" N SER A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 597 removed outlier: 4.079A pdb=" N LYS A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 655 through 672 removed outlier: 3.808A pdb=" N ALA A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 Processing helix chain 'A' and resid 682 through 699 removed outlier: 4.214A pdb=" N ARG A 688 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 720 removed outlier: 4.112A pdb=" N ILE A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 Processing helix chain 'A' and resid 772 through 784 removed outlier: 3.509A pdb=" N GLU A 782 " --> pdb=" O ALA A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 815 removed outlier: 3.943A pdb=" N ASP A 807 " --> pdb=" O SER A 803 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 853 removed outlier: 3.953A pdb=" N MET A 849 " --> pdb=" O CYS A 845 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 850 " --> pdb=" O TYR A 846 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN A 851 " --> pdb=" O GLY A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 860 removed outlier: 3.924A pdb=" N ARG A 858 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 859 " --> pdb=" O GLY A 856 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP A 860 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 889 removed outlier: 3.602A pdb=" N ALA A 880 " --> pdb=" O HIS A 876 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.096A 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 899 through 903 removed outlier: 4.128A pdb=" N THR A 903 " --> pdb=" O LEU A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 949 Processing helix chain 'A' and resid 965 through 982 removed outlier: 3.753A 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 Processing helix chain 'A' and resid 1024 through 1027 Processing helix chain 'A' and resid 1028 through 1050 removed outlier: 4.315A pdb=" N PHE A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A1034 " --> pdb=" O THR A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1083 removed outlier: 3.915A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A1077 " --> pdb=" O LEU A1073 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A1080 " --> pdb=" O GLN A1076 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1104 Proline residue: A1091 - end of helix removed outlier: 4.355A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A1098 " --> pdb=" O GLY A1094 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A1101 " --> pdb=" O ARG A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1119 removed outlier: 4.144A pdb=" N ALA A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A1117 " --> pdb=" O THR A1113 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 104 removed outlier: 4.221A pdb=" N ILE C 103 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 108 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 172 removed outlier: 3.781A pdb=" N LYS C 170 " --> pdb=" O TRP C 167 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 171 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 4.136A pdb=" N GLY C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 226 Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 56 through 85 Processing helix chain 'F' and resid 91 through 103 removed outlier: 3.859A pdb=" N ILE F 95 " --> pdb=" O THR F 91 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 124 removed outlier: 3.625A pdb=" N ALA F 108 " --> pdb=" O PRO F 104 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS F 109 " --> pdb=" O GLY F 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.484A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA G 70 " --> pdb=" O LEU G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.594A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 96 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 4.377A pdb=" N GLU A 20 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 10.906A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 14.965A pdb=" N CYS A 171 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 20.125A pdb=" N SER A 797 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU A 798 " --> pdb=" O TYR A 739 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR A 739 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA4, first strand: chain 'A' and resid 561 through 565 Processing sheet with id=AA5, first strand: chain 'A' and resid 598 through 600 removed outlier: 6.798A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY A 629 " --> pdb=" O LYS A 626 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 862 through 865 removed outlier: 3.672A pdb=" N VAL A 711 " --> pdb=" O PHE A 870 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 927 through 930 Processing sheet with id=AA8, first strand: chain 'C' and resid 113 through 122 removed outlier: 5.617A pdb=" N LEU C 117 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER C 147 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 119 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N THR C 143 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 10.288A pdb=" N SER C 152 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N LEU C 204 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG C 154 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL C 206 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 156 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ARG C 208 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASP C 186 " --> pdb=" O ASP C 207 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE C 209 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU C 184 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU C 211 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU C 182 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ARG C 180 " --> pdb=" O PRO C 213 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG C 180 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 54 through 55 removed outlier: 7.095A pdb=" N GLY F 54 " --> pdb=" O ILE G 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 89 through 90 487 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 172 hydrogen bonds 322 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 121 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3466 1.33 - 1.46: 4257 1.46 - 1.58: 7098 1.58 - 1.70: 427 1.70 - 1.82: 55 Bond restraints: 15303 Sorted by residual: bond pdb=" C21 55C A1201 " pdb=" O23 55C A1201 " ideal model delta sigma weight residual 1.237 1.327 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" CA PRO A 474 " pdb=" C PRO A 474 " ideal model delta sigma weight residual 1.514 1.497 0.017 5.50e-03 3.31e+04 9.62e+00 bond pdb=" C1' DT D 19 " pdb=" N1 DT D 19 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.51e+00 bond pdb=" C18 55C A1201 " pdb=" C21 55C A1201 " ideal model delta sigma weight residual 1.527 1.472 0.055 2.00e-02 2.50e+03 7.62e+00 bond pdb=" C3' DG D 16 " pdb=" C2' DG D 16 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.29e+00 ... (remaining 15298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 20489 1.51 - 3.01: 1139 3.01 - 4.52: 111 4.52 - 6.03: 22 6.03 - 7.54: 4 Bond angle restraints: 21765 Sorted by residual: angle pdb=" O5' C B 311 " pdb=" C5' C B 311 " pdb=" C4' C B 311 " ideal model delta sigma weight residual 109.40 113.04 -3.64 8.00e-01 1.56e+00 2.07e+01 angle pdb=" C1' C B 56 " pdb=" N1 C B 56 " pdb=" C2 C B 56 " ideal model delta sigma weight residual 118.80 123.71 -4.91 1.10e+00 8.26e-01 1.99e+01 angle pdb=" O5' U B 68 " pdb=" C5' U B 68 " pdb=" C4' U B 68 " ideal model delta sigma weight residual 109.40 112.95 -3.55 8.00e-01 1.56e+00 1.97e+01 angle pdb=" O5' U B 139 " pdb=" C5' U B 139 " pdb=" C4' U B 139 " ideal model delta sigma weight residual 109.40 112.93 -3.53 8.00e-01 1.56e+00 1.95e+01 angle pdb=" O5' U B 115 " pdb=" C5' U B 115 " pdb=" C4' U B 115 " ideal model delta sigma weight residual 109.40 112.87 -3.47 8.00e-01 1.56e+00 1.88e+01 ... (remaining 21760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 8955 35.20 - 70.41: 499 70.41 - 105.61: 86 105.61 - 140.82: 3 140.82 - 176.02: 4 Dihedral angle restraints: 9547 sinusoidal: 5920 harmonic: 3627 Sorted by residual: dihedral pdb=" O4' C B 56 " pdb=" C1' C B 56 " pdb=" N1 C B 56 " pdb=" C2 C B 56 " ideal model delta sinusoidal sigma weight residual 200.00 59.52 140.48 1 1.50e+01 4.44e-03 7.56e+01 dihedral pdb=" O4' U B 133 " pdb=" C1' U B 133 " pdb=" N1 U B 133 " pdb=" C2 U B 133 " ideal model delta sinusoidal sigma weight residual -128.00 48.02 -176.02 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C B 75 " pdb=" C1' C B 75 " pdb=" N1 C B 75 " pdb=" C2 C B 75 " ideal model delta sinusoidal sigma weight residual 232.00 63.83 168.17 1 1.70e+01 3.46e-03 6.57e+01 ... (remaining 9544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1739 0.038 - 0.077: 530 0.077 - 0.115: 167 0.115 - 0.154: 188 0.154 - 0.192: 6 Chirality restraints: 2630 Sorted by residual: chirality pdb=" C1' A B 174 " pdb=" O4' A B 174 " pdb=" C2' A B 174 " pdb=" N9 A B 174 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" C1' C B 56 " pdb=" O4' C B 56 " pdb=" C2' C B 56 " pdb=" N1 C B 56 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" C3' G B 71 " pdb=" C4' G B 71 " pdb=" O3' G B 71 " pdb=" C2' G B 71 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.18 2.00e-01 2.50e+01 8.52e-01 ... (remaining 2627 not shown) Planarity restraints: 1978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 134 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO C 135 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 135 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 135 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 390 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A 391 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 391 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 391 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 457 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 458 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " 0.019 5.00e-02 4.00e+02 ... (remaining 1975 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 221 2.64 - 3.21: 12253 3.21 - 3.77: 22134 3.77 - 4.34: 31091 4.34 - 4.90: 47864 Nonbonded interactions: 113563 Sorted by model distance: nonbonded pdb=" O ASN C 225 " pdb=" OD1 ASN C 225 " model vdw 2.078 3.040 nonbonded pdb=" O2' A B 37 " pdb=" OP1 U B 38 " model vdw 2.204 3.040 nonbonded pdb=" NE ARG A 385 " pdb=" OP1 G B 260 " model vdw 2.222 3.120 nonbonded pdb=" OG SER A 679 " pdb=" NH2 ARG A 865 " model vdw 2.232 3.120 nonbonded pdb=" OP1 C B 320 " pdb=" OH TYR F 41 " model vdw 2.241 3.040 ... (remaining 113558 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: 5.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.390 Find NCS groups from input model: 0.050 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 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 0.090 15303 Z= 0.232 Angle : 0.740 7.536 21765 Z= 0.555 Chirality : 0.052 0.192 2630 Planarity : 0.005 0.038 1978 Dihedral : 19.464 176.020 7199 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -1.41 (0.23), residues: 1234 helix: -1.08 (0.20), residues: 584 sheet: 0.07 (0.46), residues: 122 loop : -0.82 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 865 TYR 0.011 0.002 TYR A 122 PHE 0.018 0.002 PHE A 331 TRP 0.010 0.001 TRP A1026 HIS 0.005 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.23 (15303) covalent geometry : angle 0.73953 / 0.55 (21765) hydrogen bonds : bond 0.23826 / 15.73 ( 659) hydrogen bonds : angle 7.42639 / 5.38 ( 1690) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 210 SER cc_start: 0.4780 (t) cc_final: 0.3900 (t) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1563 time to fit residues: 37.5896 Evaluate side-chains 85 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 799 ASN A 829 GLN A 925 HIS ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN ** G 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.134336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.095276 restraints weight = 45265.376| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.77 r_work: 0.3365 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15303 Z= 0.210 Angle : 0.742 14.551 21765 Z= 0.396 Chirality : 0.046 0.284 2630 Planarity : 0.006 0.055 1978 Dihedral : 21.553 177.584 4794 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.82 % Allowed : 10.24 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -1.04 (0.23), residues: 1234 helix: -0.37 (0.21), residues: 599 sheet: 0.45 (0.49), residues: 116 loop : -1.23 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 610 TYR 0.019 0.002 TYR G 51 PHE 0.026 0.003 PHE G 26 TRP 0.016 0.002 TRP C 98 HIS 0.010 0.002 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (15303) covalent geometry : angle 0.74199 / 0.40 (21765) hydrogen bonds : bond 0.07165 / 4.79 ( 659) hydrogen bonds : angle 4.82240 / 3.49 ( 1690) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8682 (m-80) cc_final: 0.8306 (t80) REVERT: C 98 TRP cc_start: 0.8839 (p-90) cc_final: 0.8421 (p-90) REVERT: C 203 TYR cc_start: 0.7011 (p90) cc_final: 0.6631 (p90) REVERT: G 32 HIS cc_start: 0.8559 (t-90) cc_final: 0.8336 (t70) outliers start: 41 outliers final: 18 residues processed: 125 average time/residue: 0.1087 time to fit residues: 20.2014 Evaluate side-chains 95 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 896 CYS Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 58 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 67 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 120 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 HIS A 799 ASN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN G 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.134853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.095599 restraints weight = 45596.035| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.90 r_work: 0.3376 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15303 Z= 0.145 Angle : 0.631 12.562 21765 Z= 0.333 Chirality : 0.041 0.410 2630 Planarity : 0.005 0.055 1978 Dihedral : 21.484 176.707 4794 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.98 % Allowed : 12.10 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.68 (0.24), residues: 1234 helix: 0.02 (0.21), residues: 602 sheet: 0.21 (0.49), residues: 119 loop : -1.09 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 175 TYR 0.013 0.001 TYR A 825 PHE 0.015 0.002 PHE A 331 TRP 0.014 0.001 TRP A1072 HIS 0.006 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (15303) covalent geometry : angle 0.63088 / 0.33 (21765) hydrogen bonds : bond 0.05942 / 4.01 ( 659) hydrogen bonds : angle 4.58281 / 3.32 ( 1690) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8771 (m-80) cc_final: 0.8443 (m-80) REVERT: A 844 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8234 (mp) REVERT: C 98 TRP cc_start: 0.8908 (p-90) cc_final: 0.8518 (p-90) REVERT: C 156 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8733 (tt) REVERT: C 204 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8863 (tt) outliers start: 32 outliers final: 23 residues processed: 108 average time/residue: 0.1032 time to fit residues: 16.7381 Evaluate side-chains 98 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 116 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 HIS A 799 ASN A 995 GLN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.133419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.094136 restraints weight = 45077.875| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.86 r_work: 0.3349 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15303 Z= 0.182 Angle : 0.643 10.442 21765 Z= 0.340 Chirality : 0.043 0.477 2630 Planarity : 0.005 0.047 1978 Dihedral : 21.482 178.553 4794 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.10 % Allowed : 13.13 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.61 (0.24), residues: 1234 helix: 0.14 (0.21), residues: 601 sheet: -0.04 (0.49), residues: 121 loop : -1.06 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 48 TYR 0.012 0.001 TYR A 825 PHE 0.020 0.002 PHE A 331 TRP 0.015 0.001 TRP A1072 HIS 0.006 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (15303) covalent geometry : angle 0.64281 / 0.34 (21765) hydrogen bonds : bond 0.05853 / 3.96 ( 659) hydrogen bonds : angle 4.52984 / 3.27 ( 1690) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 73 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8808 (m-80) cc_final: 0.8430 (m-80) REVERT: A 631 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7701 (ttm-80) REVERT: A 736 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: A 782 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8623 (pt0) REVERT: A 799 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7815 (t0) REVERT: A 844 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8164 (mp) REVERT: C 98 TRP cc_start: 0.9028 (p-90) cc_final: 0.8517 (p-90) REVERT: C 156 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8709 (tt) REVERT: C 219 LEU cc_start: 0.5311 (OUTLIER) cc_final: 0.4281 (mp) REVERT: F 44 LYS cc_start: 0.7711 (mtmm) cc_final: 0.7487 (mtpp) REVERT: G 32 HIS cc_start: 0.8507 (t70) cc_final: 0.8263 (t70) outliers start: 44 outliers final: 32 residues processed: 107 average time/residue: 0.1075 time to fit residues: 17.4254 Evaluate side-chains 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 896 CYS Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 943 GLN Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 34 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 108 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 139 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 799 ASN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.133771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.096162 restraints weight = 45277.938| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.84 r_work: 0.3385 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15303 Z= 0.134 Angle : 0.586 11.804 21765 Z= 0.311 Chirality : 0.039 0.281 2630 Planarity : 0.005 0.044 1978 Dihedral : 21.468 179.916 4794 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.82 % Allowed : 13.31 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 (0.24), residues: 1234 helix: 0.35 (0.22), residues: 603 sheet: -0.11 (0.48), residues: 126 loop : -1.00 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 100 TYR 0.011 0.001 TYR A 825 PHE 0.015 0.002 PHE C 174 TRP 0.014 0.001 TRP A1072 HIS 0.007 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (15303) covalent geometry : angle 0.58637 / 0.31 (21765) hydrogen bonds : bond 0.05241 / 3.55 ( 659) hydrogen bonds : angle 4.35486 / 3.15 ( 1690) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 79 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8867 (m-80) cc_final: 0.8465 (m-80) REVERT: A 631 ARG cc_start: 0.8114 (ttm110) cc_final: 0.7761 (ttm-80) REVERT: A 736 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7800 (pm20) REVERT: A 799 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7810 (t0) REVERT: A 844 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8163 (mp) REVERT: A 985 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8544 (tt) REVERT: C 98 TRP cc_start: 0.9027 (p-90) cc_final: 0.8503 (p-90) REVERT: C 156 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8609 (tt) REVERT: C 219 LEU cc_start: 0.5174 (OUTLIER) cc_final: 0.4105 (mp) REVERT: F 117 LYS cc_start: 0.9120 (pttm) cc_final: 0.8870 (pttt) outliers start: 41 outliers final: 26 residues processed: 110 average time/residue: 0.1064 time to fit residues: 17.5428 Evaluate side-chains 100 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 28 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 109 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 799 ASN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.133734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.096229 restraints weight = 45380.448| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.67 r_work: 0.3385 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15303 Z= 0.129 Angle : 0.588 12.353 21765 Z= 0.308 Chirality : 0.038 0.384 2630 Planarity : 0.005 0.042 1978 Dihedral : 21.443 178.187 4794 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.45 % Allowed : 14.80 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.31 (0.24), residues: 1234 helix: 0.50 (0.22), residues: 602 sheet: -0.20 (0.48), residues: 126 loop : -0.98 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 100 TYR 0.012 0.001 TYR G 51 PHE 0.017 0.002 PHE A 159 TRP 0.017 0.001 TRP A 459 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (15303) covalent geometry : angle 0.58773 / 0.31 (21765) hydrogen bonds : bond 0.05060 / 3.43 ( 659) hydrogen bonds : angle 4.27544 / 3.09 ( 1690) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8844 (m-80) cc_final: 0.8423 (m-80) REVERT: A 55 LEU cc_start: 0.9150 (tt) cc_final: 0.8933 (tp) REVERT: A 631 ARG cc_start: 0.8060 (ttm110) cc_final: 0.7713 (ttm-80) REVERT: A 736 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: A 782 GLU cc_start: 0.9004 (pt0) cc_final: 0.8773 (pp20) REVERT: A 844 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8194 (mp) REVERT: C 98 TRP cc_start: 0.9034 (p-90) cc_final: 0.8529 (p-90) REVERT: C 219 LEU cc_start: 0.5210 (OUTLIER) cc_final: 0.4298 (mp) REVERT: F 44 LYS cc_start: 0.7674 (mtmm) cc_final: 0.7473 (mtpp) outliers start: 37 outliers final: 27 residues processed: 104 average time/residue: 0.0990 time to fit residues: 15.6029 Evaluate side-chains 104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 70 optimal weight: 0.4980 chunk 131 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 185 GLN G 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.134867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.097083 restraints weight = 45617.580| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.67 r_work: 0.3383 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15303 Z= 0.121 Angle : 0.568 12.589 21765 Z= 0.297 Chirality : 0.037 0.274 2630 Planarity : 0.004 0.044 1978 Dihedral : 21.415 175.582 4794 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.07 % Allowed : 15.64 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.22 (0.24), residues: 1234 helix: 0.59 (0.22), residues: 603 sheet: -0.24 (0.48), residues: 126 loop : -0.92 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 672 TYR 0.016 0.001 TYR A 667 PHE 0.018 0.002 PHE C 174 TRP 0.015 0.001 TRP A 459 HIS 0.006 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (15303) covalent geometry : angle 0.56805 / 0.30 (21765) hydrogen bonds : bond 0.04801 / 3.24 ( 659) hydrogen bonds : angle 4.20051 / 3.03 ( 1690) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8820 (m-80) cc_final: 0.8375 (m-80) REVERT: A 631 ARG cc_start: 0.8089 (ttm110) cc_final: 0.7755 (ttm-80) REVERT: A 736 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: A 844 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8181 (mp) REVERT: C 98 TRP cc_start: 0.9010 (p-90) cc_final: 0.8497 (p-90) REVERT: C 122 GLN cc_start: 0.7864 (mp10) cc_final: 0.7656 (pm20) REVERT: C 143 THR cc_start: 0.8710 (p) cc_final: 0.7988 (p) REVERT: C 219 LEU cc_start: 0.5374 (OUTLIER) cc_final: 0.4521 (mp) REVERT: F 44 LYS cc_start: 0.7711 (mtmm) cc_final: 0.7509 (mtpp) REVERT: F 117 LYS cc_start: 0.9225 (pttt) cc_final: 0.9005 (pttm) outliers start: 33 outliers final: 22 residues processed: 100 average time/residue: 0.1030 time to fit residues: 15.3950 Evaluate side-chains 97 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain G residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 122 optimal weight: 0.0060 chunk 125 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.133739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.096054 restraints weight = 44758.951| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.81 r_work: 0.3447 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15303 Z= 0.123 Angle : 0.574 12.776 21765 Z= 0.294 Chirality : 0.037 0.260 2630 Planarity : 0.004 0.038 1978 Dihedral : 21.384 172.232 4794 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.51 % Allowed : 16.01 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.13 (0.24), residues: 1234 helix: 0.66 (0.22), residues: 604 sheet: -0.19 (0.48), residues: 124 loop : -0.89 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 100 TYR 0.014 0.001 TYR G 51 PHE 0.020 0.002 PHE C 174 TRP 0.014 0.001 TRP A 459 HIS 0.006 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (15303) covalent geometry : angle 0.57386 / 0.29 (21765) hydrogen bonds : bond 0.04787 / 3.23 ( 659) hydrogen bonds : angle 4.16954 / 3.00 ( 1690) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8785 (m-80) cc_final: 0.8327 (m-80) REVERT: A 631 ARG cc_start: 0.8095 (ttm110) cc_final: 0.7758 (ttm-80) REVERT: A 736 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7815 (pm20) REVERT: A 844 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8169 (mp) REVERT: C 98 TRP cc_start: 0.8970 (p-90) cc_final: 0.8455 (p-90) REVERT: C 122 GLN cc_start: 0.7775 (mp10) cc_final: 0.7574 (pm20) REVERT: C 219 LEU cc_start: 0.5392 (OUTLIER) cc_final: 0.4514 (mp) outliers start: 27 outliers final: 23 residues processed: 95 average time/residue: 0.1109 time to fit residues: 15.8637 Evaluate side-chains 93 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain G residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 54 optimal weight: 8.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.133364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.095720 restraints weight = 45079.540| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.50 r_work: 0.3397 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15303 Z= 0.126 Angle : 0.569 13.713 21765 Z= 0.291 Chirality : 0.038 0.428 2630 Planarity : 0.004 0.037 1978 Dihedral : 21.382 172.161 4794 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.42 % Allowed : 16.39 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.11 (0.24), residues: 1234 helix: 0.69 (0.22), residues: 611 sheet: -0.33 (0.48), residues: 124 loop : -0.88 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 446 TYR 0.011 0.001 TYR C 203 PHE 0.019 0.002 PHE C 174 TRP 0.013 0.001 TRP A 459 HIS 0.006 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (15303) covalent geometry : angle 0.56928 / 0.29 (21765) hydrogen bonds : bond 0.04758 / 3.21 ( 659) hydrogen bonds : angle 4.15775 / 2.99 ( 1690) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8879 (m-80) cc_final: 0.8413 (m-80) REVERT: A 631 ARG cc_start: 0.8101 (ttm110) cc_final: 0.7772 (ttm-80) REVERT: A 736 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7817 (pm20) REVERT: A 844 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8158 (mp) REVERT: C 98 TRP cc_start: 0.8969 (p-90) cc_final: 0.8445 (p-90) REVERT: C 143 THR cc_start: 0.8802 (p) cc_final: 0.8102 (p) REVERT: C 210 SER cc_start: 0.8680 (t) cc_final: 0.8442 (t) REVERT: C 219 LEU cc_start: 0.5443 (OUTLIER) cc_final: 0.4549 (mp) REVERT: G 95 ASN cc_start: 0.8152 (m-40) cc_final: 0.7685 (m-40) outliers start: 26 outliers final: 22 residues processed: 97 average time/residue: 0.1100 time to fit residues: 15.9168 Evaluate side-chains 95 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain G residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 73 optimal weight: 0.0980 chunk 102 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 96 optimal weight: 30.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 775 GLN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.134543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.099299 restraints weight = 45270.097| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.64 r_work: 0.3435 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15303 Z= 0.118 Angle : 0.579 13.353 21765 Z= 0.296 Chirality : 0.037 0.299 2630 Planarity : 0.004 0.058 1978 Dihedral : 21.373 172.301 4794 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.61 % Allowed : 16.48 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.13 (0.24), residues: 1234 helix: 0.68 (0.22), residues: 611 sheet: -0.33 (0.48), residues: 127 loop : -0.89 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG G 89 TYR 0.009 0.001 TYR A 176 PHE 0.014 0.002 PHE A 393 TRP 0.022 0.001 TRP A 459 HIS 0.006 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (15303) covalent geometry : angle 0.57877 / 0.30 (21765) hydrogen bonds : bond 0.04632 / 3.12 ( 659) hydrogen bonds : angle 4.13535 / 2.97 ( 1690) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8914 (m-80) cc_final: 0.8437 (m-80) REVERT: A 631 ARG cc_start: 0.8110 (ttm110) cc_final: 0.7785 (ttm-80) REVERT: A 736 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: A 844 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8150 (mp) REVERT: C 98 TRP cc_start: 0.8989 (p-90) cc_final: 0.8468 (p-90) REVERT: C 210 SER cc_start: 0.8747 (t) cc_final: 0.8526 (t) REVERT: C 219 LEU cc_start: 0.5356 (OUTLIER) cc_final: 0.4480 (mp) REVERT: G 95 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.7457 (m-40) outliers start: 28 outliers final: 21 residues processed: 96 average time/residue: 0.1031 time to fit residues: 15.0047 Evaluate side-chains 94 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.134283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.098605 restraints weight = 45300.259| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.74 r_work: 0.3429 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15303 Z= 0.125 Angle : 0.579 13.311 21765 Z= 0.294 Chirality : 0.037 0.269 2630 Planarity : 0.004 0.037 1978 Dihedral : 21.362 172.269 4794 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.42 % Allowed : 16.57 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.10 (0.24), residues: 1234 helix: 0.71 (0.22), residues: 609 sheet: -0.31 (0.48), residues: 127 loop : -0.89 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 446 TYR 0.013 0.001 TYR A 894 PHE 0.014 0.002 PHE A 47 TRP 0.021 0.001 TRP A 459 HIS 0.006 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (15303) covalent geometry : angle 0.57895 / 0.29 (21765) hydrogen bonds : bond 0.04669 / 3.15 ( 659) hydrogen bonds : angle 4.11505 / 2.96 ( 1690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3508.07 seconds wall clock time: 60 minutes 39.99 seconds (3639.99 seconds total)