Starting phenix.real_space_refine on Thu Aug 6 11:50:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q10_72112/08_2026/9q10_72112.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q10_72112/08_2026/9q10_72112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q10_72112/08_2026/9q10_72112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q10_72112/08_2026/9q10_72112.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q10_72112/08_2026/9q10_72112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q10_72112/08_2026/9q10_72112.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 226 5.49 5 S 42 5.16 5 C 8541 2.51 5 N 2695 2.21 5 O 3325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14829 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 4605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 4605 Classifications: {'RNA': 217} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 21, 'rna3p_pur': 86, 'rna3p_pyr': 96} Link IDs: {'rna2p': 35, 'rna3p': 181} Chain breaks: 2 Chain: "A" Number of atoms: 7556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 942, 7556 Classifications: {'peptide': 942} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 885} Chain breaks: 4 Chain: "D" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "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: "F" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 642 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "G" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'1FZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.54, per 1000 atoms: 0.17 Number of scatterers: 14829 At special positions: 0 Unit cell: (146.3, 124.3, 125.4, 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 226 15.00 O 3325 8.00 N 2695 7.00 C 8541 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: 0.98 Conformation dependent library (CDL) restraints added in 394.1 milliseconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 9 sheets defined 53.7% alpha, 12.5% beta 60 base pairs and 113 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 removed outlier: 4.332A pdb=" N ARG A 11 " --> pdb=" O CYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 32 removed outlier: 4.518A pdb=" N ARG A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.527A pdb=" N ALA A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 92 Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.551A pdb=" N ALA A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.655A pdb=" N LEU A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.626A pdb=" N ARG A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 389 through 403 removed outlier: 3.518A pdb=" N LEU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.537A pdb=" N LYS A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 452 removed outlier: 3.907A pdb=" N VAL A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 473 removed outlier: 3.658A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.674A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) removed outlier: 3.566A 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 497 removed outlier: 3.640A pdb=" N ASN A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.781A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 521 " --> pdb=" O ALA A 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 517 through 521' Processing helix chain 'A' and resid 530 through 551 removed outlier: 3.653A pdb=" N ILE A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.856A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 3.569A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.594A pdb=" N ARG A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 672 removed outlier: 3.733A pdb=" N SER A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ARG A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A 668 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.618A pdb=" N LEU A 676 " --> pdb=" O PRO A 673 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 677 " --> pdb=" O GLY A 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 677' Processing helix chain 'A' and resid 682 through 698 removed outlier: 3.503A pdb=" N ARG A 688 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 720 removed outlier: 3.682A pdb=" N THR A 719 " --> pdb=" O GLY A 715 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 715 through 720' Processing helix chain 'A' and resid 723 through 733 removed outlier: 3.569A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 769 removed outlier: 3.813A pdb=" N LEU A 769 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 783 removed outlier: 3.578A pdb=" N HIS A 779 " --> pdb=" O GLN A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 815 removed outlier: 4.005A pdb=" N VAL A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 Processing helix chain 'A' and resid 876 through 889 removed outlier: 3.600A pdb=" N ALA A 880 " --> pdb=" O HIS A 876 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 889 " --> pdb=" O ARG A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 915 Processing helix chain 'A' and resid 967 through 982 removed outlier: 3.751A pdb=" N ARG A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 973 " --> pdb=" O ASN A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 993 through 1017 removed outlier: 3.503A pdb=" N LYS A1003 " --> pdb=" O THR A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1051 removed outlier: 3.685A pdb=" N ILE A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1083 removed outlier: 3.764A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A1077 " --> pdb=" O LEU A1073 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A1080 " --> pdb=" O GLN A1076 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1098 Proline residue: A1091 - end of helix removed outlier: 4.447A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A1098 " --> pdb=" O GLY A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1107 removed outlier: 3.657A pdb=" N SER A1104 " --> pdb=" O GLN A1100 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A1106 " --> pdb=" O GLN A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1119 removed outlier: 3.685A pdb=" N ALA A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 104 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 173 removed outlier: 3.658A pdb=" N GLU C 171 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 240 through 241 No H-bonds generated for 'chain 'C' and resid 240 through 241' Processing helix chain 'F' and resid 18 through 23 removed outlier: 3.645A pdb=" N ARG F 21 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 38 removed outlier: 3.531A pdb=" N VAL F 31 " --> pdb=" O PRO F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 73 removed outlier: 4.340A pdb=" N VAL F 50 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 89 Processing helix chain 'F' and resid 91 through 96 Processing helix chain 'G' and resid 38 through 50 removed outlier: 3.605A pdb=" N VAL G 42 " --> pdb=" O TYR G 38 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN G 48 " --> pdb=" O LYS G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 85 removed outlier: 3.552A pdb=" N ASN G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 103 removed outlier: 3.845A pdb=" N ILE G 95 " --> pdb=" O THR G 91 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU G 103 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 125 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 removed outlier: 3.622A pdb=" N PHE A 159 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU A 798 " --> pdb=" O TYR A 739 " (cutoff:3.500A) removed outlier: 6.031A 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: 6.583A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) removed outlier: 4.063A 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 Processing sheet with id=AA7, first strand: chain 'A' and resid 927 through 929 Processing sheet with id=AA8, first strand: chain 'C' and resid 113 through 122 removed outlier: 5.323A pdb=" N LEU C 117 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N SER C 147 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR C 143 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 10.404A pdb=" N SER C 152 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N LEU C 204 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ARG C 154 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL C 206 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU C 156 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ARG C 208 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP C 186 " --> pdb=" O ASP C 207 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE C 209 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU C 184 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU C 211 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 182 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ARG C 180 " --> pdb=" O PRO C 213 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG C 180 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 78 through 79 460 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 158 hydrogen bonds 308 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 113 stacking parallelities Total time for adding SS restraints: 3.24 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2190 1.32 - 1.45: 5247 1.45 - 1.57: 7658 1.57 - 1.69: 447 1.69 - 1.81: 55 Bond restraints: 15597 Sorted by residual: bond pdb=" O3B 1FZ A1201 " pdb=" PG 1FZ A1201 " ideal model delta sigma weight residual 1.703 1.628 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" N3A 1FZ A1201 " pdb=" PB 1FZ A1201 " ideal model delta sigma weight residual 1.698 1.629 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O5' 1FZ A1201 " pdb=" PA 1FZ A1201 " ideal model delta sigma weight residual 1.640 1.575 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C VAL A 514 " pdb=" O VAL A 514 " ideal model delta sigma weight residual 1.242 1.206 0.036 1.13e-02 7.83e+03 1.03e+01 bond pdb=" O2A 1FZ A1201 " pdb=" PA 1FZ A1201 " ideal model delta sigma weight residual 1.497 1.558 -0.061 2.00e-02 2.50e+03 9.25e+00 ... (remaining 15592 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 21520 1.99 - 3.98: 637 3.98 - 5.97: 34 5.97 - 7.96: 8 7.96 - 9.95: 1 Bond angle restraints: 22200 Sorted by residual: angle pdb=" O4' DG D 17 " pdb=" C4' DG D 17 " pdb=" C3' DG D 17 " ideal model delta sigma weight residual 106.00 99.98 6.02 6.00e-01 2.78e+00 1.01e+02 angle pdb=" C4' DG D 17 " pdb=" C3' DG D 17 " pdb=" C2' DG D 17 " ideal model delta sigma weight residual 103.10 97.17 5.93 9.00e-01 1.23e+00 4.34e+01 angle pdb=" O5' G B 310 " pdb=" C5' G B 310 " pdb=" C4' G B 310 " ideal model delta sigma weight residual 109.40 112.87 -3.47 8.00e-01 1.56e+00 1.88e+01 angle pdb=" N PRO C 97 " pdb=" CA PRO C 97 " pdb=" C PRO C 97 " ideal model delta sigma weight residual 110.50 117.24 -6.74 1.57e+00 4.06e-01 1.84e+01 angle pdb=" C LYS A 626 " pdb=" N PRO A 627 " pdb=" CA PRO A 627 " ideal model delta sigma weight residual 120.23 114.95 5.28 1.23e+00 6.61e-01 1.84e+01 ... (remaining 22195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 9127 35.85 - 71.69: 559 71.69 - 107.54: 93 107.54 - 143.39: 6 143.39 - 179.24: 6 Dihedral angle restraints: 9791 sinusoidal: 6117 harmonic: 3674 Sorted by residual: dihedral pdb=" O4' U B 57 " pdb=" C1' U B 57 " pdb=" N1 U B 57 " pdb=" C2 U B 57 " ideal model delta sinusoidal sigma weight residual 200.00 50.53 149.47 1 1.50e+01 4.44e-03 7.94e+01 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 232.00 52.76 179.24 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 43 " pdb=" C1' U B 43 " pdb=" N1 U B 43 " pdb=" C2 U B 43 " ideal model delta sinusoidal sigma weight residual -128.00 48.53 -176.53 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 9788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2482 0.099 - 0.199: 200 0.199 - 0.298: 2 0.298 - 0.398: 2 0.398 - 0.497: 1 Chirality restraints: 2687 Sorted by residual: chirality pdb=" P DG D 16 " pdb=" OP1 DG D 16 " pdb=" OP2 DG D 16 " pdb=" O5' DG D 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.83 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" P DG D 18 " pdb=" OP1 DG D 18 " pdb=" OP2 DG D 18 " pdb=" O5' DG D 18 " both_signs ideal model delta sigma weight residual True 2.34 -2.70 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" P DG D 17 " pdb=" OP1 DG D 17 " pdb=" OP2 DG D 17 " pdb=" O5' DG D 17 " both_signs ideal model delta sigma weight residual True 2.34 -2.68 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 2684 not shown) Planarity restraints: 2006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 529 " 0.062 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO A 530 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 530 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 530 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 624 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.30e+00 pdb=" N PRO A 625 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 625 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 625 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 300 " -0.025 2.00e-02 2.50e+03 1.17e-02 4.13e+00 pdb=" N9 G B 300 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G B 300 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G B 300 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G B 300 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G B 300 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G B 300 " -0.003 2.00e-02 2.50e+03 pdb=" N1 G B 300 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 300 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G B 300 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 300 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 300 " 0.003 2.00e-02 2.50e+03 ... (remaining 2003 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 91 2.58 - 3.16: 11520 3.16 - 3.74: 22328 3.74 - 4.32: 33594 4.32 - 4.90: 50908 Nonbonded interactions: 118441 Sorted by model distance: nonbonded pdb=" O2' A B 48 " pdb=" O5' A B 49 " model vdw 2.005 3.040 nonbonded pdb=" O2' C B 313 " pdb=" O TRP A 510 " model vdw 2.061 3.040 nonbonded pdb=" O2' G B 71 " pdb=" OP1 C B 72 " model vdw 2.094 3.040 nonbonded pdb=" O2' U B 146 " pdb=" OP1 U B 147 " model vdw 2.116 3.040 nonbonded pdb=" OG SER A 679 " pdb=" NH2 ARG A 865 " model vdw 2.141 3.120 ... (remaining 118436 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: 5.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 0.075 15597 Z= 0.247 Angle : 0.697 9.946 22200 Z= 0.515 Chirality : 0.048 0.497 2687 Planarity : 0.005 0.094 2006 Dihedral : 20.232 179.237 7413 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.18 % Allowed : 4.14 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.91 (0.18), residues: 1250 helix: -3.75 (0.13), residues: 611 sheet: -1.62 (0.41), residues: 143 loop : -2.86 (0.23), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 515 TYR 0.008 0.001 TYR A 552 PHE 0.016 0.002 PHE A 331 TRP 0.009 0.001 TRP A 581 HIS 0.005 0.001 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.25 (15597) covalent geometry : angle 0.69699 / 0.51 (22200) hydrogen bonds : bond 0.26614 / 27.39 ( 618) hydrogen bonds : angle 9.50350 / 11.66 ( 1622) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 58 LYS cc_start: 0.7649 (mttt) cc_final: 0.6845 (pttt) outliers start: 2 outliers final: 0 residues processed: 131 average time/residue: 0.7045 time to fit residues: 98.9122 Evaluate side-chains 65 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 608 GLN C 216 GLN C 225 ASN G 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.136468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.079367 restraints weight = 31301.891| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.52 r_work: 0.2944 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15597 Z= 0.235 Angle : 0.684 8.528 22200 Z= 0.369 Chirality : 0.044 0.238 2687 Planarity : 0.006 0.077 2006 Dihedral : 22.313 179.565 4972 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.30 % Allowed : 9.66 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.21), residues: 1250 helix: -1.84 (0.18), residues: 615 sheet: -1.19 (0.42), residues: 140 loop : -2.21 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1105 TYR 0.013 0.002 TYR A 949 PHE 0.024 0.002 PHE C 172 TRP 0.014 0.002 TRP A 581 HIS 0.005 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.24 (15597) covalent geometry : angle 0.68354 / 0.37 (22200) hydrogen bonds : bond 0.07244 / 7.72 ( 618) hydrogen bonds : angle 4.98393 / 6.04 ( 1622) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 654 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7385 (tt) REVERT: A 659 LYS cc_start: 0.8290 (mttt) cc_final: 0.8070 (mtpt) REVERT: A 787 ARG cc_start: 0.8338 (mtp180) cc_final: 0.8105 (mtp85) REVERT: A 849 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.9123 (ttm) REVERT: C 186 ASP cc_start: 0.9455 (t0) cc_final: 0.9113 (p0) REVERT: F 83 HIS cc_start: 0.8011 (m170) cc_final: 0.7517 (m90) outliers start: 25 outliers final: 10 residues processed: 81 average time/residue: 0.4675 time to fit residues: 42.2463 Evaluate side-chains 66 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 44 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 906 ASN C 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.137577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.080688 restraints weight = 31622.916| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.51 r_work: 0.2980 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15597 Z= 0.137 Angle : 0.557 7.105 22200 Z= 0.308 Chirality : 0.038 0.213 2687 Planarity : 0.005 0.060 2006 Dihedral : 22.224 179.796 4972 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.93 % Allowed : 10.30 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -1.74 (0.22), residues: 1250 helix: -0.54 (0.20), residues: 621 sheet: -0.72 (0.44), residues: 135 loop : -1.97 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1105 TYR 0.010 0.001 TYR A 949 PHE 0.056 0.002 PHE C 174 TRP 0.012 0.001 TRP A 581 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (15597) covalent geometry : angle 0.55706 / 0.31 (22200) hydrogen bonds : bond 0.05302 / 5.68 ( 618) hydrogen bonds : angle 4.34249 / 5.37 ( 1622) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.300 Fit side-chains REVERT: A 787 ARG cc_start: 0.8295 (mtp180) cc_final: 0.8074 (mtp85) REVERT: A 970 MET cc_start: 0.9456 (OUTLIER) cc_final: 0.9243 (ttp) REVERT: C 186 ASP cc_start: 0.9408 (t0) cc_final: 0.9102 (p0) REVERT: C 225 ASN cc_start: 0.5119 (OUTLIER) cc_final: 0.4701 (m-40) REVERT: F 83 HIS cc_start: 0.7977 (m170) cc_final: 0.7525 (m90) outliers start: 21 outliers final: 7 residues processed: 76 average time/residue: 0.5028 time to fit residues: 42.6071 Evaluate side-chains 65 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 1059 LYS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain F residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 94 optimal weight: 0.9990 chunk 66 optimal weight: 0.0170 chunk 15 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.136878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.079775 restraints weight = 31293.942| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.50 r_work: 0.2964 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15597 Z= 0.157 Angle : 0.554 7.169 22200 Z= 0.303 Chirality : 0.038 0.220 2687 Planarity : 0.005 0.052 2006 Dihedral : 22.185 179.284 4972 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.02 % Allowed : 11.96 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -1.29 (0.23), residues: 1250 helix: -0.06 (0.21), residues: 622 sheet: -0.62 (0.44), residues: 135 loop : -1.90 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 83 TYR 0.011 0.001 TYR A 949 PHE 0.022 0.002 PHE C 172 TRP 0.012 0.001 TRP A 581 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (15597) covalent geometry : angle 0.55412 / 0.30 (22200) hydrogen bonds : bond 0.05035 / 5.34 ( 618) hydrogen bonds : angle 4.21021 / 5.19 ( 1622) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 372 MET cc_start: 0.6525 (tpp) cc_final: 0.6243 (tpt) REVERT: A 659 LYS cc_start: 0.8225 (mttt) cc_final: 0.8018 (mtpt) REVERT: A 773 MET cc_start: 0.7574 (tpt) cc_final: 0.7350 (tpp) REVERT: A 787 ARG cc_start: 0.8291 (mtp180) cc_final: 0.8051 (mtp85) REVERT: A 970 MET cc_start: 0.9469 (OUTLIER) cc_final: 0.9237 (ttp) REVERT: C 172 PHE cc_start: 0.7674 (t80) cc_final: 0.7465 (t80) REVERT: C 186 ASP cc_start: 0.9381 (t0) cc_final: 0.9110 (p0) REVERT: F 83 HIS cc_start: 0.7970 (m170) cc_final: 0.7476 (m90) outliers start: 22 outliers final: 12 residues processed: 75 average time/residue: 0.4597 time to fit residues: 38.6721 Evaluate side-chains 66 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 1059 LYS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain G residue 63 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 122 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 0.0370 chunk 46 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 86 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 GLN C 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.136303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.078956 restraints weight = 31411.508| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.47 r_work: 0.2948 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15597 Z= 0.170 Angle : 0.559 7.936 22200 Z= 0.302 Chirality : 0.038 0.225 2687 Planarity : 0.005 0.055 2006 Dihedral : 22.163 178.492 4972 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.76 % Allowed : 11.87 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -0.95 (0.23), residues: 1250 helix: 0.28 (0.21), residues: 629 sheet: -0.62 (0.45), residues: 134 loop : -1.81 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 220 TYR 0.012 0.001 TYR A 949 PHE 0.024 0.002 PHE C 172 TRP 0.013 0.001 TRP A 581 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (15597) covalent geometry : angle 0.55870 / 0.30 (22200) hydrogen bonds : bond 0.05042 / 5.34 ( 618) hydrogen bonds : angle 4.05902 / 5.01 ( 1622) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 659 LYS cc_start: 0.8235 (mttt) cc_final: 0.8031 (mtpt) REVERT: A 734 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7910 (mttp) REVERT: A 787 ARG cc_start: 0.8351 (mtp180) cc_final: 0.8126 (mtp85) REVERT: C 172 PHE cc_start: 0.7664 (t80) cc_final: 0.7361 (t80) REVERT: C 174 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7847 (t80) REVERT: C 186 ASP cc_start: 0.9348 (t0) cc_final: 0.9064 (p0) REVERT: F 83 HIS cc_start: 0.8065 (m170) cc_final: 0.7525 (m90) outliers start: 30 outliers final: 16 residues processed: 80 average time/residue: 0.4140 time to fit residues: 37.5220 Evaluate side-chains 73 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 752 HIS Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain G residue 63 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 0.0070 chunk 137 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 30.0000 chunk 19 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 GLN C 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.136418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.079346 restraints weight = 30717.749| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.43 r_work: 0.2974 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15597 Z= 0.131 Angle : 0.514 8.258 22200 Z= 0.280 Chirality : 0.036 0.229 2687 Planarity : 0.005 0.058 2006 Dihedral : 22.113 178.205 4972 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.84 % Allowed : 13.16 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -0.66 (0.24), residues: 1250 helix: 0.56 (0.22), residues: 630 sheet: -0.49 (0.45), residues: 134 loop : -1.73 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 938 TYR 0.010 0.001 TYR A 949 PHE 0.014 0.001 PHE C 172 TRP 0.011 0.001 TRP A 581 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (15597) covalent geometry : angle 0.51438 / 0.28 (22200) hydrogen bonds : bond 0.04486 / 4.76 ( 618) hydrogen bonds : angle 3.91249 / 4.80 ( 1622) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 372 MET cc_start: 0.6748 (tpp) cc_final: 0.6064 (tpt) REVERT: A 659 LYS cc_start: 0.8196 (mttt) cc_final: 0.7990 (mtpt) REVERT: A 734 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7870 (mttp) REVERT: A 787 ARG cc_start: 0.8369 (mtp180) cc_final: 0.8148 (mtp85) REVERT: A 970 MET cc_start: 0.9466 (OUTLIER) cc_final: 0.9256 (ttp) REVERT: C 172 PHE cc_start: 0.7637 (t80) cc_final: 0.7327 (t80) REVERT: C 174 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7816 (t80) REVERT: F 83 HIS cc_start: 0.8098 (m170) cc_final: 0.7538 (m90) outliers start: 20 outliers final: 13 residues processed: 66 average time/residue: 0.4331 time to fit residues: 32.6843 Evaluate side-chains 68 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 1059 LYS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain G residue 63 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 126 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 GLN C 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.136537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.079015 restraints weight = 31024.896| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.45 r_work: 0.2951 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15597 Z= 0.152 Angle : 0.525 7.211 22200 Z= 0.283 Chirality : 0.037 0.234 2687 Planarity : 0.005 0.058 2006 Dihedral : 22.034 178.382 4972 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.21 % Allowed : 13.06 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -0.56 (0.23), residues: 1250 helix: 0.65 (0.21), residues: 631 sheet: -0.33 (0.45), residues: 132 loop : -1.74 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1011 TYR 0.011 0.001 TYR A 825 PHE 0.017 0.002 PHE A 331 TRP 0.013 0.001 TRP A 581 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (15597) covalent geometry : angle 0.52459 / 0.28 (22200) hydrogen bonds : bond 0.04714 / 4.97 ( 618) hydrogen bonds : angle 3.87973 / 4.70 ( 1622) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 734 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7889 (mttp) REVERT: A 787 ARG cc_start: 0.8339 (mtp180) cc_final: 0.8048 (mtp85) REVERT: C 172 PHE cc_start: 0.7650 (t80) cc_final: 0.7311 (t80) REVERT: C 174 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7923 (t80) REVERT: F 83 HIS cc_start: 0.8124 (m170) cc_final: 0.7558 (m90) REVERT: G 58 LYS cc_start: 0.7098 (mttt) cc_final: 0.6088 (pttt) outliers start: 24 outliers final: 17 residues processed: 74 average time/residue: 0.5020 time to fit residues: 41.6404 Evaluate side-chains 72 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 752 HIS Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain G residue 63 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 96 optimal weight: 0.0170 chunk 41 optimal weight: 0.0050 chunk 116 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 146 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.4032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.137206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.080117 restraints weight = 30889.269| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.43 r_work: 0.2996 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15597 Z= 0.101 Angle : 0.482 6.936 22200 Z= 0.263 Chirality : 0.034 0.236 2687 Planarity : 0.004 0.057 2006 Dihedral : 21.992 177.903 4972 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.75 % Allowed : 14.08 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -0.29 (0.24), residues: 1250 helix: 0.91 (0.22), residues: 630 sheet: -0.33 (0.45), residues: 132 loop : -1.61 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 657 TYR 0.010 0.001 TYR A 949 PHE 0.023 0.001 PHE A 99 TRP 0.012 0.001 TRP A 371 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (15597) covalent geometry : angle 0.48181 / 0.26 (22200) hydrogen bonds : bond 0.04093 / 4.35 ( 618) hydrogen bonds : angle 3.76209 / 4.59 ( 1622) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 506 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8179 (tm-30) REVERT: A 787 ARG cc_start: 0.8326 (mtp180) cc_final: 0.8040 (mtp85) REVERT: C 172 PHE cc_start: 0.7628 (t80) cc_final: 0.7278 (t80) REVERT: C 174 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7978 (t80) REVERT: F 83 HIS cc_start: 0.8140 (m170) cc_final: 0.7531 (m90) outliers start: 19 outliers final: 14 residues processed: 68 average time/residue: 0.4237 time to fit residues: 32.7557 Evaluate side-chains 67 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain G residue 63 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 82 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 GLN A 460 GLN A 737 ASN A1102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.136083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.078909 restraints weight = 30880.723| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.44 r_work: 0.2967 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15597 Z= 0.142 Angle : 0.510 7.556 22200 Z= 0.274 Chirality : 0.036 0.238 2687 Planarity : 0.005 0.056 2006 Dihedral : 21.935 178.296 4972 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.02 % Allowed : 13.89 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -0.27 (0.24), residues: 1250 helix: 0.94 (0.22), residues: 631 sheet: -0.33 (0.45), residues: 132 loop : -1.62 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 657 TYR 0.010 0.001 TYR A 825 PHE 0.019 0.002 PHE A 99 TRP 0.013 0.001 TRP A 581 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (15597) covalent geometry : angle 0.50972 / 0.27 (22200) hydrogen bonds : bond 0.04477 / 4.71 ( 618) hydrogen bonds : angle 3.79122 / 4.58 ( 1622) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 506 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: A 787 ARG cc_start: 0.8322 (mtp180) cc_final: 0.8025 (mtp85) REVERT: C 172 PHE cc_start: 0.7597 (t80) cc_final: 0.7240 (t80) REVERT: C 174 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8057 (t80) REVERT: F 83 HIS cc_start: 0.8163 (m170) cc_final: 0.7551 (m90) REVERT: G 58 LYS cc_start: 0.7086 (mttt) cc_final: 0.6083 (pttt) outliers start: 22 outliers final: 17 residues processed: 67 average time/residue: 0.3976 time to fit residues: 30.4180 Evaluate side-chains 68 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain G residue 63 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 145 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 3 optimal weight: 30.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 GLN A1102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.136115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.078799 restraints weight = 30938.262| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.48 r_work: 0.2966 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15597 Z= 0.139 Angle : 0.507 7.360 22200 Z= 0.273 Chirality : 0.035 0.238 2687 Planarity : 0.004 0.055 2006 Dihedral : 21.915 178.391 4972 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.12 % Allowed : 13.80 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -0.25 (0.24), residues: 1250 helix: 0.96 (0.21), residues: 631 sheet: -0.31 (0.45), residues: 132 loop : -1.62 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 657 TYR 0.011 0.001 TYR A 949 PHE 0.022 0.002 PHE A 99 TRP 0.014 0.001 TRP A 371 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15597) covalent geometry : angle 0.50741 / 0.27 (22200) hydrogen bonds : bond 0.04409 / 4.65 ( 618) hydrogen bonds : angle 3.78210 / 4.58 ( 1622) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 506 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8176 (tm-30) REVERT: A 787 ARG cc_start: 0.8318 (mtp180) cc_final: 0.8019 (mtp85) REVERT: C 172 PHE cc_start: 0.7560 (t80) cc_final: 0.7178 (t80) REVERT: C 174 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8093 (t80) REVERT: F 83 HIS cc_start: 0.8156 (m170) cc_final: 0.7573 (m90) REVERT: G 58 LYS cc_start: 0.7083 (mttt) cc_final: 0.6073 (pttt) outliers start: 23 outliers final: 17 residues processed: 69 average time/residue: 0.4491 time to fit residues: 34.8012 Evaluate side-chains 68 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 752 HIS Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain G residue 63 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 35 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 GLN A1102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.136026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.078765 restraints weight = 30831.535| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.44 r_work: 0.2966 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15597 Z= 0.143 Angle : 0.523 11.022 22200 Z= 0.278 Chirality : 0.036 0.270 2687 Planarity : 0.004 0.052 2006 Dihedral : 21.901 178.378 4972 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.02 % Allowed : 14.17 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.29 (0.24), residues: 1250 helix: 0.92 (0.21), residues: 632 sheet: -0.33 (0.45), residues: 132 loop : -1.64 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 87 TYR 0.013 0.001 TYR A 18 PHE 0.022 0.002 PHE A 99 TRP 0.015 0.001 TRP A 371 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (15597) covalent geometry : angle 0.52330 / 0.28 (22200) hydrogen bonds : bond 0.04467 / 4.70 ( 618) hydrogen bonds : angle 3.81035 / 4.61 ( 1622) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4029.38 seconds wall clock time: 69 minutes 20.00 seconds (4160.00 seconds total)