Starting phenix.real_space_refine on Thu Aug 6 14:58:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qax_52978/08_2026/9qax_52978.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qax_52978/08_2026/9qax_52978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qax_52978/08_2026/9qax_52978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qax_52978/08_2026/9qax_52978.map" model { file = "/net/cci-nas-00/data/ceres_data/9qax_52978/08_2026/9qax_52978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qax_52978/08_2026/9qax_52978.cif" } resolution = 3.3 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= 0.002 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 260 5.49 5 S 42 5.16 5 C 8819 2.51 5 N 2812 2.21 5 O 3538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 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: 15471 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7649 Classifications: {'peptide': 954} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 55, 'TRANS': 895} Chain breaks: 3 Chain: "B" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 5371 Classifications: {'RNA': 253} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 18, 'rna3p_pur': 99, 'rna3p_pyr': 119} Link IDs: {'rna2p': 35, 'rna3p': 217} Chain breaks: 3 Chain: "L" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 632 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "M" 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: "N" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "O" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain breaks: 3 Time building chain proxies: 3.23, per 1000 atoms: 0.21 Number of scatterers: 15471 At special positions: 0 Unit cell: (167.322, 124.962, 144.024, 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 260 15.00 O 3538 8.00 N 2812 7.00 C 8819 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: 0.99 Conformation dependent library (CDL) restraints added in 396.2 milliseconds 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 54.3% alpha, 12.7% beta 71 base pairs and 125 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 removed outlier: 3.903A pdb=" N ARG A 11 " --> pdb=" O CYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.589A pdb=" N VAL A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 92 removed outlier: 3.590A pdb=" N VAL A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 87 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.863A pdb=" N GLY A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.805A pdb=" N ARG A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.730A pdb=" N LEU A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing helix 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 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 389 through 402 removed outlier: 3.643A pdb=" N PHE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.505A pdb=" N LEU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 454 removed outlier: 3.536A pdb=" N ARG A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.901A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.701A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 497 removed outlier: 3.508A pdb=" N LYS A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 496 " --> pdb=" O LYS A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.679A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 551 removed outlier: 3.528A pdb=" N LYS A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.656A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 597 removed outlier: 3.722A pdb=" N LYS A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.687A pdb=" N GLU A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 672 removed outlier: 4.095A pdb=" N LYS A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 Processing helix chain 'A' and resid 682 through 698 removed outlier: 3.849A pdb=" N THR A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 734 removed outlier: 3.667A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 733 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 769 removed outlier: 3.570A pdb=" N LEU A 769 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 Processing helix chain 'A' and resid 802 through 814 Processing helix chain 'A' and resid 837 through 854 removed outlier: 3.670A pdb=" N CYS A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 843 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 859 Processing helix chain 'A' and resid 876 through 890 removed outlier: 3.674A pdb=" N ALA A 880 " --> pdb=" O HIS A 876 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 890 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 950 removed outlier: 3.613A pdb=" N TYR A 949 " --> pdb=" O TYR A 946 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 950 " --> pdb=" O SER A 947 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 946 through 950' Processing helix chain 'A' and resid 965 through 982 removed outlier: 3.562A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 993 through 1017 removed outlier: 3.563A pdb=" N LEU A1007 " --> pdb=" O LYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1028 removed outlier: 3.545A pdb=" N LYS A1027 " --> pdb=" O GLN A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1051 removed outlier: 3.573A pdb=" N ASP A1038 " --> pdb=" O ARG A1034 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS A1043 " --> pdb=" O THR A1039 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A1051 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1085 removed outlier: 3.902A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS A1075 " --> pdb=" O GLN A1071 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.580A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Proline residue: A1091 - end of helix removed outlier: 4.086A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A1102 " --> pdb=" O THR A1098 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A1106 " --> pdb=" O GLN A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1119 removed outlier: 3.860A pdb=" N THR A1113 " --> pdb=" O GLY A1109 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A1117 " --> pdb=" O THR A1113 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 38 removed outlier: 4.418A pdb=" N LEU L 34 " --> pdb=" O ARG L 30 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU L 35 " --> pdb=" O VAL L 31 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 73 removed outlier: 4.499A pdb=" N VAL L 50 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR L 51 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 91 removed outlier: 3.967A pdb=" N LEU L 84 " --> pdb=" O ILE L 80 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG L 89 " --> pdb=" O GLN L 85 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 99 removed outlier: 3.638A pdb=" N ASN L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS L 96 " --> pdb=" O GLU L 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 50 removed outlier: 3.659A pdb=" N VAL M 45 " --> pdb=" O TYR M 41 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS M 47 " --> pdb=" O TYR M 43 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL M 49 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 86 removed outlier: 4.007A pdb=" N SER M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS M 83 " --> pdb=" O SER M 79 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR M 84 " --> pdb=" O ARG M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 103 removed outlier: 3.781A pdb=" N ILE M 95 " --> pdb=" O THR M 91 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN M 96 " --> pdb=" O SER M 92 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THR M 97 " --> pdb=" O ARG M 93 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU M 103 " --> pdb=" O VAL M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.751A pdb=" N SER M 113 " --> pdb=" O LYS M 109 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU M 114 " --> pdb=" O HIS M 110 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY M 115 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR M 120 " --> pdb=" O THR M 116 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER M 125 " --> pdb=" O LYS M 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 104 removed outlier: 3.841A pdb=" N ILE O 103 " --> pdb=" O ILE O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 164 removed outlier: 3.628A pdb=" N LEU O 162 " --> pdb=" O THR O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 238 removed outlier: 3.530A pdb=" N LYS O 232 " --> pdb=" O LEU O 228 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS O 233 " --> pdb=" O ASP O 229 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU O 234 " --> pdb=" O VAL O 230 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR O 235 " --> pdb=" O GLN O 231 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP O 236 " --> pdb=" O LYS O 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS O 237 " --> pdb=" O LYS O 233 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU O 238 " --> pdb=" O LEU O 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.776A pdb=" N ALA A 157 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 11.341A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.776A pdb=" N ALA A 157 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 11.341A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 739 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA6, first strand: chain 'A' and resid 599 through 600 removed outlier: 7.340A pdb=" N LEU A 617 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ARG A 819 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 679 through 680 removed outlier: 3.709A pdb=" N LEU A 866 " --> pdb=" O ASP A 869 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 869 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 711 " --> pdb=" O PHE A 870 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 709 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 905 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 927 through 930 Processing sheet with id=AA9, first strand: chain 'O' and resid 181 through 184 removed outlier: 7.214A pdb=" N LEU O 145 " --> pdb=" O LEU O 118 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL O 120 " --> pdb=" O THR O 143 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR O 143 " --> pdb=" O VAL O 120 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N LEU O 204 " --> pdb=" O SER O 152 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ARG O 154 " --> pdb=" O LEU O 204 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL O 206 " --> pdb=" O ARG O 154 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU O 156 " --> pdb=" O VAL O 206 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 187 hydrogen bonds 346 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 125 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1919 1.31 - 1.44: 5730 1.44 - 1.57: 8104 1.57 - 1.70: 515 1.70 - 1.82: 55 Bond restraints: 16323 Sorted by residual: bond pdb=" C GLN A 454 " pdb=" O GLN A 454 " ideal model delta sigma weight residual 1.233 1.183 0.051 1.06e-02 8.90e+03 2.29e+01 bond pdb=" C2' U B 307 " pdb=" C1' U B 307 " ideal model delta sigma weight residual 1.526 1.499 0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C GLN A 585 " pdb=" O GLN A 585 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" C VAL A 554 " pdb=" O VAL A 554 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.19e-02 7.06e+03 1.08e+01 bond pdb=" O5' DG N 28 " pdb=" C5' DG N 28 " ideal model delta sigma weight residual 1.418 1.499 -0.081 2.50e-02 1.60e+03 1.06e+01 ... (remaining 16318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 22241 2.53 - 5.06: 1064 5.06 - 7.59: 32 7.59 - 10.12: 5 10.12 - 12.65: 4 Bond angle restraints: 23346 Sorted by residual: angle pdb=" O3' C B 119 " pdb=" P G B 120 " pdb=" O5' G B 120 " ideal model delta sigma weight residual 104.00 91.35 12.65 1.90e+00 2.77e-01 4.43e+01 angle pdb=" O6 G B 58 " pdb=" C6 G B 58 " pdb=" N1 G B 58 " ideal model delta sigma weight residual 119.90 116.19 3.71 6.00e-01 2.78e+00 3.82e+01 angle pdb=" C LYS A 338 " pdb=" CA LYS A 338 " pdb=" CB LYS A 338 " ideal model delta sigma weight residual 109.84 101.72 8.12 1.50e+00 4.44e-01 2.93e+01 angle pdb=" C HIS A1022 " pdb=" CA HIS A1022 " pdb=" CB HIS A1022 " ideal model delta sigma weight residual 110.42 120.51 -10.09 1.99e+00 2.53e-01 2.57e+01 angle pdb=" O4' U B 307 " pdb=" C4' U B 307 " pdb=" C3' U B 307 " ideal model delta sigma weight residual 106.10 102.18 3.92 8.00e-01 1.56e+00 2.40e+01 ... (remaining 23341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 9450 35.84 - 71.68: 704 71.68 - 107.52: 111 107.52 - 143.35: 8 143.35 - 179.19: 11 Dihedral angle restraints: 10284 sinusoidal: 6663 harmonic: 3621 Sorted by residual: dihedral pdb=" C4' U B 307 " pdb=" C3' U B 307 " pdb=" C2' U B 307 " pdb=" C1' U B 307 " ideal model delta sinusoidal sigma weight residual -35.00 36.96 -71.96 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C5' A B 176 " pdb=" C4' A B 176 " pdb=" C3' A B 176 " pdb=" O3' A B 176 " ideal model delta sinusoidal sigma weight residual 147.00 75.57 71.43 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' A B 176 " pdb=" C3' A B 176 " pdb=" C2' A B 176 " pdb=" C1' A B 176 " ideal model delta sinusoidal sigma weight residual -35.00 35.50 -70.50 1 8.00e+00 1.56e-02 9.99e+01 ... (remaining 10281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2531 0.117 - 0.235: 300 0.235 - 0.352: 13 0.352 - 0.470: 2 0.470 - 0.587: 4 Chirality restraints: 2850 Sorted by residual: chirality pdb=" P DG N 24 " pdb=" OP1 DG N 24 " pdb=" OP2 DG N 24 " pdb=" O5' DG N 24 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.59 2.00e-01 2.50e+01 8.62e+00 chirality pdb=" P C B 238 " pdb=" OP1 C B 238 " pdb=" OP2 C B 238 " pdb=" O5' C B 238 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" P G B 163 " pdb=" OP1 G B 163 " pdb=" OP2 G B 163 " pdb=" O5' G B 163 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.34e+00 ... (remaining 2847 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 142 " -0.208 2.00e-02 2.50e+03 1.05e-01 2.50e+02 pdb=" N1 C B 142 " 0.051 2.00e-02 2.50e+03 pdb=" C2 C B 142 " 0.057 2.00e-02 2.50e+03 pdb=" O2 C B 142 " 0.055 2.00e-02 2.50e+03 pdb=" N3 C B 142 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C B 142 " 0.054 2.00e-02 2.50e+03 pdb=" N4 C B 142 " -0.176 2.00e-02 2.50e+03 pdb=" C5 C B 142 " 0.067 2.00e-02 2.50e+03 pdb=" C6 C B 142 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 307 " -0.114 2.00e-02 2.50e+03 6.11e-02 8.40e+01 pdb=" N1 U B 307 " 0.108 2.00e-02 2.50e+03 pdb=" C2 U B 307 " 0.026 2.00e-02 2.50e+03 pdb=" O2 U B 307 " 0.036 2.00e-02 2.50e+03 pdb=" N3 U B 307 " -0.047 2.00e-02 2.50e+03 pdb=" C4 U B 307 " -0.038 2.00e-02 2.50e+03 pdb=" O4 U B 307 " -0.021 2.00e-02 2.50e+03 pdb=" C5 U B 307 " 0.052 2.00e-02 2.50e+03 pdb=" C6 U B 307 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 291 " -0.057 2.00e-02 2.50e+03 4.12e-02 3.82e+01 pdb=" N1 U B 291 " 0.017 2.00e-02 2.50e+03 pdb=" C2 U B 291 " -0.028 2.00e-02 2.50e+03 pdb=" O2 U B 291 " 0.074 2.00e-02 2.50e+03 pdb=" N3 U B 291 " -0.050 2.00e-02 2.50e+03 pdb=" C4 U B 291 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U B 291 " -0.019 2.00e-02 2.50e+03 pdb=" C5 U B 291 " 0.049 2.00e-02 2.50e+03 pdb=" C6 U B 291 " 0.015 2.00e-02 2.50e+03 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 4 2.02 - 2.74: 1058 2.74 - 3.46: 20409 3.46 - 4.18: 39932 4.18 - 4.90: 60870 Nonbonded interactions: 122273 Sorted by model distance: nonbonded pdb=" O TRP A 510 " pdb=" O2' C B 313 " model vdw 1.305 3.040 nonbonded pdb=" CA HIS A 752 " pdb=" O6 G B 58 " model vdw 1.830 3.470 nonbonded pdb=" OG SER A 12 " pdb=" O2' A B 61 " model vdw 1.837 3.040 nonbonded pdb=" C HIS A 752 " pdb=" O6 G B 58 " model vdw 2.004 3.270 nonbonded pdb=" O PHE A1021 " pdb=" O2' U B 312 " model vdw 2.050 3.040 ... (remaining 122268 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: 1.490 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 15.690 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.009 0.093 16323 Z= 0.612 Angle : 1.182 12.653 23346 Z= 0.820 Chirality : 0.078 0.587 2850 Planarity : 0.011 0.187 2013 Dihedral : 22.040 179.192 7938 Min Nonbonded Distance : 1.305 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.28 % Favored : 93.32 % Rotamer: Outliers : 0.09 % Allowed : 1.77 % Favored : 98.14 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.55 % 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: -3.15 (0.19), residues: 1227 helix: -1.93 (0.17), residues: 538 sheet: -1.96 (0.42), residues: 106 loop : -2.20 (0.22), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.002 ARG A 470 TYR 0.043 0.007 TYR A 946 PHE 0.057 0.008 PHE A 544 TRP 0.078 0.010 TRP A 510 HIS 0.019 0.003 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00868 / 0.61 (16323) covalent geometry : angle 1.18232 / 0.82 (23346) hydrogen bonds : bond 0.27598 / 18.46 ( 624) hydrogen bonds : angle 8.36241 / 5.91 ( 1648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8568 (mtpt) REVERT: A 726 THR cc_start: 0.8879 (m) cc_final: 0.8606 (p) REVERT: A 824 SER cc_start: 0.8106 (m) cc_final: 0.7748 (p) REVERT: A 850 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7039 (tp30) REVERT: A 873 VAL cc_start: 0.7444 (t) cc_final: 0.6947 (m) REVERT: A 972 ARG cc_start: 0.8966 (ttm170) cc_final: 0.8701 (mtp85) REVERT: L 63 ILE cc_start: 0.6909 (tt) cc_final: 0.6517 (tp) REVERT: M 58 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8421 (mmmm) REVERT: O 116 GLN cc_start: 0.4017 (tt0) cc_final: 0.3630 (tm-30) REVERT: O 151 HIS cc_start: 0.8001 (m90) cc_final: 0.6972 (m-70) REVERT: O 154 ARG cc_start: 0.7406 (ttp80) cc_final: 0.6970 (ptt-90) REVERT: O 182 LEU cc_start: 0.4433 (mt) cc_final: 0.4217 (mm) REVERT: O 203 TYR cc_start: 0.7871 (p90) cc_final: 0.7562 (p90) outliers start: 1 outliers final: 1 residues processed: 161 average time/residue: 0.1481 time to fit residues: 32.8178 Evaluate side-chains 77 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 40 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 50.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 GLN ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS A 879 HIS A 906 ASN A1013 HIS O 185 GLN O 216 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.124916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.096977 restraints weight = 62490.860| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 3.12 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 16323 Z= 0.207 Angle : 0.772 12.576 23346 Z= 0.409 Chirality : 0.048 0.609 2850 Planarity : 0.006 0.098 2013 Dihedral : 23.967 177.979 5520 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.58 % Rotamer: Outliers : 1.30 % Allowed : 6.42 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.51 (0.21), residues: 1227 helix: -0.19 (0.20), residues: 571 sheet: -1.93 (0.40), residues: 133 loop : -1.58 (0.24), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 96 TYR 0.034 0.002 TYR O 203 PHE 0.023 0.003 PHE A 544 TRP 0.039 0.003 TRP O 167 HIS 0.007 0.002 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 (16323) covalent geometry : angle 0.77248 / 0.41 (23346) hydrogen bonds : bond 0.07277 / 5.01 ( 624) hydrogen bonds : angle 5.00169 / 3.61 ( 1648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 HIS cc_start: 0.7163 (m170) cc_final: 0.6676 (m170) REVERT: O 151 HIS cc_start: 0.5763 (m90) cc_final: 0.4930 (m-70) outliers start: 14 outliers final: 5 residues processed: 98 average time/residue: 0.1313 time to fit residues: 18.4734 Evaluate side-chains 71 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain M residue 123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 26 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN A 609 HIS A 748 GLN A 879 HIS ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.123068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.093336 restraints weight = 62147.339| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.31 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 16323 Z= 0.189 Angle : 0.644 10.980 23346 Z= 0.350 Chirality : 0.043 0.493 2850 Planarity : 0.006 0.079 2013 Dihedral : 23.835 178.977 5519 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.42 % Favored : 96.41 % Rotamer: Outliers : 1.21 % Allowed : 8.47 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.79 (0.22), residues: 1227 helix: 0.48 (0.21), residues: 573 sheet: -1.59 (0.41), residues: 134 loop : -1.30 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 378 TYR 0.039 0.002 TYR O 203 PHE 0.018 0.002 PHE A 561 TRP 0.019 0.002 TRP A 510 HIS 0.010 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (16323) covalent geometry : angle 0.64433 / 0.35 (23346) hydrogen bonds : bond 0.06991 / 4.98 ( 624) hydrogen bonds : angle 4.54329 / 3.28 ( 1648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 50 HIS cc_start: 0.7506 (m170) cc_final: 0.7095 (m170) outliers start: 13 outliers final: 6 residues processed: 82 average time/residue: 0.1356 time to fit residues: 16.1508 Evaluate side-chains 67 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain O residue 166 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 115 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 140 optimal weight: 30.0000 chunk 26 optimal weight: 0.6980 chunk 96 optimal weight: 50.0000 chunk 90 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 HIS ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 GLN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.122646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.092630 restraints weight = 61900.930| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.27 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16323 Z= 0.147 Angle : 0.597 10.043 23346 Z= 0.320 Chirality : 0.039 0.361 2850 Planarity : 0.005 0.067 2013 Dihedral : 23.741 176.677 5519 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.85 % Favored : 96.98 % Rotamer: Outliers : 0.93 % Allowed : 9.03 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.45 (0.23), residues: 1227 helix: 0.80 (0.21), residues: 564 sheet: -1.17 (0.43), residues: 132 loop : -1.23 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 610 TYR 0.012 0.001 TYR A 707 PHE 0.015 0.002 PHE A 883 TRP 0.012 0.001 TRP A 547 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (16323) covalent geometry : angle 0.59675 / 0.32 (23346) hydrogen bonds : bond 0.05738 / 3.95 ( 624) hydrogen bonds : angle 4.30768 / 3.09 ( 1648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 766 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7474 (pt) REVERT: A 813 MET cc_start: 0.7827 (tpp) cc_final: 0.7467 (tpp) REVERT: M 50 HIS cc_start: 0.7485 (m170) cc_final: 0.7108 (m170) outliers start: 10 outliers final: 5 residues processed: 75 average time/residue: 0.1415 time to fit residues: 15.5332 Evaluate side-chains 65 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain O residue 166 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 105 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.0370 chunk 114 optimal weight: 20.0000 chunk 47 optimal weight: 0.3980 chunk 134 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN A 609 HIS ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN O 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.123205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.093444 restraints weight = 61925.666| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.12 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16323 Z= 0.115 Angle : 0.539 9.009 23346 Z= 0.292 Chirality : 0.037 0.335 2850 Planarity : 0.004 0.067 2013 Dihedral : 23.699 173.928 5519 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 1.40 % Allowed : 9.59 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.01 (0.23), residues: 1227 helix: 1.11 (0.22), residues: 574 sheet: -0.66 (0.45), residues: 132 loop : -1.07 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 208 TYR 0.013 0.001 TYR A 176 PHE 0.012 0.001 PHE A 919 TRP 0.012 0.001 TRP A 510 HIS 0.003 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 (16323) covalent geometry : angle 0.53928 / 0.29 (23346) hydrogen bonds : bond 0.05247 / 3.65 ( 624) hydrogen bonds : angle 4.06867 / 2.93 ( 1648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 402 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7426 (tp-100) REVERT: A 766 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7573 (pt) REVERT: M 50 HIS cc_start: 0.7716 (m170) cc_final: 0.7390 (m170) REVERT: M 68 ASN cc_start: 0.8395 (m-40) cc_final: 0.8013 (p0) outliers start: 15 outliers final: 6 residues processed: 74 average time/residue: 0.1495 time to fit residues: 16.0508 Evaluate side-chains 63 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain O residue 221 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 30.0000 chunk 35 optimal weight: 0.0870 chunk 137 optimal weight: 0.0270 chunk 75 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.0218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 HIS A 737 ASN A 748 GLN ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.122679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.091309 restraints weight = 61480.804| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.20 r_work: 0.3627 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 16323 Z= 0.122 Angle : 0.545 10.510 23346 Z= 0.295 Chirality : 0.038 0.343 2850 Planarity : 0.004 0.065 2013 Dihedral : 23.684 172.365 5519 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.93 % Favored : 96.90 % Rotamer: Outliers : 1.40 % Allowed : 10.43 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.03 (0.23), residues: 1227 helix: 1.13 (0.22), residues: 580 sheet: -0.63 (0.45), residues: 132 loop : -1.05 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 859 TYR 0.011 0.001 TYR A 176 PHE 0.013 0.001 PHE A 919 TRP 0.010 0.001 TRP A 547 HIS 0.004 0.001 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (16323) covalent geometry : angle 0.54490 / 0.30 (23346) hydrogen bonds : bond 0.05104 / 3.57 ( 624) hydrogen bonds : angle 4.03408 / 2.91 ( 1648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7995 (tp-100) REVERT: A 766 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7747 (pt) REVERT: L 30 ARG cc_start: 0.7743 (ttm170) cc_final: 0.7464 (mmm160) REVERT: M 50 HIS cc_start: 0.7337 (m170) cc_final: 0.6757 (m170) outliers start: 15 outliers final: 9 residues processed: 71 average time/residue: 0.1511 time to fit residues: 15.1075 Evaluate side-chains 65 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain O residue 221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 546 HIS A 609 HIS ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.121419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.089379 restraints weight = 60718.556| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.18 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16323 Z= 0.139 Angle : 0.555 9.860 23346 Z= 0.297 Chirality : 0.038 0.331 2850 Planarity : 0.004 0.058 2013 Dihedral : 23.730 172.669 5519 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.50 % Favored : 96.33 % Rotamer: Outliers : 1.30 % Allowed : 11.36 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.21 (0.24), residues: 1227 helix: 1.23 (0.22), residues: 577 sheet: -0.54 (0.46), residues: 132 loop : -0.89 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 859 TYR 0.012 0.001 TYR A 739 PHE 0.013 0.002 PHE A 883 TRP 0.016 0.001 TRP A 510 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (16323) covalent geometry : angle 0.55549 / 0.30 (23346) hydrogen bonds : bond 0.05198 / 3.69 ( 624) hydrogen bonds : angle 4.04478 / 2.91 ( 1648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7756 (tp-100) REVERT: A 813 MET cc_start: 0.7914 (mmm) cc_final: 0.7529 (tpp) REVERT: A 969 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7782 (t0) REVERT: L 78 ARG cc_start: 0.5388 (mtt90) cc_final: 0.5179 (mtt-85) REVERT: M 50 HIS cc_start: 0.7785 (m170) cc_final: 0.7421 (m170) REVERT: M 68 ASN cc_start: 0.8406 (m-40) cc_final: 0.8155 (p0) REVERT: O 98 TRP cc_start: 0.6105 (m100) cc_final: 0.5890 (m100) outliers start: 14 outliers final: 8 residues processed: 72 average time/residue: 0.1266 time to fit residues: 13.3021 Evaluate side-chains 67 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain O residue 221 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 121 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 HIS A 748 GLN ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.121811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.089727 restraints weight = 61231.898| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.27 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16323 Z= 0.117 Angle : 0.528 10.205 23346 Z= 0.285 Chirality : 0.036 0.333 2850 Planarity : 0.004 0.056 2013 Dihedral : 23.731 171.191 5519 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.58 % Rotamer: Outliers : 1.77 % Allowed : 11.45 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.26 (0.24), residues: 1227 helix: 1.26 (0.22), residues: 578 sheet: -0.53 (0.46), residues: 132 loop : -0.85 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 968 TYR 0.010 0.001 TYR A 176 PHE 0.013 0.001 PHE A 919 TRP 0.010 0.001 TRP A 547 HIS 0.003 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (16323) covalent geometry : angle 0.52769 / 0.28 (23346) hydrogen bonds : bond 0.04971 / 3.52 ( 624) hydrogen bonds : angle 3.99787 / 2.88 ( 1648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7716 (tp-100) REVERT: A 766 LEU cc_start: 0.5586 (pt) cc_final: 0.5270 (pt) REVERT: A 813 MET cc_start: 0.7915 (mmm) cc_final: 0.7449 (tpp) REVERT: L 78 ARG cc_start: 0.5449 (mtt90) cc_final: 0.5228 (mtt-85) REVERT: M 50 HIS cc_start: 0.7581 (m170) cc_final: 0.7275 (m170) REVERT: O 98 TRP cc_start: 0.6121 (m100) cc_final: 0.5905 (m100) outliers start: 19 outliers final: 10 residues processed: 74 average time/residue: 0.1448 time to fit residues: 15.2831 Evaluate side-chains 70 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1054 MET Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain O residue 221 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 129 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 111 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 HIS A 748 GLN ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.122507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.090378 restraints weight = 60882.850| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.31 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16323 Z= 0.107 Angle : 0.535 12.573 23346 Z= 0.282 Chirality : 0.036 0.329 2850 Planarity : 0.004 0.055 2013 Dihedral : 23.704 171.438 5519 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.58 % Rotamer: Outliers : 0.93 % Allowed : 12.48 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.39 (0.24), residues: 1227 helix: 1.38 (0.22), residues: 580 sheet: -0.58 (0.46), residues: 132 loop : -0.77 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 30 TYR 0.011 0.001 TYR A 176 PHE 0.014 0.001 PHE A 919 TRP 0.011 0.001 TRP A 510 HIS 0.003 0.001 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 (16323) covalent geometry : angle 0.53500 / 0.28 (23346) hydrogen bonds : bond 0.04744 / 3.37 ( 624) hydrogen bonds : angle 3.91331 / 2.82 ( 1648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7712 (tp-100) REVERT: A 766 LEU cc_start: 0.5443 (pt) cc_final: 0.5150 (pt) REVERT: A 813 MET cc_start: 0.7949 (mmm) cc_final: 0.7478 (tpp) REVERT: A 940 LEU cc_start: 0.8367 (pp) cc_final: 0.8059 (tp) REVERT: L 78 ARG cc_start: 0.5346 (mtt90) cc_final: 0.5138 (mtt-85) REVERT: M 50 HIS cc_start: 0.7578 (m170) cc_final: 0.7316 (m170) REVERT: O 98 TRP cc_start: 0.6135 (m100) cc_final: 0.5915 (m100) outliers start: 10 outliers final: 8 residues processed: 65 average time/residue: 0.1355 time to fit residues: 13.0829 Evaluate side-chains 66 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1054 MET Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain O residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 126 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN A 609 HIS ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.120339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.087872 restraints weight = 60404.636| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.24 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16323 Z= 0.162 Angle : 0.579 11.257 23346 Z= 0.303 Chirality : 0.038 0.327 2850 Planarity : 0.004 0.054 2013 Dihedral : 23.773 171.670 5519 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.42 % Favored : 96.41 % Rotamer: Outliers : 1.02 % Allowed : 12.57 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1227 helix: 1.25 (0.22), residues: 581 sheet: -0.77 (0.46), residues: 130 loop : -0.78 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 30 TYR 0.009 0.001 TYR A 552 PHE 0.018 0.002 PHE A1078 TRP 0.009 0.002 TRP A 547 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (16323) covalent geometry : angle 0.57897 / 0.30 (23346) hydrogen bonds : bond 0.05260 / 3.75 ( 624) hydrogen bonds : angle 4.05309 / 2.92 ( 1648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7763 (tp-100) REVERT: A 766 LEU cc_start: 0.5425 (pt) cc_final: 0.5162 (pt) REVERT: A 969 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7739 (t0) REVERT: L 78 ARG cc_start: 0.5564 (mtt90) cc_final: 0.5341 (mtt-85) REVERT: M 50 HIS cc_start: 0.7704 (m170) cc_final: 0.7434 (m170) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.1272 time to fit residues: 12.2378 Evaluate side-chains 64 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain O residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 144 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 0.0030 chunk 116 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 114 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 72 optimal weight: 0.0770 chunk 41 optimal weight: 0.2980 overall best weight: 0.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 HIS ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.122061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.091505 restraints weight = 60810.228| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.23 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16323 Z= 0.102 Angle : 0.536 14.722 23346 Z= 0.284 Chirality : 0.036 0.327 2850 Planarity : 0.004 0.059 2013 Dihedral : 23.773 171.500 5519 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.58 % Rotamer: Outliers : 0.56 % Allowed : 13.22 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.37 (0.24), residues: 1227 helix: 1.37 (0.22), residues: 582 sheet: -0.75 (0.47), residues: 132 loop : -0.74 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 968 TYR 0.012 0.001 TYR A 176 PHE 0.015 0.001 PHE A 919 TRP 0.012 0.001 TRP A1072 HIS 0.003 0.000 HIS A 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (16323) covalent geometry : angle 0.53609 / 0.28 (23346) hydrogen bonds : bond 0.04667 / 3.36 ( 624) hydrogen bonds : angle 3.94280 / 2.84 ( 1648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3180.32 seconds wall clock time: 55 minutes 19.27 seconds (3319.27 seconds total)