Starting phenix.real_space_refine on Thu Sep 18 09:49:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qax_52978/09_2025/9qax_52978.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qax_52978/09_2025/9qax_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_52978/09_2025/9qax_52978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qax_52978/09_2025/9qax_52978.map" model { file = "/net/cci-nas-00/data/ceres_data/9qax_52978/09_2025/9qax_52978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qax_52978/09_2025/9qax_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-2.0-5805/lib/python3.9/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: 4.26, per 1000 atoms: 0.28 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: 1.34 Conformation dependent library (CDL) restraints added in 614.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.72 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: 5.37 Time building geometry restraints manager: 1.87 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=" O5' G B 259 " pdb=" C5' G B 259 " ideal model delta sigma weight residual 1.420 1.471 -0.051 1.50e-02 4.44e+03 1.13e+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' U B 306 " pdb=" C5' U B 306 " ideal model delta sigma weight residual 1.420 1.468 -0.048 1.50e-02 4.44e+03 1.03e+01 ... (remaining 16318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 22212 2.53 - 5.06: 1093 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 1.50e+00 4.44e-01 7.12e+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=" P DG N 28 " pdb=" O5' DG N 28 " pdb=" C5' DG N 28 " ideal model delta sigma weight residual 120.00 126.63 -6.63 1.50e+00 4.44e-01 1.95e+01 angle pdb=" N PRO A 530 " pdb=" CA PRO A 530 " pdb=" C PRO A 530 " ideal model delta sigma weight residual 110.40 117.40 -7.00 1.61e+00 3.86e-01 1.89e+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 - 0.115: 2463 0.115 - 0.231: 368 0.231 - 0.346: 13 0.346 - 0.462: 2 0.462 - 0.577: 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 2.35 -2.92 -0.58 2.00e-01 2.50e+01 8.32e+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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.280 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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= 0.550 Angle : 1.201 12.653 23346 Z= 0.770 Chirality : 0.081 0.577 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 aren 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 covalent geometry : bond 0.00867 (16323) covalent geometry : angle 1.20073 (23346) hydrogen bonds : bond 0.27598 ( 624) hydrogen bonds : angle 8.36241 ( 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 : 0.559 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: 0.8880 (m) cc_final: 0.8606 (p) REVERT: A 824 SER cc_start: 0.8106 (m) cc_final: 0.7747 (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: 0.6516 (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: 0.1888 time to fit residues: 41.0758 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 : 0.512 ------------------------------------------------------------------------------- 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: 20.0000 chunk 107 optimal weight: 10.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: A 340 GLN A 388 GLN A 460 GLN ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS A 879 HIS A 906 ASN A 983 HIS A1013 HIS ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 185 GLN O 216 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.124078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.093538 restraints weight = 62257.984| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 3.37 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16323 Z= 0.204 Angle : 0.738 9.491 23346 Z= 0.372 Chirality : 0.041 0.294 2850 Planarity : 0.006 0.112 2013 Dihedral : 23.957 176.138 5520 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.93 % Favored : 96.90 % Rotamer: Outliers : 1.40 % Allowed : 5.87 % Favored : 92.74 % 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 aren not related in a simple way. whole: -1.37 (0.21), residues: 1227 helix: -0.04 (0.20), residues: 570 sheet: -1.81 (0.39), residues: 133 loop : -1.56 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 180 TYR 0.019 0.002 TYR O 203 PHE 0.024 0.002 PHE A1078 TRP 0.033 0.002 TRP O 167 HIS 0.008 0.002 HIS A 876 Details of bonding type rmsd covalent geometry : bond 0.00428 (16323) covalent geometry : angle 0.73832 (23346) hydrogen bonds : bond 0.06145 ( 624) hydrogen bonds : angle 4.65765 ( 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 101 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 813 MET cc_start: 0.7911 (tpp) cc_final: 0.7346 (tpp) REVERT: L 30 ARG cc_start: 0.7764 (ttm170) cc_final: 0.7410 (mtp85) REVERT: M 50 HIS cc_start: 0.6986 (m170) cc_final: 0.6503 (m170) REVERT: O 151 HIS cc_start: 0.6834 (m90) cc_final: 0.6574 (m-70) outliers start: 15 outliers final: 5 residues processed: 95 average time/residue: 0.1614 time to fit residues: 21.8173 Evaluate side-chains 65 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 1054 MET Chi-restraints excluded: chain O residue 166 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 146 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 60 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 388 GLN A 879 HIS A1023 GLN M 85 ASN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.123152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.091772 restraints weight = 61824.382| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.35 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16323 Z= 0.146 Angle : 0.624 9.581 23346 Z= 0.313 Chirality : 0.037 0.234 2850 Planarity : 0.005 0.062 2013 Dihedral : 23.777 178.777 5519 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.17 % Rotamer: Outliers : 0.93 % Allowed : 8.47 % Favored : 90.60 % 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 aren not related in a simple way. whole: -0.46 (0.22), residues: 1227 helix: 0.83 (0.21), residues: 572 sheet: -1.18 (0.41), residues: 133 loop : -1.30 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 132 TYR 0.020 0.002 TYR O 203 PHE 0.013 0.002 PHE A1078 TRP 0.013 0.001 TRP A 547 HIS 0.004 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00302 (16323) covalent geometry : angle 0.62365 (23346) hydrogen bonds : bond 0.05053 ( 624) hydrogen bonds : angle 4.20713 ( 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 82 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 723 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8378 (p0) REVERT: A 766 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7461 (pt) REVERT: L 30 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7361 (mtp85) REVERT: M 50 HIS cc_start: 0.7175 (m170) cc_final: 0.6800 (m170) REVERT: M 68 ASN cc_start: 0.8499 (m-40) cc_final: 0.8248 (p0) REVERT: O 151 HIS cc_start: 0.6879 (m90) cc_final: 0.6511 (m-70) outliers start: 10 outliers final: 3 residues processed: 79 average time/residue: 0.1537 time to fit residues: 17.6038 Evaluate side-chains 59 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 ASP 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 M residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 115 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 0.0470 chunk 79 optimal weight: 3.9990 chunk 140 optimal weight: 40.0000 chunk 26 optimal weight: 0.0070 chunk 96 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 HIS A 748 GLN A 799 ASN ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.122575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.090933 restraints weight = 61016.192| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.23 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16323 Z= 0.130 Angle : 0.593 9.606 23346 Z= 0.297 Chirality : 0.036 0.215 2850 Planarity : 0.004 0.051 2013 Dihedral : 23.695 179.175 5519 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.53 % Favored : 97.31 % Rotamer: Outliers : 1.12 % Allowed : 9.12 % Favored : 89.76 % 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 aren not related in a simple way. whole: -0.02 (0.23), residues: 1227 helix: 1.08 (0.21), residues: 582 sheet: -0.65 (0.43), residues: 132 loop : -1.07 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 610 TYR 0.015 0.001 TYR A 176 PHE 0.014 0.001 PHE A 883 TRP 0.012 0.001 TRP A 547 HIS 0.004 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00267 (16323) covalent geometry : angle 0.59317 (23346) hydrogen bonds : bond 0.04450 ( 624) hydrogen bonds : angle 3.99218 ( 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 72 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 723 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8459 (p0) REVERT: A 766 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7632 (pt) REVERT: A 773 MET cc_start: 0.5643 (tpp) cc_final: 0.5392 (mmp) REVERT: L 30 ARG cc_start: 0.7917 (ttm170) cc_final: 0.7677 (mtp85) REVERT: M 50 HIS cc_start: 0.7393 (m170) cc_final: 0.6860 (m170) outliers start: 12 outliers final: 7 residues processed: 68 average time/residue: 0.1698 time to fit residues: 16.3653 Evaluate side-chains 62 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 723 ASP 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 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: 0.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 114 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 134 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 799 ASN ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN L 74 ASN ** L 85 GLN ** 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 = 0.4419 r_free = 0.4419 target = 0.121682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.089534 restraints weight = 61096.301| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.24 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16323 Z= 0.132 Angle : 0.583 9.488 23346 Z= 0.290 Chirality : 0.035 0.213 2850 Planarity : 0.004 0.051 2013 Dihedral : 23.644 177.357 5519 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % Rotamer: Outliers : 1.40 % Allowed : 9.96 % Favored : 88.64 % 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 aren not related in a simple way. whole: 0.29 (0.24), residues: 1227 helix: 1.34 (0.22), residues: 578 sheet: -0.55 (0.43), residues: 139 loop : -0.90 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 32 TYR 0.010 0.001 TYR A 707 PHE 0.011 0.001 PHE A1078 TRP 0.010 0.001 TRP A 547 HIS 0.004 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00271 (16323) covalent geometry : angle 0.58271 (23346) hydrogen bonds : bond 0.04405 ( 624) hydrogen bonds : angle 3.90391 ( 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 71 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 723 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8325 (p0) REVERT: L 30 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7878 (mtp85) REVERT: M 50 HIS cc_start: 0.7691 (m170) cc_final: 0.7026 (m170) REVERT: M 68 ASN cc_start: 0.8413 (m-40) cc_final: 0.8081 (p0) outliers start: 15 outliers final: 6 residues processed: 65 average time/residue: 0.1729 time to fit residues: 16.0898 Evaluate side-chains 60 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 723 ASP 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 108 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 137 optimal weight: 0.4980 chunk 75 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 HIS A 906 ASN L 74 ASN ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.118866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.086053 restraints weight = 59904.120| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.38 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.6231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16323 Z= 0.182 Angle : 0.630 10.206 23346 Z= 0.314 Chirality : 0.037 0.216 2850 Planarity : 0.005 0.061 2013 Dihedral : 23.814 179.617 5519 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.02 % Favored : 96.82 % Rotamer: Outliers : 1.21 % Allowed : 11.27 % Favored : 87.52 % 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 aren not related in a simple way. whole: 0.22 (0.24), residues: 1227 helix: 1.20 (0.22), residues: 587 sheet: -0.50 (0.45), residues: 132 loop : -0.89 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 89 TYR 0.016 0.001 TYR M 122 PHE 0.018 0.002 PHE A 883 TRP 0.010 0.001 TRP A 547 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00382 (16323) covalent geometry : angle 0.63027 (23346) hydrogen bonds : bond 0.04816 ( 624) hydrogen bonds : angle 4.05257 ( 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 70 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.470 Fit side-chains REVERT: A 723 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8485 (p0) REVERT: A 813 MET cc_start: 0.8084 (mmm) cc_final: 0.7644 (tpp) REVERT: A 848 ASP cc_start: 0.7944 (t70) cc_final: 0.7331 (t0) REVERT: A 969 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8008 (t0) REVERT: L 30 ARG cc_start: 0.8397 (ttm170) cc_final: 0.7842 (mtp85) REVERT: M 50 HIS cc_start: 0.7800 (m170) cc_final: 0.7449 (m170) outliers start: 13 outliers final: 5 residues processed: 66 average time/residue: 0.1625 time to fit residues: 15.4086 Evaluate side-chains 56 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 723 ASP 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 12 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN L 74 ASN ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.120515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.088034 restraints weight = 60129.606| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.21 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.6482 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= 0.120 Angle : 0.565 10.416 23346 Z= 0.280 Chirality : 0.034 0.215 2850 Planarity : 0.004 0.045 2013 Dihedral : 23.735 176.344 5519 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.42 % Favored : 96.41 % Rotamer: Outliers : 1.02 % Allowed : 11.64 % 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 aren not related in a simple way. whole: 0.43 (0.24), residues: 1227 helix: 1.42 (0.22), residues: 587 sheet: -0.50 (0.44), residues: 141 loop : -0.80 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 535 TYR 0.011 0.001 TYR M 43 PHE 0.010 0.001 PHE A 883 TRP 0.009 0.001 TRP A 547 HIS 0.002 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00251 (16323) covalent geometry : angle 0.56490 (23346) hydrogen bonds : bond 0.04119 ( 624) hydrogen bonds : angle 3.86131 ( 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 67 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.492 Fit side-chains REVERT: A 848 ASP cc_start: 0.7807 (t70) cc_final: 0.7204 (t0) REVERT: A 969 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7915 (t0) REVERT: L 30 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7792 (mtp85) REVERT: M 50 HIS cc_start: 0.7860 (m170) cc_final: 0.7548 (m170) outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 0.1615 time to fit residues: 14.8307 Evaluate side-chains 60 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 580 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 121 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 74 ASN ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** 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 = 0.4372 r_free = 0.4372 target = 0.118404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.085692 restraints weight = 59986.457| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.19 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16323 Z= 0.173 Angle : 0.620 11.345 23346 Z= 0.306 Chirality : 0.036 0.216 2850 Planarity : 0.004 0.056 2013 Dihedral : 23.877 179.473 5519 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 0.93 % Allowed : 12.20 % Favored : 86.87 % 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 aren not related in a simple way. whole: 0.26 (0.24), residues: 1227 helix: 1.20 (0.22), residues: 595 sheet: -0.46 (0.46), residues: 127 loop : -0.85 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 82 TYR 0.021 0.002 TYR M 122 PHE 0.014 0.002 PHE A 883 TRP 0.009 0.001 TRP A 137 HIS 0.007 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00366 (16323) covalent geometry : angle 0.62042 (23346) hydrogen bonds : bond 0.04784 ( 624) hydrogen bonds : angle 4.05338 ( 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 70 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 848 ASP cc_start: 0.7941 (t70) cc_final: 0.7230 (t0) REVERT: A 969 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.7953 (t0) REVERT: L 30 ARG cc_start: 0.8176 (ttm170) cc_final: 0.7873 (mtp85) REVERT: M 50 HIS cc_start: 0.7975 (m170) cc_final: 0.7519 (m170) outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 0.1560 time to fit residues: 15.6637 Evaluate side-chains 62 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1088 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 129 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 995 GLN L 74 ASN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.119862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.087455 restraints weight = 59565.494| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.24 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.7103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 16323 Z= 0.118 Angle : 0.570 11.212 23346 Z= 0.281 Chirality : 0.034 0.209 2850 Planarity : 0.004 0.043 2013 Dihedral : 23.752 175.542 5519 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 1.12 % Allowed : 11.92 % Favored : 86.96 % 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 aren not related in a simple way. whole: 0.47 (0.24), residues: 1227 helix: 1.45 (0.22), residues: 592 sheet: -0.60 (0.44), residues: 141 loop : -0.75 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 865 TYR 0.011 0.001 TYR A 168 PHE 0.018 0.001 PHE A 159 TRP 0.010 0.001 TRP A 547 HIS 0.002 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00246 (16323) covalent geometry : angle 0.57043 (23346) hydrogen bonds : bond 0.04075 ( 624) hydrogen bonds : angle 3.89436 ( 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 70 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 848 ASP cc_start: 0.7874 (t70) cc_final: 0.7231 (t0) REVERT: A 969 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7953 (t0) REVERT: L 30 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7854 (mtp85) REVERT: M 50 HIS cc_start: 0.7930 (m170) cc_final: 0.7547 (m170) outliers start: 12 outliers final: 7 residues processed: 65 average time/residue: 0.1658 time to fit residues: 15.4595 Evaluate side-chains 61 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 897 VAL 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 L residue 74 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 126 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 74 ASN ** O 116 GLN ** 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 = 0.4367 r_free = 0.4367 target = 0.118197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.085561 restraints weight = 59857.082| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.19 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16323 Z= 0.167 Angle : 0.610 11.617 23346 Z= 0.302 Chirality : 0.035 0.228 2850 Planarity : 0.004 0.046 2013 Dihedral : 23.831 176.232 5519 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 0.84 % Allowed : 12.10 % Favored : 87.06 % 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 aren not related in a simple way. whole: 0.39 (0.24), residues: 1227 helix: 1.32 (0.22), residues: 593 sheet: -0.55 (0.46), residues: 132 loop : -0.75 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 938 TYR 0.018 0.001 TYR M 122 PHE 0.017 0.002 PHE A 159 TRP 0.009 0.001 TRP A 137 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00354 (16323) covalent geometry : angle 0.60999 (23346) hydrogen bonds : bond 0.04648 ( 624) hydrogen bonds : angle 4.04782 ( 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 63 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 744 TYR cc_start: 0.8017 (p90) cc_final: 0.7755 (p90) REVERT: A 848 ASP cc_start: 0.7934 (t70) cc_final: 0.7255 (t0) REVERT: A 969 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7982 (t0) REVERT: L 30 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7844 (mtp85) REVERT: M 50 HIS cc_start: 0.8046 (m170) cc_final: 0.7597 (m170) outliers start: 9 outliers final: 6 residues processed: 62 average time/residue: 0.1639 time to fit residues: 14.3901 Evaluate side-chains 58 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1088 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 144 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 74 ASN ** O 116 GLN ** 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 = 0.4369 r_free = 0.4369 target = 0.118154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.085805 restraints weight = 59634.614| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.20 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.7667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16323 Z= 0.154 Angle : 0.598 12.337 23346 Z= 0.297 Chirality : 0.035 0.218 2850 Planarity : 0.004 0.049 2013 Dihedral : 23.884 175.447 5519 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.83 % Favored : 96.01 % Rotamer: Outliers : 0.74 % Allowed : 12.48 % 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 aren not related in a simple way. whole: 0.39 (0.24), residues: 1227 helix: 1.32 (0.22), residues: 599 sheet: -0.73 (0.44), residues: 141 loop : -0.70 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 865 TYR 0.016 0.001 TYR A 744 PHE 0.019 0.001 PHE A 759 TRP 0.010 0.001 TRP A 137 HIS 0.003 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00329 (16323) covalent geometry : angle 0.59783 (23346) hydrogen bonds : bond 0.04432 ( 624) hydrogen bonds : angle 4.07937 ( 1648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3689.90 seconds wall clock time: 64 minutes 7.71 seconds (3847.71 seconds total)