Starting phenix.real_space_refine on Thu Aug 6 11:25:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q0z_72111/08_2026/9q0z_72111.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q0z_72111/08_2026/9q0z_72111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q0z_72111/08_2026/9q0z_72111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q0z_72111/08_2026/9q0z_72111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q0z_72111/08_2026/9q0z_72111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q0z_72111/08_2026/9q0z_72111.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 223 5.49 5 S 42 5.16 5 C 8481 2.51 5 N 2666 2.21 5 O 3294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 14706 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 4605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 4605 Classifications: {'RNA': 217} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 18, 'rna3p_pur': 86, 'rna3p_pyr': 99} Link IDs: {'rna2p': 32, 'rna3p': 184} Chain breaks: 2 Chain: "A" Number of atoms: 7437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7437 Classifications: {'peptide': 928} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 871} Chain breaks: 4 Chain: "D" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "G" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 642 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "C" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1171 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'55C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.78, per 1000 atoms: 0.19 Number of scatterers: 14706 At special positions: 0 Unit cell: (114.4, 138.6, 147.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 223 15.00 O 3294 8.00 N 2666 7.00 C 8481 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: 1.03 Conformation dependent library (CDL) restraints added in 414.0 milliseconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 10 sheets defined 57.5% alpha, 13.0% beta 67 base pairs and 117 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 removed outlier: 3.917A pdb=" N ARG A 11 " --> pdb=" O CYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.651A pdb=" N ARG A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 76 through 92 Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.533A pdb=" N ALA A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.513A pdb=" N ARG A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 329 through 332 removed outlier: 3.690A pdb=" N LEU A 332 " --> pdb=" O LYS A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.519A pdb=" N GLN A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 401 Processing helix chain 'A' and resid 404 through 413 Processing helix chain 'A' and resid 445 through 452 removed outlier: 4.095A pdb=" N VAL A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.748A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.776A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.818A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 551 removed outlier: 3.595A pdb=" N ILE A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 559 Processing helix chain 'A' and resid 578 through 597 removed outlier: 4.402A pdb=" N LYS A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.619A pdb=" N HIS A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 672 removed outlier: 3.788A pdb=" N ALA A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 677 Processing helix chain 'A' and resid 682 through 698 removed outlier: 3.683A pdb=" N ARG A 688 " --> pdb=" O ASP A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 720 removed outlier: 3.514A pdb=" N ILE A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 removed outlier: 3.526A pdb=" N LEU A 725 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 Processing helix chain 'A' and resid 801 through 815 Processing helix chain 'A' and resid 837 through 851 removed outlier: 3.600A pdb=" N MET A 849 " --> pdb=" O CYS A 845 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 851 " --> pdb=" O GLY A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 889 removed outlier: 3.630A pdb=" N ARG A 889 " --> pdb=" O ARG A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 895 Processing helix chain 'A' and resid 899 through 903 removed outlier: 3.781A pdb=" N THR A 903 " --> pdb=" O LEU A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 915 Processing helix chain 'A' and resid 946 through 950 removed outlier: 3.650A pdb=" N TYR A 949 " --> pdb=" O TYR A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 982 removed outlier: 3.574A pdb=" N MET A 970 " --> pdb=" O ALA A 966 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 972 " --> pdb=" O ARG A 968 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 980 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 993 through 1017 removed outlier: 3.540A pdb=" N LEU A1017 " --> pdb=" O HIS A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1027 Processing helix chain 'A' and resid 1028 through 1051 removed outlier: 4.318A pdb=" N PHE A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1082 removed outlier: 3.802A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A1077 " --> pdb=" O LEU A1073 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.714A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Proline residue: A1091 - end of helix removed outlier: 4.048A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A1098 " --> pdb=" O GLY A1094 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A1101 " --> pdb=" O ARG A1097 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1119 removed outlier: 3.610A pdb=" N ALA A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1130 removed outlier: 3.929A pdb=" N THR A1129 " --> pdb=" O ASP A1126 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 removed outlier: 3.641A pdb=" N GLN F 48 " --> pdb=" O LYS F 44 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 49 " --> pdb=" O VAL F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 85 removed outlier: 3.724A pdb=" N ASN F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 103 removed outlier: 3.621A pdb=" N ILE F 95 " --> pdb=" O THR F 91 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU F 103 " --> pdb=" O VAL F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 124 Processing helix chain 'G' and resid 19 through 23 Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.151A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 removed outlier: 3.722A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'C' and resid 98 through 104 removed outlier: 3.798A pdb=" N ILE C 103 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 108 Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 158 through 165 Processing helix chain 'C' and resid 167 through 177 removed outlier: 3.666A pdb=" N GLU C 171 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE C 174 " --> pdb=" O GLU C 171 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG C 175 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.803A pdb=" N GLU C 239 " --> pdb=" O TYR C 235 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.933A pdb=" N GLU A 20 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 11.492A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 14.947A pdb=" N CYS A 171 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 19.521A pdb=" N SER A 797 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N HIS A 754 " --> pdb=" O ALA A 750 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA4, first strand: chain 'A' and resid 561 through 565 Processing sheet with id=AA5, first strand: chain 'A' and resid 598 through 600 removed outlier: 5.915A pdb=" N GLN A 827 " --> pdb=" O HIS A 816 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N HIS A 816 " --> pdb=" O GLN A 827 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 862 through 865 Processing sheet with id=AA7, first strand: chain 'A' and resid 927 through 930 Processing sheet with id=AA8, first strand: chain 'F' and resid 54 through 55 removed outlier: 7.061A pdb=" N GLY F 54 " --> pdb=" O ILE G 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 89 through 90 Processing sheet with id=AB1, first strand: chain 'C' and resid 113 through 122 removed outlier: 6.902A pdb=" N LEU C 145 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL C 120 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR C 143 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N SER C 152 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N LEU C 204 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG C 154 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL C 206 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU C 156 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ARG C 208 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE C 202 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C 191 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU C 204 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL C 189 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL C 206 " --> pdb=" O CYS C 187 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS C 187 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG C 208 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU C 181 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG C 180 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 117 " --> pdb=" O ARG C 180 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 172 hydrogen bonds 328 hydrogen bond angles 0 basepair planarities 67 basepair parallelities 117 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3272 1.33 - 1.45: 4353 1.45 - 1.57: 7352 1.57 - 1.69: 442 1.69 - 1.81: 55 Bond restraints: 15474 Sorted by residual: bond pdb=" C1' DT D 13 " pdb=" N1 DT D 13 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.76e+00 bond pdb=" C3' DT D 14 " pdb=" C2' DT D 14 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.31e+00 bond pdb=" N9 A B 62 " pdb=" C4 A B 62 " ideal model delta sigma weight residual 1.374 1.360 0.014 6.00e-03 2.78e+04 5.12e+00 bond pdb=" O4' DT D 14 " pdb=" C1' DT D 14 " ideal model delta sigma weight residual 1.420 1.399 0.021 1.10e-02 8.26e+03 3.52e+00 bond pdb=" N1 U B 133 " pdb=" C2 U B 133 " ideal model delta sigma weight residual 1.381 1.397 -0.016 9.00e-03 1.23e+04 3.15e+00 ... (remaining 15469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 21001 1.47 - 2.94: 918 2.94 - 4.41: 95 4.41 - 5.88: 12 5.88 - 7.36: 4 Bond angle restraints: 22030 Sorted by residual: angle pdb=" C1' U B 133 " pdb=" N1 U B 133 " pdb=" C2 U B 133 " ideal model delta sigma weight residual 117.70 125.06 -7.36 1.20e+00 6.94e-01 3.76e+01 angle pdb=" N1 U B 133 " pdb=" C2 U B 133 " pdb=" O2 U B 133 " ideal model delta sigma weight residual 122.80 126.92 -4.12 7.00e-01 2.04e+00 3.47e+01 angle pdb=" C2 C B 148 " pdb=" N1 C B 148 " pdb=" C6 C B 148 " ideal model delta sigma weight residual 120.30 122.45 -2.15 4.00e-01 6.25e+00 2.89e+01 angle pdb=" O2 U B 133 " pdb=" C2 U B 133 " pdb=" N3 U B 133 " ideal model delta sigma weight residual 122.20 118.59 3.61 7.00e-01 2.04e+00 2.67e+01 angle pdb=" O5' A B 49 " pdb=" C5' A B 49 " pdb=" C4' A B 49 " ideal model delta sigma weight residual 109.40 113.25 -3.85 8.00e-01 1.56e+00 2.31e+01 ... (remaining 22025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 9095 35.45 - 70.89: 486 70.89 - 106.34: 93 106.34 - 141.78: 4 141.78 - 177.23: 2 Dihedral angle restraints: 9680 sinusoidal: 6047 harmonic: 3633 Sorted by residual: dihedral pdb=" O4' U B 43 " pdb=" C1' U B 43 " pdb=" N1 U B 43 " pdb=" C2 U B 43 " ideal model delta sinusoidal sigma weight residual -128.00 49.23 -177.23 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 291 " pdb=" C1' U B 291 " pdb=" N1 U B 291 " pdb=" C2 U B 291 " ideal model delta sinusoidal sigma weight residual -128.00 40.28 -168.28 1 1.70e+01 3.46e-03 6.57e+01 dihedral pdb=" O4' U B 133 " pdb=" C1' U B 133 " pdb=" N1 U B 133 " pdb=" C2 U B 133 " ideal model delta sinusoidal sigma weight residual 200.00 86.55 113.45 1 1.50e+01 4.44e-03 5.96e+01 ... (remaining 9677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1986 0.043 - 0.086: 401 0.086 - 0.128: 131 0.128 - 0.171: 149 0.171 - 0.214: 1 Chirality restraints: 2668 Sorted by residual: chirality pdb=" C3' G B 71 " pdb=" C4' G B 71 " pdb=" O3' G B 71 " pdb=" C2' G B 71 " both_signs ideal model delta sigma weight residual False -2.48 -2.26 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1' G B 44 " pdb=" O4' G B 44 " pdb=" C2' G B 44 " pdb=" N9 G B 44 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" C1' U B 133 " pdb=" O4' U B 133 " pdb=" C2' U B 133 " pdb=" N1 U B 133 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.46e-01 ... (remaining 2665 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 55C A1201 " 0.055 2.00e-02 2.50e+03 6.13e-02 4.69e+01 pdb=" C11 55C A1201 " -0.019 2.00e-02 2.50e+03 pdb=" C12 55C A1201 " -0.100 2.00e-02 2.50e+03 pdb=" C13 55C A1201 " 0.073 2.00e-02 2.50e+03 pdb=" C14 55C A1201 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 55C A1201 " 0.027 2.00e-02 2.50e+03 2.95e-02 1.09e+01 pdb=" C13 55C A1201 " -0.014 2.00e-02 2.50e+03 pdb=" C15 55C A1201 " 0.035 2.00e-02 2.50e+03 pdb=" N1 55C A1201 " -0.047 2.00e-02 2.50e+03 pdb=" O21 55C A1201 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 163 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO A 164 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.024 5.00e-02 4.00e+02 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 6842 2.98 - 3.46: 13722 3.46 - 3.94: 24706 3.94 - 4.42: 28580 4.42 - 4.90: 41506 Nonbonded interactions: 115356 Sorted by model distance: nonbonded pdb=" O4' C B 142 " pdb=" C6 C B 142 " model vdw 2.505 2.672 nonbonded pdb=" O5' A B 302 " pdb=" O4' A B 302 " model vdw 2.534 2.432 nonbonded pdb=" O5' C B 278 " pdb=" O4' C B 278 " model vdw 2.541 2.432 nonbonded pdb=" O2' G B 71 " pdb=" OP1 C B 72 " model vdw 2.567 3.040 nonbonded pdb=" N1 G B 305 " pdb=" C4 G B 305 " model vdw 2.572 2.672 ... (remaining 115351 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: 4.250 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.870 Find NCS groups from input model: 0.040 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15474 Z= 0.245 Angle : 0.656 7.355 22030 Z= 0.478 Chirality : 0.050 0.214 2668 Planarity : 0.004 0.061 1988 Dihedral : 19.133 177.230 7328 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.12 % Allowed : 3.53 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.23), residues: 1236 helix: -1.53 (0.19), residues: 608 sheet: -0.53 (0.43), residues: 140 loop : -0.79 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 979 TYR 0.008 0.001 TYR A 772 PHE 0.016 0.001 PHE A 331 TRP 0.009 0.001 TRP C 167 HIS 0.004 0.001 HIS A 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.24 (15474) covalent geometry : angle 0.65577 / 0.48 (22030) hydrogen bonds : bond 0.25342 / 27.03 ( 672) hydrogen bonds : angle 7.99848 / 10.13 ( 1726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 MET cc_start: 0.1370 (ttm) cc_final: 0.1089 (tpt) REVERT: A 512 MET cc_start: 0.8910 (mmm) cc_final: 0.8596 (mmt) REVERT: A 962 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7953 (pmt-80) REVERT: C 191 VAL cc_start: 0.6026 (OUTLIER) cc_final: 0.5799 (m) outliers start: 12 outliers final: 1 residues processed: 134 average time/residue: 0.1458 time to fit residues: 26.7281 Evaluate side-chains 102 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain C residue 191 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN A 340 GLN ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN A 995 GLN A1100 GLN F 50 HIS G 32 HIS ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.109750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.065464 restraints weight = 45287.813| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.43 r_work: 0.2947 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15474 Z= 0.159 Angle : 0.606 9.216 22030 Z= 0.333 Chirality : 0.039 0.271 2668 Planarity : 0.005 0.055 1988 Dihedral : 21.651 177.702 4924 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.21 % Allowed : 6.78 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.23), residues: 1236 helix: -0.29 (0.20), residues: 617 sheet: -0.46 (0.43), residues: 140 loop : -0.91 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 901 TYR 0.021 0.001 TYR F 41 PHE 0.014 0.002 PHE A 331 TRP 0.008 0.001 TRP A1072 HIS 0.007 0.001 HIS F 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (15474) covalent geometry : angle 0.60646 / 0.33 (22030) hydrogen bonds : bond 0.07285 / 7.79 ( 672) hydrogen bonds : angle 4.80957 / 5.98 ( 1726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 MET cc_start: 0.8944 (mmm) cc_final: 0.8740 (mmt) REVERT: A 760 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7837 (ptpp) REVERT: A 772 TYR cc_start: 0.7183 (m-80) cc_final: 0.6770 (m-80) REVERT: A 901 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8804 (tpp-160) REVERT: A 962 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8119 (pmt-80) REVERT: F 74 ILE cc_start: 0.9306 (mm) cc_final: 0.9055 (mm) REVERT: F 90 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.8842 (pt) REVERT: F 94 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7626 (mt-10) REVERT: F 117 LYS cc_start: 0.9246 (tmmt) cc_final: 0.8986 (tmmt) REVERT: F 121 LYS cc_start: 0.9029 (ttmm) cc_final: 0.8764 (mtmm) REVERT: G 65 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8301 (tm-30) REVERT: G 73 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7580 (p0) REVERT: C 123 ASP cc_start: 0.7436 (m-30) cc_final: 0.7060 (t70) outliers start: 13 outliers final: 6 residues processed: 118 average time/residue: 0.1279 time to fit residues: 21.1950 Evaluate side-chains 109 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 901 ARG Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain G residue 73 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 54 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 125 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.109789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.065690 restraints weight = 45367.798| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.49 r_work: 0.2957 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15474 Z= 0.146 Angle : 0.569 9.811 22030 Z= 0.313 Chirality : 0.038 0.272 2668 Planarity : 0.005 0.058 1988 Dihedral : 21.695 177.998 4923 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.21 % Allowed : 9.11 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.24), residues: 1236 helix: 0.11 (0.21), residues: 627 sheet: -0.42 (0.43), residues: 140 loop : -0.81 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 93 TYR 0.034 0.001 TYR F 41 PHE 0.028 0.002 PHE F 66 TRP 0.008 0.001 TRP A1072 HIS 0.008 0.001 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (15474) covalent geometry : angle 0.56903 / 0.31 (22030) hydrogen bonds : bond 0.05648 / 6.03 ( 672) hydrogen bonds : angle 4.44173 / 5.55 ( 1726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 TYR cc_start: 0.7351 (m-80) cc_final: 0.6759 (m-80) REVERT: A 901 ARG cc_start: 0.8962 (tpm170) cc_final: 0.8652 (tpp-160) REVERT: A 962 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8179 (pmt-80) REVERT: F 77 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8590 (tm-30) REVERT: F 110 HIS cc_start: 0.8791 (m90) cc_final: 0.8169 (m90) REVERT: G 73 ASP cc_start: 0.7776 (p0) cc_final: 0.7304 (p0) REVERT: C 123 ASP cc_start: 0.7470 (m-30) cc_final: 0.7085 (t70) outliers start: 13 outliers final: 8 residues processed: 117 average time/residue: 0.1164 time to fit residues: 19.3501 Evaluate side-chains 109 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain C residue 227 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 77 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 84 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 141 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN ** C 225 ASN ** 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 = 0.4137 r_free = 0.4137 target = 0.109677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.065638 restraints weight = 45388.863| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.49 r_work: 0.2956 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15474 Z= 0.151 Angle : 0.581 11.112 22030 Z= 0.314 Chirality : 0.039 0.420 2668 Planarity : 0.005 0.058 1988 Dihedral : 21.708 178.086 4923 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.58 % Allowed : 9.57 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.24), residues: 1236 helix: 0.33 (0.21), residues: 621 sheet: -0.34 (0.43), residues: 140 loop : -0.87 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 80 TYR 0.031 0.001 TYR F 41 PHE 0.015 0.001 PHE A 331 TRP 0.007 0.001 TRP A1072 HIS 0.009 0.001 HIS F 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (15474) covalent geometry : angle 0.58060 / 0.31 (22030) hydrogen bonds : bond 0.05329 / 5.59 ( 672) hydrogen bonds : angle 4.31875 / 5.39 ( 1726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 760 LYS cc_start: 0.8997 (mtmm) cc_final: 0.8681 (ptpp) REVERT: A 772 TYR cc_start: 0.6999 (m-80) cc_final: 0.6535 (m-80) REVERT: A 901 ARG cc_start: 0.8992 (tpm170) cc_final: 0.8675 (tpp-160) REVERT: A 962 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8185 (pmt-80) REVERT: F 77 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8619 (tm-30) REVERT: F 83 HIS cc_start: 0.9192 (m-70) cc_final: 0.8989 (p-80) REVERT: F 90 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9164 (tp) REVERT: G 73 ASP cc_start: 0.7654 (p0) cc_final: 0.7218 (p0) REVERT: C 123 ASP cc_start: 0.7480 (m-30) cc_final: 0.7097 (t70) outliers start: 17 outliers final: 10 residues processed: 116 average time/residue: 0.1216 time to fit residues: 19.9527 Evaluate side-chains 109 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain C residue 191 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 74 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 73 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 ASN ** C 225 ASN ** 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 = 0.4111 r_free = 0.4111 target = 0.108025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.063345 restraints weight = 45446.356| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.50 r_work: 0.2900 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15474 Z= 0.259 Angle : 0.652 12.211 22030 Z= 0.345 Chirality : 0.043 0.394 2668 Planarity : 0.005 0.056 1988 Dihedral : 21.821 177.557 4923 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.32 % Allowed : 10.13 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.24), residues: 1236 helix: 0.34 (0.21), residues: 623 sheet: -0.54 (0.41), residues: 153 loop : -0.97 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 93 TYR 0.017 0.002 TYR F 41 PHE 0.028 0.002 PHE C 172 TRP 0.010 0.001 TRP C 167 HIS 0.010 0.001 HIS F 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.26 (15474) covalent geometry : angle 0.65240 / 0.35 (22030) hydrogen bonds : bond 0.05943 / 6.31 ( 672) hydrogen bonds : angle 4.45744 / 5.62 ( 1726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 760 LYS cc_start: 0.8965 (mtmm) cc_final: 0.8517 (ptpp) REVERT: A 772 TYR cc_start: 0.7138 (m-80) cc_final: 0.6344 (m-80) REVERT: A 901 ARG cc_start: 0.9021 (tpm170) cc_final: 0.8718 (tpp-160) REVERT: A 962 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8275 (pmt-80) REVERT: F 90 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9128 (tp) REVERT: F 100 ARG cc_start: 0.9180 (tpp80) cc_final: 0.8734 (mmm-85) REVERT: F 106 GLU cc_start: 0.9008 (tp30) cc_final: 0.8640 (tp30) REVERT: G 73 ASP cc_start: 0.7661 (p0) cc_final: 0.7179 (p0) REVERT: C 166 ASP cc_start: 0.8585 (m-30) cc_final: 0.7453 (t70) outliers start: 25 outliers final: 14 residues processed: 108 average time/residue: 0.1196 time to fit residues: 18.1005 Evaluate side-chains 105 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain C residue 191 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 139 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.108638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.064412 restraints weight = 45321.204| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.43 r_work: 0.2927 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15474 Z= 0.170 Angle : 0.599 13.047 22030 Z= 0.318 Chirality : 0.039 0.405 2668 Planarity : 0.005 0.055 1988 Dihedral : 21.847 177.809 4923 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.86 % Allowed : 11.71 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.24), residues: 1236 helix: 0.53 (0.21), residues: 620 sheet: -0.47 (0.43), residues: 140 loop : -0.87 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 80 TYR 0.014 0.001 TYR G 51 PHE 0.024 0.002 PHE C 172 TRP 0.015 0.001 TRP C 167 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (15474) covalent geometry : angle 0.59856 / 0.32 (22030) hydrogen bonds : bond 0.05307 / 5.64 ( 672) hydrogen bonds : angle 4.24103 / 5.34 ( 1726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 MET cc_start: 0.8927 (mmt) cc_final: 0.8692 (mmt) REVERT: A 760 LYS cc_start: 0.8923 (mtmm) cc_final: 0.8602 (ptpp) REVERT: A 772 TYR cc_start: 0.7069 (m-80) cc_final: 0.6708 (m-80) REVERT: A 901 ARG cc_start: 0.9002 (tpm170) cc_final: 0.8698 (tpp-160) REVERT: A 962 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8223 (pmt-80) REVERT: F 90 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9080 (tp) REVERT: G 73 ASP cc_start: 0.7715 (p0) cc_final: 0.7294 (p0) REVERT: C 166 ASP cc_start: 0.8591 (m-30) cc_final: 0.8285 (m-30) outliers start: 20 outliers final: 15 residues processed: 104 average time/residue: 0.1321 time to fit residues: 19.0575 Evaluate side-chains 107 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain C residue 191 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 35 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 GLN A1085 HIS ** C 225 ASN ** 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 = 0.4128 r_free = 0.4128 target = 0.109012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.064954 restraints weight = 45019.450| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.48 r_work: 0.2942 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15474 Z= 0.147 Angle : 0.576 12.927 22030 Z= 0.306 Chirality : 0.038 0.407 2668 Planarity : 0.005 0.060 1988 Dihedral : 21.833 177.864 4923 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.58 % Allowed : 11.99 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.24), residues: 1236 helix: 0.66 (0.21), residues: 620 sheet: -0.35 (0.41), residues: 153 loop : -0.78 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 93 TYR 0.017 0.001 TYR F 41 PHE 0.016 0.001 PHE A 331 TRP 0.009 0.001 TRP A1072 HIS 0.015 0.001 HIS F 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (15474) covalent geometry : angle 0.57612 / 0.31 (22030) hydrogen bonds : bond 0.04933 / 5.23 ( 672) hydrogen bonds : angle 4.11101 / 5.16 ( 1726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 760 LYS cc_start: 0.8858 (mtmm) cc_final: 0.8256 (ptpp) REVERT: A 772 TYR cc_start: 0.7003 (m-80) cc_final: 0.6484 (m-80) REVERT: A 901 ARG cc_start: 0.8985 (tpm170) cc_final: 0.8694 (tpp-160) REVERT: A 962 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8206 (pmt-80) REVERT: F 90 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.8875 (tp) REVERT: F 121 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8544 (mtmm) REVERT: G 73 ASP cc_start: 0.7726 (p0) cc_final: 0.7342 (p0) REVERT: C 166 ASP cc_start: 0.8590 (m-30) cc_final: 0.7264 (p0) outliers start: 17 outliers final: 14 residues processed: 102 average time/residue: 0.1361 time to fit residues: 19.5795 Evaluate side-chains 104 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain C residue 191 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 108 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 97 optimal weight: 0.0000 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 0.0870 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 overall best weight: 0.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.109682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.065804 restraints weight = 45091.171| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.47 r_work: 0.2966 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 15474 Z= 0.115 Angle : 0.556 12.764 22030 Z= 0.295 Chirality : 0.036 0.402 2668 Planarity : 0.006 0.153 1988 Dihedral : 21.819 177.890 4923 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.39 % Allowed : 12.45 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.25), residues: 1236 helix: 0.78 (0.22), residues: 619 sheet: -0.20 (0.45), residues: 140 loop : -0.76 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 80 TYR 0.018 0.001 TYR F 41 PHE 0.035 0.001 PHE C 172 TRP 0.008 0.001 TRP A1072 HIS 0.006 0.001 HIS F 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (15474) covalent geometry : angle 0.55632 / 0.30 (22030) hydrogen bonds : bond 0.04558 / 4.84 ( 672) hydrogen bonds : angle 4.00758 / 5.04 ( 1726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 760 LYS cc_start: 0.8866 (mtmm) cc_final: 0.8252 (ptpp) REVERT: A 772 TYR cc_start: 0.7170 (m-80) cc_final: 0.6910 (m-10) REVERT: A 774 ARG cc_start: 0.8430 (ttt90) cc_final: 0.8106 (tpt170) REVERT: A 901 ARG cc_start: 0.8990 (tpm170) cc_final: 0.8695 (tpp-160) REVERT: A 962 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8175 (pmt-80) REVERT: F 90 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9086 (tp) REVERT: G 73 ASP cc_start: 0.7659 (p0) cc_final: 0.7293 (p0) REVERT: C 166 ASP cc_start: 0.8484 (m-30) cc_final: 0.8233 (m-30) outliers start: 15 outliers final: 11 residues processed: 98 average time/residue: 0.1220 time to fit residues: 17.0909 Evaluate side-chains 97 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain C residue 191 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 43 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 102 optimal weight: 0.2980 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.109423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.065505 restraints weight = 45305.850| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.50 r_work: 0.2959 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15474 Z= 0.128 Angle : 0.564 13.648 22030 Z= 0.298 Chirality : 0.037 0.401 2668 Planarity : 0.005 0.056 1988 Dihedral : 21.815 177.685 4922 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.58 % Allowed : 12.73 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.25), residues: 1236 helix: 0.81 (0.22), residues: 619 sheet: -0.16 (0.43), residues: 148 loop : -0.68 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG F 80 TYR 0.014 0.001 TYR G 51 PHE 0.015 0.001 PHE A 331 TRP 0.008 0.001 TRP C 167 HIS 0.007 0.001 HIS F 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (15474) covalent geometry : angle 0.56441 / 0.30 (22030) hydrogen bonds : bond 0.04580 / 4.87 ( 672) hydrogen bonds : angle 4.00730 / 5.08 ( 1726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 760 LYS cc_start: 0.8874 (mtmm) cc_final: 0.8264 (ptpp) REVERT: A 772 TYR cc_start: 0.7229 (m-80) cc_final: 0.6879 (m-80) REVERT: A 774 ARG cc_start: 0.8470 (ttt90) cc_final: 0.8120 (tpt170) REVERT: A 901 ARG cc_start: 0.8995 (tpm170) cc_final: 0.8745 (tpp-160) REVERT: A 962 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8208 (pmt-80) REVERT: F 90 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.8845 (tp) REVERT: G 73 ASP cc_start: 0.7641 (p0) cc_final: 0.7283 (p0) outliers start: 17 outliers final: 12 residues processed: 96 average time/residue: 0.1340 time to fit residues: 17.9589 Evaluate side-chains 96 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain C residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 11 optimal weight: 50.0000 chunk 75 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 GLN ** C 225 ASN ** 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 = 0.4128 r_free = 0.4128 target = 0.108816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.064789 restraints weight = 45240.856| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.55 r_work: 0.2940 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15474 Z= 0.160 Angle : 0.597 13.964 22030 Z= 0.313 Chirality : 0.038 0.397 2668 Planarity : 0.005 0.055 1988 Dihedral : 21.840 177.326 4922 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.39 % Allowed : 12.83 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1236 helix: 0.91 (0.22), residues: 610 sheet: -0.27 (0.42), residues: 157 loop : -0.70 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 80 TYR 0.017 0.001 TYR F 41 PHE 0.032 0.002 PHE C 172 TRP 0.009 0.001 TRP C 167 HIS 0.010 0.001 HIS F 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (15474) covalent geometry : angle 0.59692 / 0.31 (22030) hydrogen bonds : bond 0.04797 / 5.10 ( 672) hydrogen bonds : angle 4.06996 / 5.17 ( 1726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 760 LYS cc_start: 0.8865 (mtmm) cc_final: 0.8252 (ptpp) REVERT: A 772 TYR cc_start: 0.7239 (m-80) cc_final: 0.6886 (m-80) REVERT: A 774 ARG cc_start: 0.8478 (ttt90) cc_final: 0.8130 (tpt170) REVERT: A 901 ARG cc_start: 0.8992 (tpm170) cc_final: 0.8724 (tpp-160) REVERT: A 962 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8204 (pmt-80) REVERT: F 90 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9076 (tp) REVERT: F 110 HIS cc_start: 0.9174 (OUTLIER) cc_final: 0.8576 (m90) REVERT: G 25 GLN cc_start: 0.8056 (mm110) cc_final: 0.7848 (mm110) REVERT: G 73 ASP cc_start: 0.7640 (p0) cc_final: 0.7280 (p0) outliers start: 15 outliers final: 11 residues processed: 95 average time/residue: 0.1253 time to fit residues: 16.5910 Evaluate side-chains 98 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain C residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 18 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 754 HIS ** C 225 ASN ** 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 = 0.4137 r_free = 0.4137 target = 0.109444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.065650 restraints weight = 44915.082| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.44 r_work: 0.2966 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15474 Z= 0.129 Angle : 0.571 14.178 22030 Z= 0.300 Chirality : 0.036 0.398 2668 Planarity : 0.005 0.062 1988 Dihedral : 21.831 177.464 4922 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.39 % Allowed : 12.83 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1236 helix: 1.02 (0.22), residues: 611 sheet: -0.17 (0.42), residues: 157 loop : -0.68 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG F 93 TYR 0.014 0.001 TYR F 41 PHE 0.016 0.001 PHE A 331 TRP 0.010 0.001 TRP C 167 HIS 0.005 0.001 HIS F 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (15474) covalent geometry : angle 0.57099 / 0.30 (22030) hydrogen bonds : bond 0.04474 / 4.76 ( 672) hydrogen bonds : angle 3.99674 / 5.07 ( 1726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4184.05 seconds wall clock time: 71 minutes 57.88 seconds (4317.88 seconds total)