Starting phenix.real_space_refine on Tue Jan 21 06:28:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8t_44358/01_2025/9b8t_44358.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8t_44358/01_2025/9b8t_44358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8t_44358/01_2025/9b8t_44358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8t_44358/01_2025/9b8t_44358.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8t_44358/01_2025/9b8t_44358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8t_44358/01_2025/9b8t_44358.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.026 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 53 5.49 5 Mg 1 5.21 5 S 102 5.16 5 C 10221 2.51 5 N 2766 2.21 5 O 3252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 16399 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 9313 Classifications: {'peptide': 1146} Link IDs: {'PTRANS': 58, 'TRANS': 1087} Chain breaks: 1 Chain: "B" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "C" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "D" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "P" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' MG': 1, 'SF4': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4940 SG CYS A 663 70.973 79.154 48.069 1.00 72.87 S ATOM 4874 SG CYS A 654 75.834 75.266 45.585 1.00 88.21 S ATOM 5664 SG CYS A 747 69.867 73.512 46.501 1.00 39.67 S ATOM 4858 SG CYS A 651 72.585 74.287 51.633 1.00 72.97 S Time building chain proxies: 9.04, per 1000 atoms: 0.55 Number of scatterers: 16399 At special positions: 0 Unit cell: (101.016, 109.296, 144.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 102 16.00 P 53 15.00 Mg 1 11.99 O 3252 8.00 N 2766 7.00 C 10221 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: 4.35 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A3003 " pdb="FE3 SF4 A3003 " - pdb=" SG CYS A 747 " pdb="FE1 SF4 A3003 " - pdb=" SG CYS A 663 " pdb="FE2 SF4 A3003 " - pdb=" SG CYS A 654 " pdb="FE4 SF4 A3003 " - pdb=" SG CYS A 651 " Number of angles added : 12 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3670 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 20 sheets defined 33.4% alpha, 23.7% beta 22 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 5.21 Creating SS restraints... Processing helix chain 'A' and resid 24 through 48 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 159 through 180 Proline residue: A 172 - end of helix removed outlier: 3.609A pdb=" N LYS A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 236 removed outlier: 3.706A pdb=" N LEU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 407 through 415 removed outlier: 4.323A pdb=" N ARG A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 423 through 431 removed outlier: 4.765A pdb=" N LYS A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 474 removed outlier: 3.759A pdb=" N ALA A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N THR A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 483 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 496 through 512 Processing helix chain 'A' and resid 563 through 584 removed outlier: 4.113A pdb=" N PHE A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LYS A 576 " --> pdb=" O GLN A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.175A pdb=" N LEU A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 647 through 654 Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 711 through 731 removed outlier: 3.774A pdb=" N ARG A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 726 " --> pdb=" O ARG A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 783 Processing helix chain 'A' and resid 790 through 818 removed outlier: 3.906A pdb=" N ILE A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 821 No H-bonds generated for 'chain 'A' and resid 819 through 821' Processing helix chain 'A' and resid 828 through 851 removed outlier: 4.596A pdb=" N ALA A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY A 833 " --> pdb=" O MET A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 905 Processing helix chain 'A' and resid 980 through 989 Processing helix chain 'A' and resid 990 through 995 removed outlier: 3.883A pdb=" N LEU A 994 " --> pdb=" O GLU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1019 Processing helix chain 'A' and resid 1025 through 1031 Processing helix chain 'A' and resid 1043 through 1047 removed outlier: 3.862A pdb=" N GLY A1047 " --> pdb=" O GLU A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1065 Processing helix chain 'A' and resid 1066 through 1069 Processing helix chain 'A' and resid 1089 through 1091 No H-bonds generated for 'chain 'A' and resid 1089 through 1091' Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1106 through 1114 removed outlier: 4.367A pdb=" N TRP A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A1114 " --> pdb=" O LEU A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 3.969A pdb=" N ILE A1127 " --> pdb=" O ASP A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1145 Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1164 through 1176 removed outlier: 3.537A pdb=" N ASP A1176 " --> pdb=" O LEU A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1187 Processing helix chain 'B' and resid 9 through 21 removed outlier: 4.004A pdb=" N LYS B 13 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 217 through 222 Proline residue: B 220 - end of helix No H-bonds generated for 'chain 'B' and resid 217 through 222' Processing helix chain 'C' and resid 9 through 18 removed outlier: 3.581A pdb=" N LYS C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 141 through 152 removed outlier: 3.783A pdb=" N ARG C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARG C 149 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 216 removed outlier: 3.784A pdb=" N THR C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'D' and resid 9 through 21 removed outlier: 3.695A pdb=" N LYS D 13 " --> pdb=" O GLY D 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 3.635A pdb=" N ILE D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 152 Processing helix chain 'D' and resid 209 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.658A pdb=" N GLU A 51 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA A 97 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.658A pdb=" N GLU A 51 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA A 97 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR A 85 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP A 243 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 136 removed outlier: 3.751A pdb=" N LYS A 130 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 132 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN A 151 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N THR A 108 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 104 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP A 220 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.022A pdb=" N LEU A 272 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET A 359 " --> pdb=" O MET A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 275 through 278 removed outlier: 3.655A pdb=" N MET A 295 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY A 304 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N PHE A 335 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 306 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 534 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 545 through 546 removed outlier: 6.657A pdb=" N TRP A 865 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU A 859 " --> pdb=" O GLY A 863 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLY A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE A 622 " --> pdb=" O PRO A 936 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS A 624 " --> pdb=" O ASP A 934 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 550 through 553 removed outlier: 3.919A pdb=" N ALA A 939 " --> pdb=" O PHE A 959 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 561 Processing sheet with id=AB1, first strand: chain 'A' and resid 645 through 646 Processing sheet with id=AB2, first strand: chain 'A' and resid 876 through 879 Processing sheet with id=AB3, first strand: chain 'A' and resid 911 through 913 Processing sheet with id=AB4, first strand: chain 'A' and resid 978 through 979 removed outlier: 3.718A pdb=" N ASN A1036 " --> pdb=" O GLU A 978 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1189 through 1192 Processing sheet with id=AB6, first strand: chain 'B' and resid 59 through 62 removed outlier: 3.782A pdb=" N THR B 59 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 3 " --> pdb=" O ARG B 61 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET B 116 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.471A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 204 through 208 removed outlier: 5.218A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR D 59 " --> pdb=" O ARG D 5 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 60 through 61 removed outlier: 3.885A pdb=" N SER D 172 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA D 157 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 66 through 71 removed outlier: 3.628A pdb=" N ALA C 26 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU C 25 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET C 40 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 29 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 36 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 51 " --> pdb=" O HIS C 246 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS C 246 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 237 " --> pdb=" O TYR C 249 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 67 through 68 removed outlier: 5.462A pdb=" N SER D 230 " --> pdb=" O PRO D 234 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER D 228 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS D 240 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N THR D 224 " --> pdb=" O LYS D 240 " (cutoff:3.500A) 742 hydrogen bonds defined for protein. 2082 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 7.48 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 6711 1.40 - 1.62: 9942 1.62 - 1.84: 158 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 16823 Sorted by residual: bond pdb=" C PRO A 452 " pdb=" O PRO A 452 " ideal model delta sigma weight residual 1.237 1.177 0.061 1.16e-02 7.43e+03 2.73e+01 bond pdb=" C GLN A 451 " pdb=" O GLN A 451 " ideal model delta sigma weight residual 1.238 1.292 -0.054 1.28e-02 6.10e+03 1.78e+01 bond pdb=" N ASP A 462 " pdb=" CA ASP A 462 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.44e-02 4.82e+03 8.56e+00 bond pdb=" N ILE D 11 " pdb=" CA ILE D 11 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.99e+00 bond pdb=" N ARG A1111 " pdb=" CA ARG A1111 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.33e-02 5.65e+03 7.52e+00 ... (remaining 16818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 22504 2.92 - 5.84: 374 5.84 - 8.76: 56 8.76 - 11.68: 16 11.68 - 14.60: 2 Bond angle restraints: 22952 Sorted by residual: angle pdb=" CB MET C 244 " pdb=" CG MET C 244 " pdb=" SD MET C 244 " ideal model delta sigma weight residual 112.70 127.30 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CA GLU A 36 " pdb=" CB GLU A 36 " pdb=" CG GLU A 36 " ideal model delta sigma weight residual 114.10 123.78 -9.68 2.00e+00 2.50e-01 2.34e+01 angle pdb=" CA GLU A1173 " pdb=" CB GLU A1173 " pdb=" CG GLU A1173 " ideal model delta sigma weight residual 114.10 123.02 -8.92 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CB ARG A 154 " pdb=" CG ARG A 154 " pdb=" CD ARG A 154 " ideal model delta sigma weight residual 111.30 121.51 -10.21 2.30e+00 1.89e-01 1.97e+01 angle pdb=" N VAL A 785 " pdb=" CA VAL A 785 " pdb=" C VAL A 785 " ideal model delta sigma weight residual 108.65 102.25 6.40 1.45e+00 4.76e-01 1.95e+01 ... (remaining 22947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.46: 9302 28.46 - 56.91: 792 56.91 - 85.37: 64 85.37 - 113.83: 3 113.83 - 142.29: 3 Dihedral angle restraints: 10164 sinusoidal: 4501 harmonic: 5663 Sorted by residual: dihedral pdb=" C2 TTP A3001 " pdb=" C1' TTP A3001 " pdb=" N1 TTP A3001 " pdb=" O4' TTP A3001 " ideal model delta sinusoidal sigma weight residual 301.68 159.40 142.29 1 2.00e+01 2.50e-03 4.30e+01 dihedral pdb=" O3A TTP A3001 " pdb=" O3B TTP A3001 " pdb=" PB TTP A3001 " pdb=" PG TTP A3001 " ideal model delta sinusoidal sigma weight residual 179.98 -53.61 -126.41 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" O5' TTP A3001 " pdb=" O3A TTP A3001 " pdb=" PA TTP A3001 " pdb=" PB TTP A3001 " ideal model delta sinusoidal sigma weight residual 180.02 54.81 125.21 1 2.00e+01 2.50e-03 3.78e+01 ... (remaining 10161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2201 0.077 - 0.154: 330 0.154 - 0.231: 23 0.231 - 0.308: 2 0.308 - 0.385: 1 Chirality restraints: 2557 Sorted by residual: chirality pdb=" CB VAL A 785 " pdb=" CA VAL A 785 " pdb=" CG1 VAL A 785 " pdb=" CG2 VAL A 785 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CG LEU A 272 " pdb=" CB LEU A 272 " pdb=" CD1 LEU A 272 " pdb=" CD2 LEU A 272 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CG LEU A 897 " pdb=" CB LEU A 897 " pdb=" CD1 LEU A 897 " pdb=" CD2 LEU A 897 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2554 not shown) Planarity restraints: 2781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 450 " 0.024 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" C GLU A 450 " -0.085 2.00e-02 2.50e+03 pdb=" O GLU A 450 " 0.032 2.00e-02 2.50e+03 pdb=" N GLN A 451 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 516 " 0.035 2.00e-02 2.50e+03 3.36e-02 1.98e+01 pdb=" CG PHE A 516 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 PHE A 516 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 516 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 516 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 516 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 516 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 103 " -0.022 2.00e-02 2.50e+03 2.18e-02 9.49e+00 pdb=" CG TYR A 103 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 103 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 103 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 103 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 103 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 103 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 103 " 0.000 2.00e-02 2.50e+03 ... (remaining 2778 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 220 2.65 - 3.21: 13288 3.21 - 3.77: 26847 3.77 - 4.34: 35556 4.34 - 4.90: 57169 Nonbonded interactions: 133080 Sorted by model distance: nonbonded pdb=" O VAL A 627 " pdb="MG MG A3002 " model vdw 2.085 2.170 nonbonded pdb=" O1G TTP A3001 " pdb="MG MG A3002 " model vdw 2.200 2.170 nonbonded pdb=" OH TYR A 754 " pdb=" O PHE A 815 " model vdw 2.278 3.040 nonbonded pdb=" O GLU B 25 " pdb=" OG SER B 39 " model vdw 2.292 3.040 nonbonded pdb=" OG SER D 43 " pdb=" OH TYR D 211 " model vdw 2.299 3.040 ... (remaining 133075 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.970 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 43.980 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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:10.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 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 : 0.005 0.071 16823 Z= 0.325 Angle : 0.957 14.604 22952 Z= 0.520 Chirality : 0.054 0.385 2557 Planarity : 0.007 0.066 2781 Dihedral : 18.825 142.286 6494 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.30 % Allowed : 25.52 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 1919 helix: -1.26 (0.19), residues: 571 sheet: -0.39 (0.23), residues: 506 loop : -1.85 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 28 HIS 0.010 0.001 HIS A 350 PHE 0.076 0.003 PHE A 516 TYR 0.054 0.003 TYR A 103 ARG 0.017 0.001 ARG A 728 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 225 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7348 (tm) cc_final: 0.7123 (mp) REVERT: A 221 MET cc_start: 0.7315 (mpt) cc_final: 0.6725 (ptt) REVERT: A 295 MET cc_start: 0.5927 (mtm) cc_final: 0.5693 (mmt) REVERT: A 715 GLN cc_start: 0.6378 (mt0) cc_final: 0.5876 (mm-40) REVERT: A 1083 LYS cc_start: 0.5645 (mmmt) cc_final: 0.5133 (mttt) REVERT: B 94 ASP cc_start: 0.3752 (m-30) cc_final: 0.3028 (p0) REVERT: B 197 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6447 (pt) REVERT: B 217 LYS cc_start: 0.6445 (mmmm) cc_final: 0.6200 (mmtt) REVERT: B 246 HIS cc_start: 0.6286 (p90) cc_final: 0.6081 (p90) REVERT: C 1 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.5196 (ttm) REVERT: C 244 MET cc_start: 0.7148 (tpp) cc_final: 0.6740 (ttm) REVERT: D 179 ASN cc_start: 0.7406 (p0) cc_final: 0.6959 (p0) REVERT: D 244 MET cc_start: 0.4896 (tpp) cc_final: 0.4599 (tpp) outliers start: 73 outliers final: 39 residues processed: 272 average time/residue: 1.1867 time to fit residues: 367.9129 Evaluate side-chains 234 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 203 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 8.9990 chunk 148 optimal weight: 0.1980 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN A 394 GLN A 475 HIS ** A1180 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 = 0.4862 r_free = 0.4862 target = 0.235435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.209692 restraints weight = 19589.874| |-----------------------------------------------------------------------------| r_work (start): 0.4637 rms_B_bonded: 2.61 r_work: 0.4232 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16823 Z= 0.195 Angle : 0.608 8.843 22952 Z= 0.319 Chirality : 0.043 0.160 2557 Planarity : 0.005 0.046 2781 Dihedral : 15.676 140.389 2732 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.77 % Allowed : 23.16 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.18), residues: 1919 helix: -0.22 (0.20), residues: 577 sheet: -0.22 (0.23), residues: 510 loop : -1.49 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 28 HIS 0.004 0.001 HIS A 229 PHE 0.035 0.002 PHE C 215 TYR 0.014 0.002 TYR A 468 ARG 0.005 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 208 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 THR cc_start: 0.6693 (m) cc_final: 0.6357 (t) REVERT: A 151 ASN cc_start: 0.5193 (p0) cc_final: 0.4572 (m-40) REVERT: A 715 GLN cc_start: 0.6697 (mt0) cc_final: 0.6382 (mm-40) REVERT: A 921 TYR cc_start: 0.5728 (OUTLIER) cc_final: 0.5030 (m-80) REVERT: A 1030 PHE cc_start: 0.6213 (t80) cc_final: 0.5937 (t80) REVERT: B 94 ASP cc_start: 0.3632 (m-30) cc_final: 0.3050 (p0) REVERT: B 116 MET cc_start: 0.5371 (OUTLIER) cc_final: 0.5107 (ptm) REVERT: B 197 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6666 (pt) REVERT: B 199 MET cc_start: 0.4321 (OUTLIER) cc_final: 0.4111 (ptm) REVERT: C 1 MET cc_start: 0.6245 (mmt) cc_final: 0.5398 (ttm) REVERT: C 216 THR cc_start: 0.5441 (OUTLIER) cc_final: 0.5124 (p) REVERT: D 138 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7240 (tmtt) outliers start: 98 outliers final: 35 residues processed: 279 average time/residue: 1.0331 time to fit residues: 329.3267 Evaluate side-chains 229 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 988 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 138 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 105 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 135 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 177 ASN ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.234276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.207244 restraints weight = 19345.839| |-----------------------------------------------------------------------------| r_work (start): 0.4615 rms_B_bonded: 2.61 r_work: 0.4217 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16823 Z= 0.205 Angle : 0.605 8.886 22952 Z= 0.315 Chirality : 0.043 0.161 2557 Planarity : 0.004 0.039 2781 Dihedral : 15.452 138.292 2686 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.60 % Allowed : 24.10 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 1919 helix: 0.06 (0.21), residues: 597 sheet: -0.07 (0.23), residues: 520 loop : -1.42 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 28 HIS 0.012 0.001 HIS A 229 PHE 0.025 0.002 PHE C 215 TYR 0.020 0.002 TYR A 631 ARG 0.009 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 212 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.5544 (mmm160) cc_final: 0.4572 (mmp80) REVERT: A 151 ASN cc_start: 0.5212 (p0) cc_final: 0.4634 (m-40) REVERT: A 715 GLN cc_start: 0.6704 (mt0) cc_final: 0.6381 (mm-40) REVERT: A 878 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6630 (m-10) REVERT: A 1189 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6971 (pp) REVERT: B 53 ARG cc_start: 0.4208 (mtp85) cc_final: 0.3713 (mmt90) REVERT: B 75 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.5585 (tmm) REVERT: B 94 ASP cc_start: 0.3680 (m-30) cc_final: 0.3125 (OUTLIER) REVERT: B 116 MET cc_start: 0.5304 (OUTLIER) cc_final: 0.5024 (ptm) REVERT: B 197 ILE cc_start: 0.6877 (OUTLIER) cc_final: 0.6600 (pt) REVERT: B 199 MET cc_start: 0.4442 (OUTLIER) cc_final: 0.4176 (ttp) REVERT: B 204 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7027 (pp30) REVERT: C 1 MET cc_start: 0.6123 (mmt) cc_final: 0.5431 (ttm) REVERT: C 41 ASP cc_start: 0.5190 (t0) cc_final: 0.4775 (t0) REVERT: C 216 THR cc_start: 0.5643 (OUTLIER) cc_final: 0.5297 (p) REVERT: D 138 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7477 (tmtt) REVERT: D 244 MET cc_start: 0.4651 (mmt) cc_final: 0.4447 (tpp) outliers start: 95 outliers final: 41 residues processed: 275 average time/residue: 1.0357 time to fit residues: 325.8824 Evaluate side-chains 237 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 255 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.2596 > 50: distance: 43 - 48: 8.813 distance: 48 - 49: 7.114 distance: 49 - 50: 7.820 distance: 49 - 52: 22.069 distance: 50 - 51: 12.153 distance: 50 - 56: 18.133 distance: 52 - 53: 11.818 distance: 53 - 54: 6.539 distance: 53 - 55: 5.296 distance: 56 - 57: 8.399 distance: 57 - 58: 20.213 distance: 57 - 60: 9.910 distance: 58 - 59: 11.469 distance: 58 - 64: 22.167 distance: 60 - 61: 15.478 distance: 61 - 62: 28.530 distance: 61 - 63: 28.389 distance: 64 - 65: 21.259 distance: 65 - 66: 24.672 distance: 65 - 68: 10.710 distance: 66 - 67: 12.197 distance: 66 - 71: 34.502 distance: 68 - 69: 17.545 distance: 68 - 70: 7.563 distance: 71 - 72: 10.514 distance: 72 - 73: 34.803 distance: 72 - 75: 12.884 distance: 73 - 74: 36.333 distance: 73 - 80: 8.217 distance: 75 - 76: 11.912 distance: 76 - 77: 16.318 distance: 77 - 78: 3.772 distance: 77 - 79: 7.380 distance: 80 - 81: 8.988 distance: 81 - 82: 24.114 distance: 81 - 84: 18.137 distance: 82 - 83: 9.095 distance: 82 - 91: 6.683 distance: 84 - 85: 22.469 distance: 85 - 86: 10.786 distance: 86 - 87: 10.843 distance: 87 - 88: 5.598 distance: 88 - 89: 3.977 distance: 88 - 90: 5.120 distance: 91 - 92: 13.751 distance: 91 - 97: 15.069 distance: 92 - 93: 7.143 distance: 92 - 95: 16.012 distance: 93 - 94: 11.383 distance: 93 - 98: 15.711 distance: 95 - 96: 20.238 distance: 96 - 97: 12.228 distance: 98 - 99: 21.574 distance: 99 - 100: 25.703 distance: 99 - 102: 20.177 distance: 100 - 101: 20.375 distance: 100 - 106: 17.930 distance: 102 - 103: 24.416 distance: 103 - 104: 21.029 distance: 103 - 105: 10.884 distance: 106 - 107: 36.087 distance: 106 - 112: 25.315 distance: 107 - 108: 16.831 distance: 107 - 110: 9.269 distance: 108 - 109: 14.133 distance: 108 - 113: 23.660 distance: 110 - 111: 15.134 distance: 111 - 112: 18.741 distance: 113 - 114: 7.948 distance: 114 - 115: 14.229 distance: 114 - 117: 4.382 distance: 115 - 116: 14.110 distance: 115 - 120: 16.259 distance: 117 - 119: 12.038 distance: 120 - 121: 9.654 distance: 121 - 122: 11.691 distance: 121 - 124: 15.007 distance: 122 - 123: 13.147 distance: 122 - 127: 15.037 distance: 124 - 125: 3.398 distance: 124 - 126: 14.596