Starting phenix.real_space_refine on Wed Jan 14 01:19:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7u_27234/01_2026/8d7u_27234.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7u_27234/01_2026/8d7u_27234.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/8d7u_27234/01_2026/8d7u_27234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7u_27234/01_2026/8d7u_27234.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d7u_27234/01_2026/8d7u_27234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7u_27234/01_2026/8d7u_27234.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= -0.001 sd= 0.072 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 57 5.16 5 C 7009 2.51 5 N 1907 2.21 5 O 2097 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11072 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 8047 Classifications: {'peptide': 1132} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1091} Chain breaks: 1 Unresolved non-hydrogen bonds: 832 Unresolved non-hydrogen angles: 1054 Unresolved non-hydrogen dihedrals: 653 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLU:plan': 24, 'ASP:plan': 17, 'ARG:plan': 14, 'GLN:plan1': 16, 'HIS:plan': 6, 'TRP:plan': 2, 'ASN:plan1': 10, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 404 Chain: "B" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2982 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 21, 'TRANS': 362} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 7, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {' ZN': 1, 'QFC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10247 SG CYS B 323 41.560 88.680 30.907 1.00 70.87 S ATOM 10263 SG CYS B 326 40.281 91.785 29.926 1.00 84.79 S ATOM 10767 SG CYS B 391 38.772 89.022 27.622 1.00 79.10 S ATOM 10786 SG CYS B 394 42.362 90.125 27.496 1.00 91.19 S Time building chain proxies: 2.64, per 1000 atoms: 0.24 Number of scatterers: 11072 At special positions: 0 Unit cell: (89.7, 109.25, 157.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 57 16.00 F 1 9.00 O 2097 8.00 N 1907 7.00 C 7009 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 562.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 326 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 391 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 323 " Number of angles added : 6 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2840 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 27 sheets defined 11.8% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.622A pdb=" N ILE A 253 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 254 " --> pdb=" O PRO A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 254' Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 595 through 599 removed outlier: 3.591A pdb=" N SER A 598 " --> pdb=" O THR A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 1044 through 1060 removed outlier: 3.886A pdb=" N LYS A1060 " --> pdb=" O ASN A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1097 through 1100 removed outlier: 3.697A pdb=" N ILE A1100 " --> pdb=" O PHE A1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1097 through 1100' Processing helix chain 'A' and resid 1101 through 1109 Processing helix chain 'A' and resid 1126 through 1138 removed outlier: 3.520A pdb=" N ILE A1130 " --> pdb=" O ALA A1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.670A pdb=" N GLY B 151 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.512A pdb=" N LYS B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.671A pdb=" N ASN B 236 " --> pdb=" O HIS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 248 removed outlier: 3.575A pdb=" N TYR B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 265 removed outlier: 3.759A pdb=" N LEU B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 303 through 318 Processing sheet with id=AA1, first strand: chain 'A' and resid 1004 through 1009 removed outlier: 3.749A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A1027 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A1040 " --> pdb=" O SER A1027 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU A1029 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY A1038 " --> pdb=" O LEU A1029 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN A 4 " --> pdb=" O ILE A1089 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 5.899A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67 removed outlier: 3.867A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 97 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 removed outlier: 4.743A pdb=" N LEU A 135 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169 removed outlier: 6.299A pdb=" N VAL A 164 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN A 183 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP A 166 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.636A pdb=" N MET A 218 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 263 removed outlier: 6.911A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 306 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N MET A 282 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU A 304 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A 284 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL A 302 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 289 through 290 removed outlier: 4.091A pdb=" N GLU A 289 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.993A pdb=" N VAL A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N SER A 331 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR A 352 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.658A pdb=" N ARG A 388 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 396 through 403 removed outlier: 6.396A pdb=" N ILE A 701 " --> pdb=" O HIS A 399 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER A 401 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 699 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AB4, first strand: chain 'A' and resid 459 through 463 removed outlier: 3.815A pdb=" N SER A 488 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 500 through 503 removed outlier: 6.171A pdb=" N GLN A 520 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLN A 528 " --> pdb=" O GLN A 520 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.334A pdb=" N GLY A 559 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 541 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA A 557 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA A 566 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS A 579 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE A 568 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 588 through 594 removed outlier: 6.907A pdb=" N ALA A 605 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 591 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A 603 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N MET A 593 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR A 601 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A 604 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 637 through 640 Processing sheet with id=AB9, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.743A pdb=" N SER A 738 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 723 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS A 803 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N SER A 762 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN A 806 " --> pdb=" O SER A 762 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 811 through 819 removed outlier: 6.715A pdb=" N GLY A 832 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 816 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 830 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER A 818 " --> pdb=" O TYR A 828 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR A 828 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLN A 845 " --> pdb=" O MET A 835 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLN A 852 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR A 860 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N SER A 854 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 870 through 875 removed outlier: 4.287A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 913 through 915 removed outlier: 3.613A pdb=" N TYR A 913 " --> pdb=" O GLY A 924 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL A 930 " --> pdb=" O ARG A 947 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG A 947 " --> pdb=" O VAL A 930 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU A 932 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 941 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 954 through 959 removed outlier: 3.638A pdb=" N ALA A 956 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 974 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 997 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL A 976 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.548A pdb=" N PHE B 135 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS B 166 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR B 137 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG B 164 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ALA B 139 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG B 162 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE B 141 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 160 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 143 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 78 through 82 removed outlier: 3.732A pdb=" N ILE B 81 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 180 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 143 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 160 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE B 141 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG B 162 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ALA B 139 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG B 164 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR B 137 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS B 166 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE B 135 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N PHE B 135 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 320 through 322 removed outlier: 4.041A pdb=" N SER B 320 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.837A pdb=" N ALA B 347 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.586A pdb=" N THR B 403 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY B 399 " --> pdb=" O ALA B 389 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1901 1.28 - 1.41: 2731 1.41 - 1.54: 6572 1.54 - 1.68: 6 1.68 - 1.81: 84 Bond restraints: 11294 Sorted by residual: bond pdb=" C LEU B 423 " pdb=" N PRO B 424 " ideal model delta sigma weight residual 1.332 1.402 -0.070 1.12e-02 7.97e+03 3.93e+01 bond pdb=" C GLU A 842 " pdb=" N PRO A 843 " ideal model delta sigma weight residual 1.332 1.411 -0.079 1.34e-02 5.57e+03 3.48e+01 bond pdb=" C GLU A1083 " pdb=" N PRO A1084 " ideal model delta sigma weight residual 1.331 1.392 -0.062 1.31e-02 5.83e+03 2.21e+01 bond pdb=" CA SER A 2 " pdb=" CB SER A 2 " ideal model delta sigma weight residual 1.535 1.458 0.077 1.69e-02 3.50e+03 2.09e+01 bond pdb=" N ILE B 81 " pdb=" CA ILE B 81 " ideal model delta sigma weight residual 1.458 1.487 -0.030 7.70e-03 1.69e+04 1.48e+01 ... (remaining 11289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 14922 2.30 - 4.60: 411 4.60 - 6.90: 55 6.90 - 9.21: 13 9.21 - 11.51: 2 Bond angle restraints: 15403 Sorted by residual: angle pdb=" N ASN B 203 " pdb=" CA ASN B 203 " pdb=" C ASN B 203 " ideal model delta sigma weight residual 113.18 103.44 9.74 1.33e+00 5.65e-01 5.36e+01 angle pdb=" N SER B 52 " pdb=" CA SER B 52 " pdb=" C SER B 52 " ideal model delta sigma weight residual 114.75 105.66 9.09 1.26e+00 6.30e-01 5.20e+01 angle pdb=" N PRO B 98 " pdb=" CA PRO B 98 " pdb=" CB PRO B 98 " ideal model delta sigma weight residual 103.15 109.99 -6.84 9.70e-01 1.06e+00 4.98e+01 angle pdb=" N LYS B 334 " pdb=" CA LYS B 334 " pdb=" C LYS B 334 " ideal model delta sigma weight residual 114.12 105.58 8.54 1.39e+00 5.18e-01 3.77e+01 angle pdb=" C GLU B 140 " pdb=" N ILE B 141 " pdb=" CA ILE B 141 " ideal model delta sigma weight residual 120.91 129.07 -8.16 1.39e+00 5.18e-01 3.44e+01 ... (remaining 15398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6071 17.92 - 35.83: 512 35.83 - 53.75: 114 53.75 - 71.67: 30 71.67 - 89.58: 14 Dihedral angle restraints: 6741 sinusoidal: 2343 harmonic: 4398 Sorted by residual: dihedral pdb=" CA ASP B 117 " pdb=" C ASP B 117 " pdb=" N ARG B 118 " pdb=" CA ARG B 118 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" C ASN B 203 " pdb=" N ASN B 203 " pdb=" CA ASN B 203 " pdb=" CB ASN B 203 " ideal model delta harmonic sigma weight residual -122.60 -108.72 -13.88 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C ARG A 391 " pdb=" N ARG A 391 " pdb=" CA ARG A 391 " pdb=" CB ARG A 391 " ideal model delta harmonic sigma weight residual -122.60 -110.39 -12.21 0 2.50e+00 1.60e-01 2.38e+01 ... (remaining 6738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1527 0.080 - 0.159: 221 0.159 - 0.239: 23 0.239 - 0.318: 8 0.318 - 0.398: 3 Chirality restraints: 1782 Sorted by residual: chirality pdb=" CA ARG A 391 " pdb=" N ARG A 391 " pdb=" C ARG A 391 " pdb=" CB ARG A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA ASN B 203 " pdb=" N ASN B 203 " pdb=" C ASN B 203 " pdb=" CB ASN B 203 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CA GLU A 842 " pdb=" N GLU A 842 " pdb=" C GLU A 842 " pdb=" CB GLU A 842 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 1779 not shown) Planarity restraints: 2020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O QFC B 502 " 0.017 2.00e-02 2.50e+03 4.68e-02 6.58e+01 pdb=" C14 QFC B 502 " 0.007 2.00e-02 2.50e+03 pdb=" C15 QFC B 502 " -0.032 2.00e-02 2.50e+03 pdb=" C16 QFC B 502 " -0.048 2.00e-02 2.50e+03 pdb=" C17 QFC B 502 " -0.023 2.00e-02 2.50e+03 pdb=" C18 QFC B 502 " 0.019 2.00e-02 2.50e+03 pdb=" C19 QFC B 502 " 0.035 2.00e-02 2.50e+03 pdb=" C20 QFC B 502 " 0.041 2.00e-02 2.50e+03 pdb=" C21 QFC B 502 " 0.031 2.00e-02 2.50e+03 pdb=" C22 QFC B 502 " -0.120 2.00e-02 2.50e+03 pdb=" N2 QFC B 502 " 0.016 2.00e-02 2.50e+03 pdb=" O1 QFC B 502 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 915 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C LYS A 915 " 0.073 2.00e-02 2.50e+03 pdb=" O LYS A 915 " -0.027 2.00e-02 2.50e+03 pdb=" N THR A 916 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 326 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C CYS B 326 " -0.066 2.00e-02 2.50e+03 pdb=" O CYS B 326 " 0.025 2.00e-02 2.50e+03 pdb=" N GLN B 327 " 0.022 2.00e-02 2.50e+03 ... (remaining 2017 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1126 2.75 - 3.28: 10336 3.28 - 3.82: 17360 3.82 - 4.36: 20768 4.36 - 4.90: 37219 Nonbonded interactions: 86809 Sorted by model distance: nonbonded pdb=" O PHE B 338 " pdb=" OG1 THR B 361 " model vdw 2.207 3.040 nonbonded pdb=" OG SER B 320 " pdb=" OG1 THR B 425 " model vdw 2.209 3.040 nonbonded pdb=" NZ LYS A1121 " pdb=" OD2 ASP A1128 " model vdw 2.215 3.120 nonbonded pdb=" NE2 GLN A 727 " pdb=" OG1 THR A 827 " model vdw 2.215 3.120 nonbonded pdb=" O SER A1071 " pdb=" OG SER A1075 " model vdw 2.216 3.040 ... (remaining 86804 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: 0.700 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.440 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 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 : 0.006 0.112 11298 Z= 0.337 Angle : 0.889 20.239 15409 Z= 0.556 Chirality : 0.059 0.398 1782 Planarity : 0.005 0.047 2020 Dihedral : 15.193 89.581 3901 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.41 % Favored : 90.79 % Rotamer: Outliers : 3.62 % Allowed : 2.10 % Favored : 94.28 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.22), residues: 1510 helix: -0.21 (0.41), residues: 169 sheet: -0.80 (0.23), residues: 593 loop : -2.22 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 301 TYR 0.020 0.002 TYR A 136 PHE 0.027 0.002 PHE A 829 TRP 0.020 0.002 TRP B 223 HIS 0.007 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00587 (11294) covalent geometry : angle 0.86236 (15403) hydrogen bonds : bond 0.22657 ( 373) hydrogen bonds : angle 8.91124 ( 1008) metal coordination : bond 0.05671 ( 4) metal coordination : angle 11.02586 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.9119 (ptp) cc_final: 0.8870 (ptm) REVERT: A 1063 LYS cc_start: 0.8074 (mtmm) cc_final: 0.7481 (tppt) REVERT: A 1080 ARG cc_start: 0.7651 (ptt90) cc_final: 0.7031 (mpp-170) REVERT: A 1104 LYS cc_start: 0.7621 (mttm) cc_final: 0.7362 (mttt) REVERT: B 187 GLU cc_start: 0.5571 (tp30) cc_final: 0.5299 (mm-30) REVERT: B 206 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.7131 (mp10) outliers start: 38 outliers final: 14 residues processed: 216 average time/residue: 0.1114 time to fit residues: 33.9418 Evaluate side-chains 148 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 335 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 HIS A 877 ASN B 68 HIS B 203 ASN B 206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.172710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129483 restraints weight = 13246.269| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.42 r_work: 0.3215 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11298 Z= 0.165 Angle : 0.611 9.353 15409 Z= 0.316 Chirality : 0.046 0.180 1782 Planarity : 0.004 0.046 2020 Dihedral : 7.426 85.802 1682 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.02 % Favored : 92.58 % Rotamer: Outliers : 1.72 % Allowed : 9.72 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.21), residues: 1510 helix: -0.11 (0.39), residues: 178 sheet: -0.75 (0.23), residues: 591 loop : -2.17 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 262 TYR 0.014 0.002 TYR B 221 PHE 0.024 0.002 PHE B 165 TRP 0.022 0.002 TRP B 264 HIS 0.004 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00391 (11294) covalent geometry : angle 0.60577 (15403) hydrogen bonds : bond 0.04028 ( 373) hydrogen bonds : angle 5.74111 ( 1008) metal coordination : bond 0.00984 ( 4) metal coordination : angle 4.05461 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.5226 (mmt) REVERT: A 312 GLU cc_start: 0.8240 (tt0) cc_final: 0.7818 (tt0) REVERT: A 1063 LYS cc_start: 0.8302 (mtmm) cc_final: 0.7717 (tppt) REVERT: A 1080 ARG cc_start: 0.8102 (ptt90) cc_final: 0.7051 (mpp-170) REVERT: B 187 GLU cc_start: 0.5636 (tp30) cc_final: 0.5352 (mm-30) REVERT: B 204 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7643 (mtmm) outliers start: 18 outliers final: 8 residues processed: 141 average time/residue: 0.0949 time to fit residues: 19.9271 Evaluate side-chains 130 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 351 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 132 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 53 optimal weight: 40.0000 chunk 44 optimal weight: 0.2980 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 0.0040 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 111 optimal weight: 0.0870 chunk 106 optimal weight: 0.9990 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN B 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132342 restraints weight = 13290.438| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.38 r_work: 0.3237 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11298 Z= 0.092 Angle : 0.506 5.662 15409 Z= 0.265 Chirality : 0.044 0.148 1782 Planarity : 0.004 0.043 2020 Dihedral : 5.533 53.735 1659 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.43 % Favored : 94.17 % Rotamer: Outliers : 1.43 % Allowed : 12.30 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.79 (0.22), residues: 1510 helix: 0.41 (0.40), residues: 175 sheet: -0.61 (0.23), residues: 585 loop : -2.08 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 262 TYR 0.008 0.001 TYR A 42 PHE 0.018 0.001 PHE B 165 TRP 0.016 0.001 TRP B 264 HIS 0.001 0.000 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00209 (11294) covalent geometry : angle 0.50314 (15403) hydrogen bonds : bond 0.02998 ( 373) hydrogen bonds : angle 5.01211 ( 1008) metal coordination : bond 0.00590 ( 4) metal coordination : angle 2.93756 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5839 (OUTLIER) cc_final: 0.5164 (mmt) REVERT: A 92 LYS cc_start: 0.8477 (tppt) cc_final: 0.8149 (ttpt) REVERT: A 1063 LYS cc_start: 0.8123 (mtmm) cc_final: 0.7630 (tppt) REVERT: A 1080 ARG cc_start: 0.8063 (ptt90) cc_final: 0.7007 (mpp-170) REVERT: B 118 ARG cc_start: 0.6007 (ptp-170) cc_final: 0.5640 (mtt180) REVERT: B 187 GLU cc_start: 0.5585 (tp30) cc_final: 0.5164 (mm-30) REVERT: B 204 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6249 (mmtt) REVERT: B 262 ARG cc_start: 0.6999 (mtm110) cc_final: 0.6711 (ttp-170) outliers start: 15 outliers final: 9 residues processed: 141 average time/residue: 0.1130 time to fit residues: 22.6254 Evaluate side-chains 128 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 351 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 96 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 6 optimal weight: 0.1980 chunk 61 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.173972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130762 restraints weight = 13333.865| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.45 r_work: 0.3218 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11298 Z= 0.105 Angle : 0.505 5.670 15409 Z= 0.263 Chirality : 0.044 0.143 1782 Planarity : 0.004 0.042 2020 Dihedral : 5.183 50.760 1656 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.56 % Favored : 94.11 % Rotamer: Outliers : 1.33 % Allowed : 13.63 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.76 (0.22), residues: 1510 helix: 0.57 (0.41), residues: 175 sheet: -0.72 (0.22), residues: 612 loop : -2.00 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 301 TYR 0.010 0.001 TYR B 355 PHE 0.018 0.001 PHE B 165 TRP 0.013 0.001 TRP B 264 HIS 0.003 0.000 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00247 (11294) covalent geometry : angle 0.50306 (15403) hydrogen bonds : bond 0.02933 ( 373) hydrogen bonds : angle 4.77792 ( 1008) metal coordination : bond 0.00448 ( 4) metal coordination : angle 2.42005 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5524 (mmt) cc_final: 0.5044 (mmt) REVERT: A 92 LYS cc_start: 0.8543 (tppt) cc_final: 0.8165 (ttpt) REVERT: A 735 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8742 (t) REVERT: A 1063 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7618 (tppt) REVERT: A 1080 ARG cc_start: 0.8095 (ptt90) cc_final: 0.7070 (mpp-170) REVERT: B 118 ARG cc_start: 0.5885 (ptp-170) cc_final: 0.5630 (mtt180) REVERT: B 187 GLU cc_start: 0.5592 (tp30) cc_final: 0.5140 (mm-30) REVERT: B 204 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6273 (mmtt) REVERT: B 262 ARG cc_start: 0.7020 (mtm110) cc_final: 0.6708 (ttp-170) outliers start: 14 outliers final: 8 residues processed: 133 average time/residue: 0.1091 time to fit residues: 20.7844 Evaluate side-chains 129 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 351 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 26 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 7 optimal weight: 0.0870 chunk 82 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 117 optimal weight: 0.0170 chunk 53 optimal weight: 40.0000 chunk 113 optimal weight: 30.0000 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.173794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.130548 restraints weight = 13142.336| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.21 r_work: 0.3235 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11298 Z= 0.105 Angle : 0.494 5.836 15409 Z= 0.259 Chirality : 0.044 0.143 1782 Planarity : 0.003 0.042 2020 Dihedral : 4.759 40.844 1653 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.43 % Favored : 94.24 % Rotamer: Outliers : 1.91 % Allowed : 14.01 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.70 (0.22), residues: 1510 helix: 0.66 (0.41), residues: 175 sheet: -0.69 (0.22), residues: 606 loop : -1.96 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 301 TYR 0.009 0.001 TYR B 355 PHE 0.014 0.001 PHE B 165 TRP 0.012 0.001 TRP A 207 HIS 0.002 0.000 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00246 (11294) covalent geometry : angle 0.49257 (15403) hydrogen bonds : bond 0.02851 ( 373) hydrogen bonds : angle 4.62290 ( 1008) metal coordination : bond 0.00379 ( 4) metal coordination : angle 2.10514 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5845 (mmt) cc_final: 0.5158 (mmt) REVERT: A 92 LYS cc_start: 0.8500 (tppt) cc_final: 0.8182 (ttpt) REVERT: A 314 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8269 (mt) REVERT: A 735 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8748 (t) REVERT: A 1063 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7639 (tppt) REVERT: A 1080 ARG cc_start: 0.8028 (ptt90) cc_final: 0.7023 (mpp-170) REVERT: B 187 GLU cc_start: 0.5754 (tp30) cc_final: 0.5253 (mm-30) REVERT: B 204 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.6330 (mmtt) REVERT: B 262 ARG cc_start: 0.7008 (mtm110) cc_final: 0.6701 (ttp-170) outliers start: 20 outliers final: 9 residues processed: 139 average time/residue: 0.1077 time to fit residues: 21.4218 Evaluate side-chains 131 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 106 optimal weight: 0.0370 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.172052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129116 restraints weight = 13298.643| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.30 r_work: 0.3181 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11298 Z= 0.137 Angle : 0.525 6.257 15409 Z= 0.273 Chirality : 0.044 0.147 1782 Planarity : 0.004 0.041 2020 Dihedral : 4.796 35.130 1653 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.03 % Favored : 93.64 % Rotamer: Outliers : 1.53 % Allowed : 15.73 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.68 (0.22), residues: 1510 helix: 0.61 (0.41), residues: 175 sheet: -0.67 (0.22), residues: 607 loop : -1.94 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 301 TYR 0.009 0.001 TYR A 42 PHE 0.016 0.002 PHE B 165 TRP 0.013 0.001 TRP A 207 HIS 0.004 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00327 (11294) covalent geometry : angle 0.52318 (15403) hydrogen bonds : bond 0.03054 ( 373) hydrogen bonds : angle 4.70303 ( 1008) metal coordination : bond 0.00428 ( 4) metal coordination : angle 2.28730 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5853 (mmt) cc_final: 0.5166 (mmt) REVERT: A 92 LYS cc_start: 0.8520 (tppt) cc_final: 0.8188 (ttpt) REVERT: A 314 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8281 (mt) REVERT: A 735 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8725 (t) REVERT: A 1063 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7672 (tppt) REVERT: A 1080 ARG cc_start: 0.8091 (ptt90) cc_final: 0.7121 (mpp-170) REVERT: B 187 GLU cc_start: 0.5734 (tp30) cc_final: 0.5086 (mm-30) REVERT: B 414 PHE cc_start: 0.6649 (t80) cc_final: 0.6214 (t80) outliers start: 16 outliers final: 7 residues processed: 133 average time/residue: 0.1091 time to fit residues: 20.7964 Evaluate side-chains 126 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 70 optimal weight: 20.0000 chunk 140 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 HIS B 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.171717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128525 restraints weight = 13160.193| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.41 r_work: 0.3144 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11298 Z= 0.149 Angle : 0.532 5.749 15409 Z= 0.277 Chirality : 0.045 0.176 1782 Planarity : 0.004 0.041 2020 Dihedral : 4.567 26.433 1649 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.42 % Favored : 93.25 % Rotamer: Outliers : 1.53 % Allowed : 15.92 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.69 (0.22), residues: 1510 helix: 0.58 (0.41), residues: 175 sheet: -0.70 (0.22), residues: 609 loop : -1.91 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 301 TYR 0.018 0.001 TYR B 221 PHE 0.016 0.002 PHE B 165 TRP 0.014 0.002 TRP A 207 HIS 0.003 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00357 (11294) covalent geometry : angle 0.53086 (15403) hydrogen bonds : bond 0.03117 ( 373) hydrogen bonds : angle 4.76292 ( 1008) metal coordination : bond 0.00385 ( 4) metal coordination : angle 2.09079 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.454 Fit side-chains REVERT: A 1 MET cc_start: 0.5731 (OUTLIER) cc_final: 0.5063 (mmt) REVERT: A 92 LYS cc_start: 0.8621 (tppt) cc_final: 0.8129 (ttpt) REVERT: A 314 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8302 (mt) REVERT: A 1063 LYS cc_start: 0.8327 (mtmm) cc_final: 0.7722 (tppt) REVERT: A 1080 ARG cc_start: 0.8226 (ptt90) cc_final: 0.7089 (mpp-170) REVERT: B 414 PHE cc_start: 0.7334 (t80) cc_final: 0.6900 (t80) outliers start: 16 outliers final: 11 residues processed: 130 average time/residue: 0.1019 time to fit residues: 19.2477 Evaluate side-chains 128 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 319 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 20 optimal weight: 0.1980 chunk 140 optimal weight: 0.9990 chunk 41 optimal weight: 0.0030 chunk 11 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 48 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 125 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.175497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133544 restraints weight = 13084.737| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.02 r_work: 0.3253 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11298 Z= 0.085 Angle : 0.478 7.157 15409 Z= 0.252 Chirality : 0.043 0.147 1782 Planarity : 0.003 0.041 2020 Dihedral : 4.090 21.604 1649 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.23 % Favored : 94.44 % Rotamer: Outliers : 1.24 % Allowed : 16.49 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.52 (0.22), residues: 1510 helix: 0.80 (0.41), residues: 175 sheet: -0.53 (0.22), residues: 601 loop : -1.88 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 301 TYR 0.013 0.001 TYR B 221 PHE 0.016 0.001 PHE B 381 TRP 0.011 0.001 TRP B 264 HIS 0.002 0.000 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00195 (11294) covalent geometry : angle 0.47662 (15403) hydrogen bonds : bond 0.02532 ( 373) hydrogen bonds : angle 4.43556 ( 1008) metal coordination : bond 0.00382 ( 4) metal coordination : angle 1.93243 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5602 (mmt) cc_final: 0.4929 (mmt) REVERT: A 92 LYS cc_start: 0.8462 (tppt) cc_final: 0.8154 (ttpt) REVERT: A 314 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8154 (mt) REVERT: A 735 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8753 (t) REVERT: A 1063 LYS cc_start: 0.8093 (mtmm) cc_final: 0.7627 (tppt) REVERT: A 1080 ARG cc_start: 0.8026 (ptt90) cc_final: 0.7009 (mpp-170) REVERT: B 414 PHE cc_start: 0.7099 (t80) cc_final: 0.6786 (t80) outliers start: 13 outliers final: 9 residues processed: 128 average time/residue: 0.1001 time to fit residues: 19.0237 Evaluate side-chains 127 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 40 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 101 optimal weight: 0.2980 chunk 104 optimal weight: 3.9990 chunk 47 optimal weight: 30.0000 chunk 39 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A1055 GLN B 276 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.168501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125638 restraints weight = 13123.529| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.22 r_work: 0.3144 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 11298 Z= 0.275 Angle : 0.654 8.230 15409 Z= 0.335 Chirality : 0.049 0.236 1782 Planarity : 0.004 0.043 2020 Dihedral : 4.907 32.845 1648 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.22 % Favored : 92.45 % Rotamer: Outliers : 1.53 % Allowed : 16.97 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.83 (0.22), residues: 1510 helix: 0.33 (0.39), residues: 174 sheet: -0.70 (0.22), residues: 600 loop : -2.06 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 301 TYR 0.015 0.002 TYR B 221 PHE 0.021 0.002 PHE B 165 TRP 0.015 0.002 TRP A 207 HIS 0.005 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00666 (11294) covalent geometry : angle 0.65203 (15403) hydrogen bonds : bond 0.03899 ( 373) hydrogen bonds : angle 5.03456 ( 1008) metal coordination : bond 0.00470 ( 4) metal coordination : angle 2.62122 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5605 (OUTLIER) cc_final: 0.4901 (mmt) REVERT: A 314 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8355 (mt) REVERT: A 1063 LYS cc_start: 0.8195 (mtmm) cc_final: 0.7695 (tppt) REVERT: A 1080 ARG cc_start: 0.8188 (ptt90) cc_final: 0.7213 (mpp-170) REVERT: B 75 ASP cc_start: 0.6031 (OUTLIER) cc_final: 0.5815 (t0) REVERT: B 363 TYR cc_start: 0.6053 (m-80) cc_final: 0.5775 (m-10) REVERT: B 414 PHE cc_start: 0.7371 (t80) cc_final: 0.7150 (t80) outliers start: 16 outliers final: 8 residues processed: 132 average time/residue: 0.1031 time to fit residues: 19.7054 Evaluate side-chains 127 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 0.0060 chunk 137 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A1055 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.129367 restraints weight = 13219.345| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.34 r_work: 0.3207 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11298 Z= 0.107 Angle : 0.515 6.797 15409 Z= 0.269 Chirality : 0.044 0.165 1782 Planarity : 0.004 0.042 2020 Dihedral : 4.346 24.563 1648 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.56 % Favored : 94.11 % Rotamer: Outliers : 1.24 % Allowed : 16.97 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.61 (0.22), residues: 1510 helix: 0.76 (0.41), residues: 174 sheet: -0.56 (0.22), residues: 590 loop : -1.97 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 301 TYR 0.013 0.001 TYR B 221 PHE 0.015 0.001 PHE B 165 TRP 0.014 0.001 TRP A 207 HIS 0.002 0.000 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00253 (11294) covalent geometry : angle 0.51331 (15403) hydrogen bonds : bond 0.02774 ( 373) hydrogen bonds : angle 4.60786 ( 1008) metal coordination : bond 0.00334 ( 4) metal coordination : angle 1.86658 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.380 Fit side-chains REVERT: A 1 MET cc_start: 0.5455 (mmt) cc_final: 0.4820 (mmt) REVERT: A 314 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8114 (mt) REVERT: A 1063 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7697 (tppt) REVERT: A 1080 ARG cc_start: 0.8148 (ptt90) cc_final: 0.7093 (mpp-170) REVERT: B 75 ASP cc_start: 0.5956 (OUTLIER) cc_final: 0.5726 (t0) REVERT: B 363 TYR cc_start: 0.6139 (m-80) cc_final: 0.5786 (m-10) outliers start: 13 outliers final: 9 residues processed: 128 average time/residue: 0.0986 time to fit residues: 18.5081 Evaluate side-chains 125 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 147 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 90 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.169367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126161 restraints weight = 13223.770| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.44 r_work: 0.3147 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11298 Z= 0.211 Angle : 0.602 7.443 15409 Z= 0.310 Chirality : 0.047 0.214 1782 Planarity : 0.004 0.043 2020 Dihedral : 4.700 29.099 1648 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.89 % Favored : 92.78 % Rotamer: Outliers : 1.53 % Allowed : 16.68 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.78 (0.22), residues: 1510 helix: 0.54 (0.40), residues: 174 sheet: -0.72 (0.22), residues: 611 loop : -2.03 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 301 TYR 0.013 0.002 TYR B 221 PHE 0.019 0.002 PHE B 165 TRP 0.015 0.002 TRP A 207 HIS 0.004 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00510 (11294) covalent geometry : angle 0.60042 (15403) hydrogen bonds : bond 0.03491 ( 373) hydrogen bonds : angle 4.86777 ( 1008) metal coordination : bond 0.00370 ( 4) metal coordination : angle 2.17614 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2899.51 seconds wall clock time: 50 minutes 18.38 seconds (3018.38 seconds total)