Starting phenix.real_space_refine on Wed Feb 4 06:22:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ltj_63371/02_2026/9ltj_63371.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ltj_63371/02_2026/9ltj_63371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ltj_63371/02_2026/9ltj_63371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ltj_63371/02_2026/9ltj_63371.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ltj_63371/02_2026/9ltj_63371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ltj_63371/02_2026/9ltj_63371.map" } resolution = 2.65 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= -0.002 sd= 0.035 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 5669 2.51 5 N 1539 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8861 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2638 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 173} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 382} Chain breaks: 5 Unresolved non-hydrogen bonds: 611 Unresolved non-hydrogen angles: 779 Unresolved non-hydrogen dihedrals: 487 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 12, 'ARG:plan': 17, 'PHE:plan': 7, 'GLU:plan': 16, 'ASP:plan': 15, 'TYR:plan': 5, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 376 Chain: "B" Number of atoms: 5852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 5852 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 5 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 12, 'ARG:plan': 3, 'GLU:plan': 24, 'GLN:plan1': 4, 'PHE:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 177 Chain: "F" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 371 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 1.74, per 1000 atoms: 0.20 Number of scatterers: 8861 At special positions: 0 Unit cell: (88.4, 109.65, 98.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1613 8.00 N 1539 7.00 C 5669 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: 0.41 Conformation dependent library (CDL) restraints added in 310.1 milliseconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 25 sheets defined 11.6% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 17 through 28 Processing helix chain 'A' and resid 34 through 41 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.823A pdb=" N GLN A 98 " --> pdb=" O ASP A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 394 through 397 Processing helix chain 'A' and resid 418 through 431 removed outlier: 3.859A pdb=" N GLN A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.716A pdb=" N ALA A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL A 441 " --> pdb=" O HIS A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 436 through 441' Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.706A pdb=" N GLN B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 384 Processing helix chain 'B' and resid 756 through 760 removed outlier: 3.749A pdb=" N ALA B 760 " --> pdb=" O SER B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1059 removed outlier: 3.625A pdb=" N ASN B1056 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1075 Processing helix chain 'B' and resid 1090 through 1097 removed outlier: 3.770A pdb=" N ILE B1094 " --> pdb=" O ASP B1090 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B1095 " --> pdb=" O GLY B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1100 No H-bonds generated for 'chain 'B' and resid 1098 through 1100' Processing helix chain 'B' and resid 1101 through 1109 Processing helix chain 'B' and resid 1130 through 1136 Processing helix chain 'F' and resid 55 through 63 removed outlier: 3.717A pdb=" N GLN F 61 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN F 62 " --> pdb=" O TYR F 58 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP F 63 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 65 removed outlier: 6.878A pdb=" N ILE A 73 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE A 65 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR A 71 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 84 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 140 removed outlier: 3.552A pdb=" N ILE A 196 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 193 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR A 206 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE A 195 " --> pdb=" O CYS A 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 224 removed outlier: 3.522A pdb=" N TYR A 223 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 230 " --> pdb=" O TYR A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 244 removed outlier: 6.334A pdb=" N GLN A 243 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASP A 252 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 342 removed outlier: 6.880A pdb=" N VAL A 367 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 369 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 374 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 466 through 467 removed outlier: 6.719A pdb=" N PHE A 489 " --> pdb=" O LYS A 498 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 4 through 10 removed outlier: 6.446A pdb=" N ILE B1037 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY B1038 " --> pdb=" O LEU B1029 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU B1029 " --> pdb=" O GLY B1038 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B1040 " --> pdb=" O SER B1027 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER B1027 " --> pdb=" O VAL B1040 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N SER B1027 " --> pdb=" O HIS B1009 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N HIS B1009 " --> pdb=" O SER B1027 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B1029 " --> pdb=" O PHE B1007 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE B1007 " --> pdb=" O LEU B1029 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY B1031 " --> pdb=" O ASN B1005 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 17 through 21 removed outlier: 3.567A pdb=" N GLY B 17 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 53 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 43 " --> pdb=" O PRO B 51 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B 45 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 67 removed outlier: 6.683A pdb=" N LEU B 80 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N MET B 64 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE B 78 " --> pdb=" O MET B 64 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU B 66 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU B 76 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA B 86 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N HIS B 105 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 88 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 94 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 121 through 124 removed outlier: 5.768A pdb=" N LYS B 153 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 164 through 169 removed outlier: 5.750A pdb=" N VAL B 164 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 183 " --> pdb=" O VAL B 164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 164 through 169 removed outlier: 5.750A pdb=" N VAL B 164 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 183 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 190 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 210 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 221 removed outlier: 3.581A pdb=" N MET B 218 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 258 through 263 removed outlier: 7.008A pdb=" N GLY B 274 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N HIS B 261 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 272 " --> pdb=" O HIS B 261 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ARG B 263 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ARG B 270 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 273 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP B 275 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 280 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 299 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLU B 288 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU B 297 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 313 through 318 removed outlier: 6.665A pdb=" N VAL B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER B 331 " --> pdb=" O THR B 352 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR B 352 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 333 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 361 through 363 removed outlier: 4.154A pdb=" N ASP B 361 " --> pdb=" O CYS B 378 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.556A pdb=" N LEU B 736 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE B 724 " --> pdb=" O GLY B 734 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLY B 734 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR B 726 " --> pdb=" O CYS B 732 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N CYS B 732 " --> pdb=" O TYR B 726 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.556A pdb=" N LEU B 736 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE B 724 " --> pdb=" O GLY B 734 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLY B 734 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR B 726 " --> pdb=" O CYS B 732 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N CYS B 732 " --> pdb=" O TYR B 726 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N HIS B 789 " --> pdb=" O GLN B 806 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLN B 806 " --> pdb=" O HIS B 789 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU B 791 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 804 " --> pdb=" O LEU B 791 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE B 793 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N SER B 764 " --> pdb=" O GLN B 806 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 811 through 819 removed outlier: 5.456A pdb=" N ALA B 813 " --> pdb=" O ALA B 834 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA B 834 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 815 " --> pdb=" O GLY B 832 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B 847 " --> pdb=" O THR B 833 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA B 862 " --> pdb=" O VAL B 850 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 872 through 876 removed outlier: 3.869A pdb=" N SER B 872 " --> pdb=" O SER B 883 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 911 through 917 removed outlier: 7.397A pdb=" N VAL B 930 " --> pdb=" O ARG B 947 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ARG B 947 " --> pdb=" O VAL B 930 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU B 932 " --> pdb=" O ILE B 945 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 954 through 959 removed outlier: 3.731A pdb=" N ALA B 956 " --> pdb=" O ALA B 968 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN B 973 " --> pdb=" O GLU B 969 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 974 " --> pdb=" O LEU B 997 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU B 997 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 976 " --> pdb=" O VAL B 995 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1076 through 1077 Processing sheet with id=AC7, first strand: chain 'B' and resid 1114 through 1115 294 hydrogen bonds defined for protein. 765 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: 1.46 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2943 1.34 - 1.46: 2104 1.46 - 1.58: 3924 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 9031 Sorted by residual: bond pdb=" CA GLY B 832 " pdb=" C GLY B 832 " ideal model delta sigma weight residual 1.520 1.512 0.008 7.30e-03 1.88e+04 1.13e+00 bond pdb=" CA MET A 331 " pdb=" C MET A 331 " ideal model delta sigma weight residual 1.519 1.531 -0.012 1.14e-02 7.69e+03 1.03e+00 bond pdb=" CA ARG F 18 " pdb=" CB ARG F 18 " ideal model delta sigma weight residual 1.526 1.543 -0.017 1.68e-02 3.54e+03 1.01e+00 bond pdb=" N ASN A 136 " pdb=" CA ASN A 136 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.73e-01 bond pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta sigma weight residual 1.449 1.463 -0.014 1.45e-02 4.76e+03 9.16e-01 ... (remaining 9026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 12195 2.46 - 4.93: 84 4.93 - 7.39: 4 7.39 - 9.86: 0 9.86 - 12.32: 3 Bond angle restraints: 12286 Sorted by residual: angle pdb=" N ASN B 36 " pdb=" CA ASN B 36 " pdb=" C ASN B 36 " ideal model delta sigma weight residual 108.31 95.99 12.32 1.52e+00 4.33e-01 6.57e+01 angle pdb=" CG1 ILE A 130 " pdb=" CB ILE A 130 " pdb=" CG2 ILE A 130 " ideal model delta sigma weight residual 110.70 99.63 11.07 3.00e+00 1.11e-01 1.36e+01 angle pdb=" CB MET B 938 " pdb=" CG MET B 938 " pdb=" SD MET B 938 " ideal model delta sigma weight residual 112.70 123.27 -10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" N ARG F 18 " pdb=" CA ARG F 18 " pdb=" C ARG F 18 " ideal model delta sigma weight residual 110.44 106.60 3.84 1.20e+00 6.94e-01 1.02e+01 angle pdb=" N ILE A 130 " pdb=" CA ILE A 130 " pdb=" C ILE A 130 " ideal model delta sigma weight residual 109.34 103.32 6.02 2.08e+00 2.31e-01 8.37e+00 ... (remaining 12281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4721 17.89 - 35.79: 467 35.79 - 53.68: 111 53.68 - 71.57: 23 71.57 - 89.46: 5 Dihedral angle restraints: 5327 sinusoidal: 1791 harmonic: 3536 Sorted by residual: dihedral pdb=" CA GLU A 103 " pdb=" C GLU A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ARG A 40 " pdb=" C ARG A 40 " pdb=" N VAL A 41 " pdb=" CA VAL A 41 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASN B 36 " pdb=" C ASN B 36 " pdb=" N THR B 37 " pdb=" CA THR B 37 " ideal model delta harmonic sigma weight residual -180.00 -162.15 -17.85 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1298 0.081 - 0.163: 136 0.163 - 0.244: 2 0.244 - 0.325: 1 0.325 - 0.407: 1 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CB ILE A 104 " pdb=" CA ILE A 104 " pdb=" CG1 ILE A 104 " pdb=" CG2 ILE A 104 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CA ASN B 36 " pdb=" N ASN B 36 " pdb=" C ASN B 36 " pdb=" CB ASN B 36 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE A 130 " pdb=" CA ILE A 130 " pdb=" CG1 ILE A 130 " pdb=" CG2 ILE A 130 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.27e-01 ... (remaining 1435 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 184 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO B 185 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 448 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO A 449 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 449 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 449 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 523 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 524 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 524 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 524 " 0.025 5.00e-02 4.00e+02 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 554 2.73 - 3.27: 8196 3.27 - 3.82: 13616 3.82 - 4.36: 15934 4.36 - 4.90: 28819 Nonbonded interactions: 67119 Sorted by model distance: nonbonded pdb=" NZ LYS B1104 " pdb=" O THR F 38 " model vdw 2.191 3.120 nonbonded pdb=" OE1 GLU B 40 " pdb=" OH TYR B 42 " model vdw 2.195 3.040 nonbonded pdb=" OE2 GLU A 86 " pdb=" NE2 HIS B 991 " model vdw 2.220 3.120 nonbonded pdb=" N GLN A 235 " pdb=" OE1 GLN A 235 " model vdw 2.247 3.120 nonbonded pdb=" O ALA A 503 " pdb=" NE2 GLN A 533 " model vdw 2.252 3.120 ... (remaining 67114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.003 0.052 9031 Z= 0.137 Angle : 0.558 12.325 12286 Z= 0.308 Chirality : 0.046 0.407 1438 Planarity : 0.004 0.054 1591 Dihedral : 15.666 89.465 3039 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.05 % Rotamer: Outliers : 0.12 % Allowed : 24.27 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.24), residues: 1192 helix: -1.07 (0.50), residues: 119 sheet: -0.87 (0.24), residues: 451 loop : -1.24 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 18 TYR 0.007 0.001 TYR B 91 PHE 0.012 0.001 PHE B1030 TRP 0.012 0.001 TRP B 893 HIS 0.006 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9031) covalent geometry : angle 0.55829 (12286) hydrogen bonds : bond 0.09995 ( 279) hydrogen bonds : angle 5.74023 ( 765) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.251 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.3082 time to fit residues: 26.0468 Evaluate side-chains 72 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.114998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.085867 restraints weight = 20630.171| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 4.07 r_work: 0.3140 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 9031 Z= 0.207 Angle : 0.554 9.823 12286 Z= 0.298 Chirality : 0.046 0.234 1438 Planarity : 0.004 0.052 1591 Dihedral : 4.288 21.614 1292 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 4.15 % Allowed : 21.10 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.24), residues: 1192 helix: -1.17 (0.50), residues: 123 sheet: -1.00 (0.24), residues: 453 loop : -1.26 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 57 TYR 0.014 0.001 TYR A 368 PHE 0.019 0.001 PHE A 42 TRP 0.014 0.002 TRP B 893 HIS 0.006 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 9031) covalent geometry : angle 0.55427 (12286) hydrogen bonds : bond 0.03418 ( 279) hydrogen bonds : angle 5.32933 ( 765) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.257 Fit side-chains REVERT: A 542 ASN cc_start: 0.8196 (m-40) cc_final: 0.7849 (t0) REVERT: B 866 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8555 (m) REVERT: F 13 LYS cc_start: 0.8467 (tptp) cc_final: 0.8144 (tptp) outliers start: 34 outliers final: 14 residues processed: 95 average time/residue: 0.3285 time to fit residues: 34.4788 Evaluate side-chains 85 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain F residue 49 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 28 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.116125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.087374 restraints weight = 20611.697| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 4.08 r_work: 0.3170 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9031 Z= 0.130 Angle : 0.507 8.292 12286 Z= 0.271 Chirality : 0.045 0.234 1438 Planarity : 0.004 0.055 1591 Dihedral : 4.069 22.616 1292 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 3.17 % Allowed : 21.83 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.24), residues: 1192 helix: -1.21 (0.48), residues: 129 sheet: -0.93 (0.24), residues: 450 loop : -1.17 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 57 TYR 0.008 0.001 TYR B 42 PHE 0.012 0.001 PHE B1030 TRP 0.014 0.001 TRP B 893 HIS 0.005 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9031) covalent geometry : angle 0.50725 (12286) hydrogen bonds : bond 0.02898 ( 279) hydrogen bonds : angle 5.01653 ( 765) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.210 Fit side-chains REVERT: A 542 ASN cc_start: 0.8106 (m-40) cc_final: 0.7827 (t0) REVERT: B 258 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8428 (mm) REVERT: F 13 LYS cc_start: 0.8517 (tptp) cc_final: 0.8116 (tptp) REVERT: F 50 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7822 (pp20) outliers start: 26 outliers final: 12 residues processed: 92 average time/residue: 0.2991 time to fit residues: 30.6344 Evaluate side-chains 86 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 50 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 0.0060 chunk 8 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.116760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.088040 restraints weight = 20707.942| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 4.08 r_work: 0.3182 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9031 Z= 0.113 Angle : 0.485 7.457 12286 Z= 0.259 Chirality : 0.044 0.200 1438 Planarity : 0.003 0.056 1591 Dihedral : 3.905 20.776 1292 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.88 % Rotamer: Outliers : 2.80 % Allowed : 22.44 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.57 (0.24), residues: 1192 helix: -1.03 (0.48), residues: 129 sheet: -0.78 (0.25), residues: 449 loop : -1.16 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 57 TYR 0.007 0.001 TYR B 42 PHE 0.012 0.001 PHE B1030 TRP 0.013 0.001 TRP B 893 HIS 0.005 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9031) covalent geometry : angle 0.48509 (12286) hydrogen bonds : bond 0.02704 ( 279) hydrogen bonds : angle 4.82875 ( 765) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.317 Fit side-chains REVERT: A 235 GLN cc_start: 0.7413 (pm20) cc_final: 0.7206 (pm20) REVERT: A 542 ASN cc_start: 0.8031 (m-40) cc_final: 0.7808 (t0) REVERT: B 258 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8444 (mm) REVERT: F 13 LYS cc_start: 0.8560 (tptp) cc_final: 0.8131 (tptp) outliers start: 23 outliers final: 14 residues processed: 87 average time/residue: 0.3229 time to fit residues: 31.2739 Evaluate side-chains 84 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 49 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 95 optimal weight: 0.0270 chunk 17 optimal weight: 9.9990 chunk 111 optimal weight: 0.0170 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.116585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.087846 restraints weight = 20554.573| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 4.00 r_work: 0.3182 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9031 Z= 0.118 Angle : 0.490 8.481 12286 Z= 0.260 Chirality : 0.044 0.151 1438 Planarity : 0.003 0.055 1591 Dihedral : 3.896 19.214 1292 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.36 % Favored : 95.55 % Rotamer: Outliers : 2.93 % Allowed : 22.44 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.50 (0.24), residues: 1192 helix: -0.82 (0.49), residues: 127 sheet: -0.76 (0.25), residues: 449 loop : -1.13 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 18 TYR 0.017 0.001 TYR A 368 PHE 0.011 0.001 PHE B1030 TRP 0.012 0.001 TRP B 893 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9031) covalent geometry : angle 0.48991 (12286) hydrogen bonds : bond 0.02689 ( 279) hydrogen bonds : angle 4.79305 ( 765) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.343 Fit side-chains REVERT: A 235 GLN cc_start: 0.7094 (pm20) cc_final: 0.6840 (pm20) REVERT: B 258 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8454 (mm) REVERT: F 13 LYS cc_start: 0.8586 (tptp) cc_final: 0.8145 (tptp) outliers start: 24 outliers final: 14 residues processed: 88 average time/residue: 0.2792 time to fit residues: 27.5743 Evaluate side-chains 85 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 49 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 46 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 26 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.117137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.088446 restraints weight = 20687.168| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 4.02 r_work: 0.3193 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9031 Z= 0.100 Angle : 0.488 10.979 12286 Z= 0.255 Chirality : 0.044 0.184 1438 Planarity : 0.003 0.056 1591 Dihedral : 3.766 16.386 1292 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 2.68 % Allowed : 22.80 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.38 (0.24), residues: 1192 helix: -0.65 (0.49), residues: 127 sheet: -0.67 (0.25), residues: 432 loop : -1.08 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 18 TYR 0.006 0.001 TYR B 42 PHE 0.010 0.001 PHE B1030 TRP 0.012 0.001 TRP B 893 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9031) covalent geometry : angle 0.48790 (12286) hydrogen bonds : bond 0.02513 ( 279) hydrogen bonds : angle 4.64966 ( 765) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.339 Fit side-chains REVERT: A 235 GLN cc_start: 0.7049 (pm20) cc_final: 0.6754 (pm20) REVERT: B 54 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8138 (tm-30) REVERT: B 258 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8437 (mm) REVERT: F 13 LYS cc_start: 0.8614 (tptp) cc_final: 0.8067 (tptp) outliers start: 22 outliers final: 14 residues processed: 87 average time/residue: 0.3216 time to fit residues: 31.2321 Evaluate side-chains 86 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 49 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 0.0870 chunk 112 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.115806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.087021 restraints weight = 20714.350| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 4.02 r_work: 0.3166 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9031 Z= 0.142 Angle : 0.509 10.659 12286 Z= 0.266 Chirality : 0.044 0.208 1438 Planarity : 0.003 0.054 1591 Dihedral : 3.903 17.477 1292 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 3.17 % Allowed : 22.44 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.40 (0.24), residues: 1192 helix: -0.57 (0.49), residues: 127 sheet: -0.71 (0.25), residues: 432 loop : -1.10 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 18 TYR 0.018 0.001 TYR A 368 PHE 0.011 0.001 PHE B1030 TRP 0.010 0.001 TRP B 893 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9031) covalent geometry : angle 0.50893 (12286) hydrogen bonds : bond 0.02805 ( 279) hydrogen bonds : angle 4.76488 ( 765) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.343 Fit side-chains REVERT: A 78 ASP cc_start: 0.8746 (p0) cc_final: 0.8473 (t0) REVERT: A 235 GLN cc_start: 0.7035 (pm20) cc_final: 0.6737 (pm20) REVERT: B 54 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8139 (tm-30) REVERT: B 258 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8483 (mm) REVERT: F 13 LYS cc_start: 0.8642 (tptp) cc_final: 0.8107 (tptp) outliers start: 26 outliers final: 14 residues processed: 87 average time/residue: 0.3078 time to fit residues: 29.9863 Evaluate side-chains 85 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 49 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 95 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 64 optimal weight: 0.1980 chunk 58 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.118014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.089248 restraints weight = 20503.998| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 4.06 r_work: 0.3212 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9031 Z= 0.085 Angle : 0.492 10.760 12286 Z= 0.254 Chirality : 0.044 0.191 1438 Planarity : 0.003 0.057 1591 Dihedral : 3.661 18.895 1292 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.48 % Rotamer: Outliers : 1.71 % Allowed : 24.27 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.24 (0.24), residues: 1192 helix: -0.44 (0.49), residues: 127 sheet: -0.55 (0.25), residues: 428 loop : -1.04 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 18 TYR 0.007 0.001 TYR B 239 PHE 0.010 0.001 PHE B1030 TRP 0.013 0.001 TRP B 893 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 9031) covalent geometry : angle 0.49174 (12286) hydrogen bonds : bond 0.02350 ( 279) hydrogen bonds : angle 4.50257 ( 765) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.339 Fit side-chains REVERT: A 16 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7953 (mm-40) REVERT: A 235 GLN cc_start: 0.7013 (pm20) cc_final: 0.6702 (pm20) REVERT: B 54 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7695 (mp0) REVERT: F 13 LYS cc_start: 0.8644 (tptp) cc_final: 0.8087 (tptp) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 0.3064 time to fit residues: 27.6691 Evaluate side-chains 82 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain F residue 49 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 25 optimal weight: 20.0000 chunk 59 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 80 optimal weight: 0.0770 chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.116605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.087252 restraints weight = 20609.255| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 4.13 r_work: 0.3184 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9031 Z= 0.124 Angle : 0.505 10.294 12286 Z= 0.263 Chirality : 0.044 0.197 1438 Planarity : 0.003 0.054 1591 Dihedral : 3.779 19.014 1292 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.64 % Rotamer: Outliers : 1.71 % Allowed : 24.39 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.27 (0.24), residues: 1192 helix: -0.36 (0.50), residues: 127 sheet: -0.64 (0.25), residues: 433 loop : -1.03 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 18 TYR 0.021 0.001 TYR A 368 PHE 0.011 0.001 PHE B 180 TRP 0.010 0.001 TRP B 893 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9031) covalent geometry : angle 0.50539 (12286) hydrogen bonds : bond 0.02658 ( 279) hydrogen bonds : angle 4.61372 ( 765) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.318 Fit side-chains REVERT: A 78 ASP cc_start: 0.8816 (p0) cc_final: 0.8501 (t0) REVERT: A 235 GLN cc_start: 0.7003 (pm20) cc_final: 0.6703 (pm20) REVERT: F 13 LYS cc_start: 0.8688 (tptp) cc_final: 0.8165 (tptp) outliers start: 14 outliers final: 11 residues processed: 80 average time/residue: 0.3183 time to fit residues: 28.4453 Evaluate side-chains 81 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain F residue 49 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 120 optimal weight: 0.0870 chunk 103 optimal weight: 0.9990 chunk 82 optimal weight: 0.0470 chunk 96 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.117774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.088715 restraints weight = 20367.422| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 4.06 r_work: 0.3212 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9031 Z= 0.092 Angle : 0.496 10.865 12286 Z= 0.257 Chirality : 0.044 0.191 1438 Planarity : 0.003 0.056 1591 Dihedral : 3.663 17.210 1292 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.94 % Favored : 95.97 % Rotamer: Outliers : 1.34 % Allowed : 24.76 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.17 (0.24), residues: 1192 helix: -0.29 (0.50), residues: 127 sheet: -0.49 (0.25), residues: 426 loop : -1.02 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 18 TYR 0.006 0.001 TYR B 239 PHE 0.010 0.001 PHE B 180 TRP 0.012 0.001 TRP B 893 HIS 0.005 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 9031) covalent geometry : angle 0.49571 (12286) hydrogen bonds : bond 0.02398 ( 279) hydrogen bonds : angle 4.49660 ( 765) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.351 Fit side-chains REVERT: A 78 ASP cc_start: 0.8809 (p0) cc_final: 0.8472 (t0) REVERT: A 228 ILE cc_start: 0.8004 (mp) cc_final: 0.7687 (tp) REVERT: A 235 GLN cc_start: 0.7010 (pm20) cc_final: 0.6708 (pm20) REVERT: F 13 LYS cc_start: 0.8702 (tptp) cc_final: 0.8182 (tptp) outliers start: 11 outliers final: 9 residues processed: 78 average time/residue: 0.3049 time to fit residues: 26.5664 Evaluate side-chains 79 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain F residue 49 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 98 optimal weight: 5.9990 chunk 82 optimal weight: 0.0970 chunk 16 optimal weight: 30.0000 chunk 1 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 0.0000 chunk 73 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 40.0000 chunk 11 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.116495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.087172 restraints weight = 20303.383| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 4.08 r_work: 0.3181 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9031 Z= 0.127 Angle : 0.516 12.009 12286 Z= 0.269 Chirality : 0.044 0.188 1438 Planarity : 0.003 0.054 1591 Dihedral : 3.819 18.846 1292 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.36 % Favored : 95.55 % Rotamer: Outliers : 1.59 % Allowed : 25.00 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.26 (0.24), residues: 1192 helix: -0.31 (0.50), residues: 127 sheet: -0.62 (0.25), residues: 439 loop : -1.04 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 18 TYR 0.018 0.001 TYR A 368 PHE 0.011 0.001 PHE B 180 TRP 0.010 0.001 TRP B 893 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9031) covalent geometry : angle 0.51594 (12286) hydrogen bonds : bond 0.02696 ( 279) hydrogen bonds : angle 4.63894 ( 765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2488.65 seconds wall clock time: 43 minutes 2.00 seconds (2582.00 seconds total)