Starting phenix.real_space_refine on Wed Jan 14 02:07:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7z_27240/01_2026/8d7z_27240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7z_27240/01_2026/8d7z_27240.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/8d7z_27240/01_2026/8d7z_27240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7z_27240/01_2026/8d7z_27240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d7z_27240/01_2026/8d7z_27240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7z_27240/01_2026/8d7z_27240.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= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 202 atoms to isotropic. 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 2 6.06 5 S 59 5.16 5 C 7104 2.51 5 N 1942 2.21 5 O 2120 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 10 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: 11228 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 8039 Classifications: {'peptide': 1132} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 262} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1091} Chain breaks: 1 Unresolved non-hydrogen bonds: 841 Unresolved non-hydrogen angles: 1067 Unresolved non-hydrogen dihedrals: 660 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLU:plan': 24, 'ASP:plan': 18, 'ARG:plan': 14, 'GLN:plan1': 17, 'HIS:plan': 7, 'TRP:plan': 2, 'ASN:plan1': 10, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 416 Chain: "B" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2944 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 20, 'TRANS': 360} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 8, 'HIS:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 201 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} 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} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10207 SG CYS B 323 44.077 88.915 31.267 1.00236.30 S ATOM 10223 SG CYS B 326 43.485 92.561 30.483 1.00238.80 S ATOM 10721 SG CYS B 391 43.064 89.721 27.543 1.00218.80 S ATOM 10740 SG CYS B 394 45.934 91.290 28.641 1.00228.55 S ATOM 11016 SG CYS C 147 56.933 86.307 20.559 1.00216.63 S Time building chain proxies: 2.76, per 1000 atoms: 0.25 Number of scatterers: 11228 At special positions: 0 Unit cell: (90.85, 110.4, 158.7, 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 2 29.99 S 59 16.00 F 1 9.00 O 2120 8.00 N 1942 7.00 C 7104 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: 0.95 Conformation dependent library (CDL) restraints added in 665.3 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 391 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 323 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 326 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 163 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 167 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 147 " Number of angles added : 6 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2880 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 29 sheets defined 12.2% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.861A pdb=" N ILE A 253 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 3.788A 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 985 through 990 removed outlier: 3.605A pdb=" N GLN A 990 " --> pdb=" O ASP A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1060 removed outlier: 3.918A pdb=" N LYS A1060 " --> pdb=" O ASN A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1075 Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1101 through 1109 removed outlier: 3.798A pdb=" N VAL A1109 " --> pdb=" O MET A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1138 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 200 through 204 removed outlier: 4.180A pdb=" N LYS B 204 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.701A pdb=" N ASN B 236 " --> pdb=" O HIS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.615A pdb=" N TYR B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 265 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 helix chain 'B' and resid 333 through 337 Processing helix chain 'C' and resid 157 through 168 Processing sheet with id=AA1, first strand: chain 'A' and resid 1004 through 1009 removed outlier: 3.677A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLY A1026 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER A1042 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 5.918A 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: 3.559A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 3.570A 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: 3.510A pdb=" N ILE A 121 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 166 removed outlier: 6.786A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 221 Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 263 removed outlier: 3.656A pdb=" N LEU A 273 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 280 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 289 through 290 removed outlier: 3.709A 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 316 removed outlier: 6.526A pdb=" N SER A 331 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR A 352 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 365 removed outlier: 4.408A pdb=" N ASP A 361 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 3.547A 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 402 removed outlier: 6.373A pdb=" N ILE A 701 " --> pdb=" O HIS A 399 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER A 401 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A 699 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 702 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.530A pdb=" N THR A 424 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 459 through 463 removed outlier: 3.768A pdb=" N GLN A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 470 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 498 through 503 removed outlier: 3.522A pdb=" N VAL A 500 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 502 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU A 516 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N HIS A 531 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N TYR A 518 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.740A pdb=" N ILE A 558 " --> pdb=" O ARG A 567 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 567 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A 578 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 588 through 595 removed outlier: 4.061A pdb=" N LYS A 627 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 637 through 639 removed outlier: 3.566A pdb=" N CYS A 652 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.362A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.362A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 811 through 819 removed outlier: 5.313A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 862 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLN A 852 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR A 860 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N SER A 854 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 874 through 876 removed outlier: 5.579A pdb=" N GLU A 892 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N THR A 901 " --> pdb=" O GLU A 892 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 913 through 914 removed outlier: 3.661A pdb=" N ALA A 946 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA A 934 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU A 944 " --> pdb=" O ALA A 934 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 954 through 961 removed outlier: 6.511A pdb=" N ALA A 968 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL A 957 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 966 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ILE A 959 " --> pdb=" O ASN A 964 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASN A 964 " --> pdb=" O ILE A 959 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN A 978 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLU A 994 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AC7, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.589A pdb=" N GLU B 65 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 144 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR B 137 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG B 164 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA B 139 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG B 162 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE B 141 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE B 160 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 143 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 78 through 83 removed outlier: 3.873A pdb=" N GLN B 178 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLN B 179 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU B 170 " --> pdb=" O GLN B 179 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LYS B 181 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 143 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE B 160 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE B 141 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG B 162 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA B 139 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG B 164 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR B 137 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AD1, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.530A pdb=" N TRP B 415 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 368 through 375 removed outlier: 3.718A pdb=" N VAL B 388 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG B 373 " --> pdb=" O TRP B 386 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TRP B 386 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER B 375 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR B 384 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 385 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 389 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY B 399 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS B 391 " --> pdb=" O HIS B 397 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N HIS B 397 " --> pdb=" O CYS B 391 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1068 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: 2.77 Time building geometry restraints manager: 1.29 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: 1921 1.28 - 1.42: 2779 1.42 - 1.55: 6662 1.55 - 1.69: 0 1.69 - 1.83: 86 Bond restraints: 11448 Sorted by residual: bond pdb=" N ILE B 154 " pdb=" CA ILE B 154 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.67e+00 bond pdb=" N PHE B 102 " pdb=" CA PHE B 102 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.17e-02 7.31e+03 6.86e+00 bond pdb=" N ILE B 152 " pdb=" CA ILE B 152 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.64e+00 bond pdb=" N VAL B 157 " pdb=" CA VAL B 157 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.18e-02 7.18e+03 6.58e+00 bond pdb=" N GLU B 146 " pdb=" CA GLU B 146 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.35e+00 ... (remaining 11443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 15332 1.93 - 3.86: 234 3.86 - 5.80: 30 5.80 - 7.73: 5 7.73 - 9.66: 3 Bond angle restraints: 15604 Sorted by residual: angle pdb=" N PRO B 98 " pdb=" CA PRO B 98 " pdb=" CB PRO B 98 " ideal model delta sigma weight residual 103.25 111.06 -7.81 1.05e+00 9.07e-01 5.54e+01 angle pdb=" C CYS C 150 " pdb=" CA CYS C 150 " pdb=" CB CYS C 150 " ideal model delta sigma weight residual 111.26 101.60 9.66 1.66e+00 3.63e-01 3.39e+01 angle pdb=" C ALA B 143 " pdb=" N TYR B 144 " pdb=" CA TYR B 144 " ideal model delta sigma weight residual 122.99 116.45 6.54 1.41e+00 5.03e-01 2.15e+01 angle pdb=" O CYS C 150 " pdb=" C CYS C 150 " pdb=" N GLY C 151 " ideal model delta sigma weight residual 121.95 126.71 -4.76 1.17e+00 7.31e-01 1.66e+01 angle pdb=" CA CYS C 150 " pdb=" C CYS C 150 " pdb=" N GLY C 151 " ideal model delta sigma weight residual 118.39 112.95 5.44 1.38e+00 5.25e-01 1.55e+01 ... (remaining 15599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.23: 6424 23.23 - 46.46: 364 46.46 - 69.69: 37 69.69 - 92.92: 12 92.92 - 116.15: 2 Dihedral angle restraints: 6839 sinusoidal: 2379 harmonic: 4460 Sorted by residual: dihedral pdb=" C CYS C 150 " pdb=" N CYS C 150 " pdb=" CA CYS C 150 " pdb=" CB CYS C 150 " ideal model delta harmonic sigma weight residual -122.60 -109.06 -13.54 0 2.50e+00 1.60e-01 2.93e+01 dihedral pdb=" N CYS C 150 " pdb=" C CYS C 150 " pdb=" CA CYS C 150 " pdb=" CB CYS C 150 " ideal model delta harmonic sigma weight residual 122.80 112.71 10.09 0 2.50e+00 1.60e-01 1.63e+01 dihedral pdb=" C29 QFC B 502 " pdb=" N QFC B 502 " pdb=" C30 QFC B 502 " pdb=" C6 QFC B 502 " ideal model delta sinusoidal sigma weight residual -52.98 63.17 -116.15 1 3.00e+01 1.11e-03 1.54e+01 ... (remaining 6836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1588 0.072 - 0.144: 214 0.144 - 0.216: 3 0.216 - 0.288: 1 0.288 - 0.360: 1 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CA CYS C 150 " pdb=" N CYS C 150 " pdb=" C CYS C 150 " pdb=" CB CYS C 150 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA VAL B 155 " pdb=" N VAL B 155 " pdb=" C VAL B 155 " pdb=" CB VAL B 155 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA VAL B 157 " pdb=" N VAL B 157 " pdb=" C VAL B 157 " pdb=" CB VAL B 157 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1804 not shown) Planarity restraints: 2043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N QFC B 502 " 0.034 2.00e-02 2.50e+03 5.02e-02 6.29e+01 pdb=" C QFC B 502 " -0.046 2.00e-02 2.50e+03 pdb=" C1 QFC B 502 " -0.092 2.00e-02 2.50e+03 pdb=" C2 QFC B 502 " -0.054 2.00e-02 2.50e+03 pdb=" C3 QFC B 502 " -0.006 2.00e-02 2.50e+03 pdb=" C31 QFC B 502 " 0.012 2.00e-02 2.50e+03 pdb=" C4 QFC B 502 " 0.013 2.00e-02 2.50e+03 pdb=" C5 QFC B 502 " -0.003 2.00e-02 2.50e+03 pdb=" F QFC B 502 " 0.072 2.00e-02 2.50e+03 pdb=" N4 QFC B 502 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 QFC B 502 " 0.025 2.00e-02 2.50e+03 3.94e-02 3.10e+01 pdb=" C11 QFC B 502 " 0.027 2.00e-02 2.50e+03 pdb=" C12 QFC B 502 " 0.015 2.00e-02 2.50e+03 pdb=" C13 QFC B 502 " -0.068 2.00e-02 2.50e+03 pdb=" C27 QFC B 502 " 0.027 2.00e-02 2.50e+03 pdb=" C28 QFC B 502 " 0.026 2.00e-02 2.50e+03 pdb=" C8 QFC B 502 " -0.067 2.00e-02 2.50e+03 pdb=" C9 QFC B 502 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O QFC B 502 " 0.030 2.00e-02 2.50e+03 2.82e-02 2.39e+01 pdb=" C14 QFC B 502 " -0.011 2.00e-02 2.50e+03 pdb=" C15 QFC B 502 " 0.005 2.00e-02 2.50e+03 pdb=" C16 QFC B 502 " 0.019 2.00e-02 2.50e+03 pdb=" C17 QFC B 502 " 0.016 2.00e-02 2.50e+03 pdb=" C18 QFC B 502 " -0.011 2.00e-02 2.50e+03 pdb=" C19 QFC B 502 " -0.012 2.00e-02 2.50e+03 pdb=" C20 QFC B 502 " -0.049 2.00e-02 2.50e+03 pdb=" C21 QFC B 502 " -0.026 2.00e-02 2.50e+03 pdb=" C22 QFC B 502 " 0.065 2.00e-02 2.50e+03 pdb=" N2 QFC B 502 " -0.014 2.00e-02 2.50e+03 pdb=" O1 QFC B 502 " -0.011 2.00e-02 2.50e+03 ... (remaining 2040 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1073 2.75 - 3.29: 10683 3.29 - 3.82: 17660 3.82 - 4.36: 20780 4.36 - 4.90: 37768 Nonbonded interactions: 87964 Sorted by model distance: nonbonded pdb=" OE2 GLU A 811 " pdb=" OG1 THR A 833 " model vdw 2.210 3.040 nonbonded pdb=" CB CYS C 150 " pdb="ZN ZN C 201 " model vdw 2.237 2.630 nonbonded pdb=" O GLY A1010 " pdb=" OG SER A1027 " model vdw 2.250 3.040 nonbonded pdb=" OG SER A 757 " pdb=" OD1 ASN A 790 " model vdw 2.252 3.040 nonbonded pdb=" OE2 GLU A 277 " pdb=" NH1 ARG A 279 " model vdw 2.259 3.120 ... (remaining 87959 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.360 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.269 11455 Z= 0.202 Angle : 0.635 18.277 15610 Z= 0.333 Chirality : 0.046 0.360 1807 Planarity : 0.004 0.091 2043 Dihedral : 14.593 116.150 3959 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.47 % Favored : 93.08 % Rotamer: Outliers : 0.66 % Allowed : 0.38 % Favored : 98.97 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.33 % 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: -2.00 (0.21), residues: 1531 helix: 0.18 (0.39), residues: 182 sheet: -1.14 (0.22), residues: 561 loop : -1.82 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 118 TYR 0.012 0.001 TYR B 227 PHE 0.020 0.001 PHE A 829 TRP 0.016 0.001 TRP B 400 HIS 0.004 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00332 (11448) covalent geometry : angle 0.59051 (15604) hydrogen bonds : bond 0.23935 ( 391) hydrogen bonds : angle 9.57611 ( 1068) metal coordination : bond 0.14100 ( 7) metal coordination : angle 11.93434 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7396 (mt-10) REVERT: A 286 GLU cc_start: 0.7036 (mp0) cc_final: 0.6418 (mp0) REVERT: A 655 ARG cc_start: 0.7098 (mmp-170) cc_final: 0.6483 (ttm-80) REVERT: A 660 TYR cc_start: 0.7137 (p90) cc_final: 0.6932 (p90) REVERT: A 1014 MET cc_start: 0.7366 (tmm) cc_final: 0.7100 (tmm) REVERT: B 357 HIS cc_start: 0.7137 (m90) cc_final: 0.6705 (m90) outliers start: 7 outliers final: 1 residues processed: 163 average time/residue: 0.1156 time to fit residues: 26.5910 Evaluate side-chains 120 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0050 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 990 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.171465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128985 restraints weight = 15132.824| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.07 r_work: 0.3234 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 11455 Z= 0.292 Angle : 0.698 16.321 15610 Z= 0.349 Chirality : 0.049 0.200 1807 Planarity : 0.005 0.065 2043 Dihedral : 6.909 84.090 1674 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.51 % Favored : 92.10 % Rotamer: Outliers : 1.60 % Allowed : 10.63 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.18 (0.20), residues: 1531 helix: 0.05 (0.39), residues: 184 sheet: -1.18 (0.22), residues: 564 loop : -2.02 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 309 TYR 0.017 0.002 TYR A 678 PHE 0.026 0.003 PHE A 829 TRP 0.016 0.002 TRP A 207 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00704 (11448) covalent geometry : angle 0.67117 (15604) hydrogen bonds : bond 0.04585 ( 391) hydrogen bonds : angle 6.62744 ( 1068) metal coordination : bond 0.00902 ( 7) metal coordination : angle 9.79418 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 655 ARG cc_start: 0.7375 (mmp-170) cc_final: 0.6765 (ttm-80) REVERT: A 670 ASN cc_start: 0.8588 (t0) cc_final: 0.8311 (t0) REVERT: A 990 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: A 1063 LYS cc_start: 0.7964 (ptpt) cc_final: 0.7672 (mmmt) REVERT: B 112 ASN cc_start: 0.6799 (m-40) cc_final: 0.6154 (p0) outliers start: 17 outliers final: 11 residues processed: 130 average time/residue: 0.1147 time to fit residues: 21.3474 Evaluate side-chains 129 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 150 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 55 optimal weight: 20.0000 chunk 53 optimal weight: 50.0000 chunk 102 optimal weight: 0.5980 chunk 101 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** 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 = 0.4103 r_free = 0.4103 target = 0.173245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120249 restraints weight = 15156.606| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.75 r_work: 0.3296 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11455 Z= 0.154 Angle : 0.566 12.307 15610 Z= 0.288 Chirality : 0.045 0.150 1807 Planarity : 0.004 0.053 2043 Dihedral : 5.727 63.114 1672 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.88 % Favored : 93.86 % Rotamer: Outliers : 1.88 % Allowed : 12.32 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.08 (0.21), residues: 1531 helix: 0.33 (0.39), residues: 183 sheet: -1.16 (0.22), residues: 561 loop : -1.97 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 230 TYR 0.013 0.001 TYR A 42 PHE 0.018 0.002 PHE A 829 TRP 0.013 0.001 TRP A 207 HIS 0.004 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00366 (11448) covalent geometry : angle 0.54546 (15604) hydrogen bonds : bond 0.03677 ( 391) hydrogen bonds : angle 5.96346 ( 1068) metal coordination : bond 0.00664 ( 7) metal coordination : angle 7.72297 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 655 ARG cc_start: 0.7285 (mmp-170) cc_final: 0.6718 (ttm-80) REVERT: A 670 ASN cc_start: 0.8629 (t0) cc_final: 0.8336 (t0) REVERT: A 1014 MET cc_start: 0.8210 (tmm) cc_final: 0.7829 (tmm) REVERT: A 1063 LYS cc_start: 0.7966 (ptpt) cc_final: 0.7682 (mmmt) REVERT: A 1073 TRP cc_start: 0.8335 (t60) cc_final: 0.7707 (t-100) REVERT: B 112 ASN cc_start: 0.6898 (m-40) cc_final: 0.6243 (p0) REVERT: B 376 THR cc_start: 0.7199 (OUTLIER) cc_final: 0.6844 (m) REVERT: B 384 TYR cc_start: 0.7047 (m-80) cc_final: 0.6755 (m-80) outliers start: 20 outliers final: 17 residues processed: 140 average time/residue: 0.1124 time to fit residues: 22.5586 Evaluate side-chains 136 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain C residue 150 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 75 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 0.0370 chunk 137 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN B 412 GLN C 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.174423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125711 restraints weight = 15149.866| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.71 r_work: 0.3280 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11455 Z= 0.122 Angle : 0.524 11.025 15610 Z= 0.269 Chirality : 0.044 0.148 1807 Planarity : 0.004 0.046 2043 Dihedral : 4.921 38.292 1672 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.53 % Favored : 93.21 % Rotamer: Outliers : 2.26 % Allowed : 13.83 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1531 helix: 0.44 (0.40), residues: 183 sheet: -1.14 (0.22), residues: 549 loop : -1.91 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.013 0.001 TYR A 678 PHE 0.016 0.001 PHE A 829 TRP 0.012 0.001 TRP A 207 HIS 0.003 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00287 (11448) covalent geometry : angle 0.50852 (15604) hydrogen bonds : bond 0.03181 ( 391) hydrogen bonds : angle 5.52031 ( 1068) metal coordination : bond 0.00598 ( 7) metal coordination : angle 6.36454 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 655 ARG cc_start: 0.7305 (mmp-170) cc_final: 0.6791 (ttm-80) REVERT: A 670 ASN cc_start: 0.8663 (t0) cc_final: 0.8378 (t0) REVERT: A 1063 LYS cc_start: 0.7902 (ptpt) cc_final: 0.7691 (mmmt) REVERT: A 1073 TRP cc_start: 0.8265 (t60) cc_final: 0.7818 (t-100) REVERT: A 1095 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8046 (mt-10) REVERT: B 376 THR cc_start: 0.7193 (OUTLIER) cc_final: 0.6818 (m) REVERT: B 384 TYR cc_start: 0.6970 (m-80) cc_final: 0.6651 (m-80) outliers start: 24 outliers final: 19 residues processed: 150 average time/residue: 0.1047 time to fit residues: 22.4652 Evaluate side-chains 142 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain C residue 150 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 42 optimal weight: 40.0000 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 115 optimal weight: 40.0000 chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 727 GLN A 991 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.168900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120227 restraints weight = 15119.902| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.58 r_work: 0.3196 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.055 11455 Z= 0.356 Angle : 0.713 10.523 15610 Z= 0.362 Chirality : 0.050 0.225 1807 Planarity : 0.005 0.049 2043 Dihedral : 5.399 34.993 1672 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.49 % Favored : 91.31 % Rotamer: Outliers : 2.82 % Allowed : 15.33 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.35 (0.20), residues: 1531 helix: 0.14 (0.39), residues: 182 sheet: -1.28 (0.22), residues: 536 loop : -2.19 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 900 TYR 0.021 0.002 TYR B 227 PHE 0.027 0.003 PHE A 998 TRP 0.016 0.002 TRP A 207 HIS 0.006 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00864 (11448) covalent geometry : angle 0.70215 (15604) hydrogen bonds : bond 0.04266 ( 391) hydrogen bonds : angle 5.87162 ( 1068) metal coordination : bond 0.00755 ( 7) metal coordination : angle 6.27847 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 655 ARG cc_start: 0.7473 (mmp-170) cc_final: 0.6827 (ttm-80) REVERT: A 670 ASN cc_start: 0.8721 (t0) cc_final: 0.8391 (t0) REVERT: A 986 ASP cc_start: 0.7886 (t0) cc_final: 0.7617 (t0) REVERT: A 1014 MET cc_start: 0.8440 (tmm) cc_final: 0.8154 (tmm) REVERT: B 81 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7797 (mp) REVERT: B 112 ASN cc_start: 0.6732 (m-40) cc_final: 0.6068 (p0) REVERT: B 376 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.6905 (m) REVERT: B 384 TYR cc_start: 0.7153 (m-80) cc_final: 0.6703 (m-80) outliers start: 30 outliers final: 25 residues processed: 143 average time/residue: 0.1013 time to fit residues: 20.9405 Evaluate side-chains 144 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain C residue 150 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 34 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 991 HIS B 203 ASN B 353 HIS C 149 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.173948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132531 restraints weight = 15068.193| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.80 r_work: 0.3267 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11455 Z= 0.113 Angle : 0.537 9.557 15610 Z= 0.277 Chirality : 0.045 0.150 1807 Planarity : 0.003 0.047 2043 Dihedral : 4.681 23.968 1672 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.01 % Favored : 93.86 % Rotamer: Outliers : 2.16 % Allowed : 16.18 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.06 (0.21), residues: 1531 helix: 0.57 (0.40), residues: 177 sheet: -1.19 (0.22), residues: 543 loop : -1.96 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.014 0.001 TYR A 678 PHE 0.012 0.001 PHE A1030 TRP 0.014 0.001 TRP B 400 HIS 0.004 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00264 (11448) covalent geometry : angle 0.52540 (15604) hydrogen bonds : bond 0.03043 ( 391) hydrogen bonds : angle 5.39499 ( 1068) metal coordination : bond 0.00525 ( 7) metal coordination : angle 5.57940 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.8164 (t80) cc_final: 0.7461 (t80) REVERT: A 655 ARG cc_start: 0.7355 (mmp-170) cc_final: 0.6817 (ttm-80) REVERT: A 670 ASN cc_start: 0.8735 (t0) cc_final: 0.8440 (t0) REVERT: A 1014 MET cc_start: 0.8319 (tmm) cc_final: 0.8096 (tmm) REVERT: A 1073 TRP cc_start: 0.8244 (t60) cc_final: 0.7813 (t-100) REVERT: B 112 ASN cc_start: 0.6820 (m-40) cc_final: 0.6199 (p0) REVERT: B 376 THR cc_start: 0.7240 (OUTLIER) cc_final: 0.6862 (m) REVERT: B 384 TYR cc_start: 0.7060 (m-80) cc_final: 0.6749 (m-80) REVERT: B 390 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6912 (mm-40) outliers start: 23 outliers final: 17 residues processed: 149 average time/residue: 0.1077 time to fit residues: 23.0597 Evaluate side-chains 143 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain C residue 150 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 120 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 115 optimal weight: 40.0000 chunk 146 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 60 optimal weight: 50.0000 chunk 53 optimal weight: 50.0000 chunk 23 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 991 HIS B 353 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.168881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121387 restraints weight = 15128.291| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.89 r_work: 0.3205 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 11455 Z= 0.332 Angle : 0.697 10.302 15610 Z= 0.353 Chirality : 0.049 0.191 1807 Planarity : 0.004 0.049 2043 Dihedral : 5.268 34.086 1672 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.36 % Favored : 91.51 % Rotamer: Outliers : 3.39 % Allowed : 15.80 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.36 (0.20), residues: 1531 helix: 0.32 (0.39), residues: 181 sheet: -1.29 (0.21), residues: 536 loop : -2.23 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 900 TYR 0.020 0.002 TYR B 227 PHE 0.025 0.003 PHE A 998 TRP 0.015 0.002 TRP A 207 HIS 0.005 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00802 (11448) covalent geometry : angle 0.68792 (15604) hydrogen bonds : bond 0.04062 ( 391) hydrogen bonds : angle 5.75321 ( 1068) metal coordination : bond 0.00726 ( 7) metal coordination : angle 5.84147 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 655 ARG cc_start: 0.7545 (mmp-170) cc_final: 0.6872 (ttm-80) REVERT: A 1014 MET cc_start: 0.8466 (tmm) cc_final: 0.8199 (tmm) REVERT: B 81 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7640 (mp) REVERT: B 112 ASN cc_start: 0.6865 (m-40) cc_final: 0.6193 (p0) REVERT: B 376 THR cc_start: 0.7334 (OUTLIER) cc_final: 0.6968 (m) REVERT: B 390 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6961 (mm-40) outliers start: 36 outliers final: 30 residues processed: 146 average time/residue: 0.1050 time to fit residues: 22.0550 Evaluate side-chains 152 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain C residue 150 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 80 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 50.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 174 GLN A 907 ASN A 991 HIS B 353 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.172967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124232 restraints weight = 14977.131| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.54 r_work: 0.3254 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11455 Z= 0.120 Angle : 0.547 9.329 15610 Z= 0.281 Chirality : 0.045 0.155 1807 Planarity : 0.003 0.046 2043 Dihedral : 4.687 24.430 1672 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.27 % Favored : 93.60 % Rotamer: Outliers : 2.54 % Allowed : 17.22 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.20), residues: 1531 helix: 0.59 (0.40), residues: 182 sheet: -1.25 (0.21), residues: 549 loop : -2.01 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 283 TYR 0.016 0.001 TYR A 678 PHE 0.012 0.001 PHE A1030 TRP 0.014 0.001 TRP A 207 HIS 0.003 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00279 (11448) covalent geometry : angle 0.53633 (15604) hydrogen bonds : bond 0.03057 ( 391) hydrogen bonds : angle 5.34690 ( 1068) metal coordination : bond 0.00533 ( 7) metal coordination : angle 5.42223 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.8136 (t80) cc_final: 0.7482 (t80) REVERT: A 655 ARG cc_start: 0.7397 (mmp-170) cc_final: 0.6775 (ttm-80) REVERT: A 1014 MET cc_start: 0.8399 (tmm) cc_final: 0.8172 (tmm) REVERT: A 1073 TRP cc_start: 0.8262 (t60) cc_final: 0.7779 (t-100) REVERT: B 81 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7422 (mp) REVERT: B 112 ASN cc_start: 0.6879 (m-40) cc_final: 0.6300 (p0) REVERT: B 384 TYR cc_start: 0.7168 (m-80) cc_final: 0.6729 (m-80) REVERT: B 390 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6919 (mm-40) outliers start: 27 outliers final: 20 residues processed: 147 average time/residue: 0.1073 time to fit residues: 22.6002 Evaluate side-chains 147 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain C residue 150 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 113 optimal weight: 20.0000 chunk 71 optimal weight: 0.4980 chunk 5 optimal weight: 0.0970 chunk 40 optimal weight: 30.0000 chunk 130 optimal weight: 0.0670 chunk 38 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 129 optimal weight: 0.2980 chunk 44 optimal weight: 30.0000 chunk 124 optimal weight: 9.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN B 57 HIS B 357 HIS C 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.175493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127813 restraints weight = 14990.000| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.56 r_work: 0.3327 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11455 Z= 0.096 Angle : 0.532 8.943 15610 Z= 0.274 Chirality : 0.044 0.149 1807 Planarity : 0.003 0.045 2043 Dihedral : 4.424 23.836 1672 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.66 % Favored : 93.21 % Rotamer: Outliers : 1.98 % Allowed : 17.97 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.93 (0.21), residues: 1531 helix: 0.68 (0.40), residues: 189 sheet: -1.14 (0.22), residues: 550 loop : -1.87 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 373 TYR 0.012 0.001 TYR B 59 PHE 0.011 0.001 PHE A1030 TRP 0.013 0.001 TRP B 400 HIS 0.004 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00221 (11448) covalent geometry : angle 0.52264 (15604) hydrogen bonds : bond 0.02679 ( 391) hydrogen bonds : angle 5.05295 ( 1068) metal coordination : bond 0.00518 ( 7) metal coordination : angle 5.00311 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.8180 (t80) cc_final: 0.7771 (t80) REVERT: A 655 ARG cc_start: 0.7293 (mmp-170) cc_final: 0.6766 (ttm-80) REVERT: A 660 TYR cc_start: 0.7318 (p90) cc_final: 0.6860 (p90) REVERT: A 969 GLU cc_start: 0.8017 (pt0) cc_final: 0.7812 (pt0) REVERT: A 1014 MET cc_start: 0.8382 (tmm) cc_final: 0.8140 (tmm) REVERT: B 112 ASN cc_start: 0.6867 (m-40) cc_final: 0.6336 (p0) REVERT: B 384 TYR cc_start: 0.6959 (m-80) cc_final: 0.6659 (m-80) REVERT: B 390 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6749 (mm110) outliers start: 21 outliers final: 14 residues processed: 150 average time/residue: 0.1114 time to fit residues: 23.8401 Evaluate side-chains 142 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain C residue 150 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 40 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 GLN A1106 GLN C 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.173913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.124580 restraints weight = 15037.081| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.85 r_work: 0.3284 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11455 Z= 0.127 Angle : 0.549 10.184 15610 Z= 0.280 Chirality : 0.045 0.151 1807 Planarity : 0.003 0.045 2043 Dihedral : 4.499 26.252 1672 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.53 % Favored : 93.40 % Rotamer: Outliers : 1.51 % Allowed : 18.34 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.93 (0.21), residues: 1531 helix: 0.75 (0.40), residues: 189 sheet: -1.13 (0.21), residues: 570 loop : -1.92 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.014 0.001 TYR A 678 PHE 0.012 0.001 PHE A 829 TRP 0.032 0.002 TRP A1073 HIS 0.005 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00301 (11448) covalent geometry : angle 0.53777 (15604) hydrogen bonds : bond 0.02917 ( 391) hydrogen bonds : angle 5.06872 ( 1068) metal coordination : bond 0.00573 ( 7) metal coordination : angle 5.70241 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.8157 (t80) cc_final: 0.7741 (t80) REVERT: A 655 ARG cc_start: 0.7343 (mmp-170) cc_final: 0.6697 (ttm-80) REVERT: A 660 TYR cc_start: 0.7350 (p90) cc_final: 0.6899 (p90) REVERT: A 1014 MET cc_start: 0.8388 (tmm) cc_final: 0.8125 (tmm) REVERT: B 112 ASN cc_start: 0.6934 (m-40) cc_final: 0.6397 (p0) REVERT: B 384 TYR cc_start: 0.6817 (m-80) cc_final: 0.6441 (m-80) REVERT: B 390 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6608 (mm110) outliers start: 16 outliers final: 15 residues processed: 131 average time/residue: 0.1101 time to fit residues: 20.7803 Evaluate side-chains 137 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 150 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 115 optimal weight: 40.0000 chunk 112 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 109 optimal weight: 0.0070 chunk 77 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 55 optimal weight: 30.0000 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.175447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.122629 restraints weight = 15014.137| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.29 r_work: 0.3324 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11455 Z= 0.100 Angle : 0.530 9.816 15610 Z= 0.270 Chirality : 0.044 0.152 1807 Planarity : 0.003 0.045 2043 Dihedral : 4.300 22.023 1672 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.66 % Rotamer: Outliers : 1.51 % Allowed : 18.34 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.21), residues: 1531 helix: 0.77 (0.40), residues: 192 sheet: -1.04 (0.21), residues: 582 loop : -1.87 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.013 0.001 TYR A 678 PHE 0.012 0.001 PHE A1030 TRP 0.022 0.001 TRP A1073 HIS 0.005 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00234 (11448) covalent geometry : angle 0.51863 (15604) hydrogen bonds : bond 0.02687 ( 391) hydrogen bonds : angle 4.95277 ( 1068) metal coordination : bond 0.00558 ( 7) metal coordination : angle 5.50982 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3694.05 seconds wall clock time: 63 minutes 42.45 seconds (3822.45 seconds total)