Starting phenix.real_space_refine on Sat Feb 7 22:57:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sok_40660/02_2026/8sok_40660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sok_40660/02_2026/8sok_40660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sok_40660/02_2026/8sok_40660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sok_40660/02_2026/8sok_40660.map" model { file = "/net/cci-nas-00/data/ceres_data/8sok_40660/02_2026/8sok_40660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sok_40660/02_2026/8sok_40660.cif" } resolution = 4.1 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= 0.002 sd= 0.033 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 922 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 9 5.49 5 S 103 5.16 5 C 11795 2.51 5 N 3210 2.21 5 O 3455 1.98 5 H 18588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s 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: 37162 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 18208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1158, 18208 Classifications: {'peptide': 1158} Link IDs: {'PCIS': 6, 'PTRANS': 88, 'TRANS': 1063} Chain breaks: 2 Chain: "B" Number of atoms: 5825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 5825 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 13, 'TRANS': 347} Chain: "C" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1897 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "D" Number of atoms: 9937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 9937 Classifications: {'peptide': 630} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 602} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 972 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "F" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 321 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" 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 15624 SG CYS A1043 78.333 92.219 70.385 1.00100.31 S ATOM 15666 SG CYS A1046 75.634 94.882 69.285 1.00 99.09 S ATOM 15802 SG CYS A1055 78.501 95.084 67.535 1.00101.81 S ATOM 15902 SG CYS A1062 79.128 95.208 71.402 1.00 99.71 S ATOM 31926 SG CYS D 382 66.292 102.038 150.553 1.00111.08 S ATOM 31973 SG CYS D 385 66.188 105.294 148.770 1.00111.92 S ATOM 33829 SG CYS D 503 69.540 103.437 150.222 1.00110.86 S ATOM 33879 SG CYS D 506 66.905 105.275 152.391 1.00116.20 S Time building chain proxies: 6.35, per 1000 atoms: 0.17 Number of scatterers: 37162 At special positions: 0 Unit cell: (111.8, 153.94, 190.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 103 16.00 P 9 15.00 O 3455 8.00 N 3210 7.00 C 11795 6.00 H 18588 1.00 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: 3.43 Conformation dependent library (CDL) restraints added in 887.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1055 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1062 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1043 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1046 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 382 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 506 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 385 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 503 " Number of angles added : 12 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4412 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 30 sheets defined 29.2% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 Processing helix chain 'A' and resid 37 through 52 removed outlier: 4.062A pdb=" N LEU A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 88 through 97 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 216 through 219 removed outlier: 3.879A pdb=" N LEU A 219 " --> pdb=" O ARG A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 265 through 274 removed outlier: 4.290A pdb=" N VAL A 270 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 388 through 393 removed outlier: 3.625A pdb=" N ARG A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 388 through 393' Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.926A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 461 removed outlier: 3.641A pdb=" N TYR A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 478 removed outlier: 4.489A pdb=" N TRP A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 507 through 515 removed outlier: 3.673A pdb=" N LEU A 513 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 551 through 567 removed outlier: 4.344A pdb=" N GLU A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 Processing helix chain 'A' and resid 582 through 591 Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 671 through 677 Processing helix chain 'A' and resid 803 through 808 Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 865 through 870 removed outlier: 4.492A pdb=" N ASP A 870 " --> pdb=" O GLN A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 removed outlier: 3.894A pdb=" N ALA A 874 " --> pdb=" O VAL A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 913 removed outlier: 3.680A pdb=" N VAL A 912 " --> pdb=" O CYS A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 951 through 955 Processing helix chain 'A' and resid 1011 through 1017 Processing helix chain 'A' and resid 1092 through 1097 Processing helix chain 'A' and resid 1100 through 1112 Processing helix chain 'A' and resid 1136 through 1148 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 30 through 37 removed outlier: 4.098A pdb=" N LEU B 35 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 125 Processing helix chain 'B' and resid 160 through 177 Proline residue: B 171 - end of helix Processing helix chain 'B' and resid 200 through 220 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 241 through 248 removed outlier: 3.730A pdb=" N HIS B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 removed outlier: 5.508A pdb=" N ASN B 253 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 277 Processing helix chain 'B' and resid 297 through 310 removed outlier: 3.980A pdb=" N ILE B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 Processing helix chain 'B' and resid 340 through 355 removed outlier: 3.538A pdb=" N GLU B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 17 removed outlier: 3.955A pdb=" N VAL C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'D' and resid 13 through 17 Processing helix chain 'D' and resid 126 through 143 Processing helix chain 'D' and resid 152 through 156 Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 210 through 215 removed outlier: 6.006A pdb=" N ASN D 215 " --> pdb=" O ARG D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 4.093A pdb=" N HIS D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.565A pdb=" N ARG D 273 " --> pdb=" O SER D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 297 removed outlier: 3.841A pdb=" N SER D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 322 removed outlier: 3.885A pdb=" N GLU D 320A" --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 320D" --> pdb=" O SER D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 353 Processing helix chain 'D' and resid 373 through 376 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 410 through 414 Processing helix chain 'D' and resid 447 through 450 Processing helix chain 'D' and resid 459 through 468 Processing helix chain 'D' and resid 511 through 518 Processing helix chain 'D' and resid 525 through 533 Processing helix chain 'D' and resid 576 through 591 Processing helix chain 'D' and resid 596 through 600 Processing helix chain 'E' and resid 176 through 193 Processing helix chain 'E' and resid 205 through 215 Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.570A pdb=" N LEU E 240 " --> pdb=" O ILE E 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 68 removed outlier: 6.329A pdb=" N SER A 66 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 114 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL A 68 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N THR A 116 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N LEU A 179 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N SER A 143 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N LEU A 181 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLU A 145 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 68 removed outlier: 6.329A pdb=" N SER A 66 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 114 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL A 68 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N THR A 116 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU A 113 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 204 removed outlier: 5.855A pdb=" N ILE A 201 " --> pdb=" O GLN A 316 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 318 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 203 " --> pdb=" O LEU A 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 237 through 238 removed outlier: 8.675A pdb=" N TRP A 299 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER A 260 " --> pdb=" O TRP A 299 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR A 301 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE A 262 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 238 removed outlier: 6.519A pdb=" N ILE A 246 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 233 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER A 248 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 352 Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 361 removed outlier: 6.214A pdb=" N LEU A 356 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N CYS A 400 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 373 through 375 removed outlier: 6.629A pdb=" N GLY A 380 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 593 through 596 removed outlier: 3.970A pdb=" N LEU A 595 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 593 through 596 removed outlier: 3.970A pdb=" N LEU A 595 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 687 " --> pdb=" O GLU A 662 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 628 through 631 removed outlier: 4.047A pdb=" N VAL A 611 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 742 through 744 Processing sheet with id=AB4, first strand: chain 'A' and resid 742 through 744 removed outlier: 7.316A pdb=" N TYR A 764 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS A 738 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 766 " --> pdb=" O CYS A 736 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 732 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLY A 772 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER A 730 " --> pdb=" O GLY A 772 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLN A 774 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY A 728 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 899 through 901 removed outlier: 6.300A pdb=" N ARG A 966 " --> pdb=" O LEU A 995 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 905 through 907 Processing sheet with id=AB7, first strand: chain 'A' and resid 1024 through 1027 removed outlier: 5.574A pdb=" N GLU A1160 " --> pdb=" O CYS A1198 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N CYS A1198 " --> pdb=" O GLU A1160 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG A1089 " --> pdb=" O CYS A1198 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N SER A1200 " --> pdb=" O ARG A1089 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A1036 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A1076 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A1034 " --> pdb=" O LEU A1076 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLU A1078 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A1032 " --> pdb=" O GLU A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1175 through 1178 Processing sheet with id=AB9, first strand: chain 'B' and resid 38 through 39 removed outlier: 3.548A pdb=" N LYS B 38 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 56 through 68 removed outlier: 6.436A pdb=" N GLY B 76 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 66 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER B 74 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU B 68 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N PHE B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N ARG B 145 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN B 85 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TRP B 89 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR B 151 " --> pdb=" O TRP B 89 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG B 135 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR B 152 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG B 133 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS B 154 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N THR B 131 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 59 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 223 through 225 Processing sheet with id=AC3, first strand: chain 'B' and resid 322 through 323 Processing sheet with id=AC4, first strand: chain 'C' and resid 24 through 36 removed outlier: 11.593A pdb=" N GLY C 30 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 10.317A pdb=" N GLN C 47 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU C 32 " --> pdb=" O MET C 45 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N MET C 45 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 13.852A pdb=" N SER C 87 " --> pdb=" O GLN C 52 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N GLN C 54 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N VAL C 89 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU C 56 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA C 91 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N CYS C 58 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL C 93 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU C 76 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU C 94 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 74 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N CYS C 96 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU C 72 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER C 24 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 36 through 37 removed outlier: 6.506A pdb=" N VAL D 50 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL D 29 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL D 25 " --> pdb=" O HIS D 82 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N HIS D 82 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLY D 27 " --> pdb=" O ARG D 80 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARG D 80 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D 29 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE D 78 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 36 through 37 removed outlier: 8.131A pdb=" N THR D 93 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR D 58 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 204 through 205 removed outlier: 6.240A pdb=" N LEU D 168 " --> pdb=" O TRP D 184 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TRP D 184 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 10.761A pdb=" N THR D 217 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N PHE D 263 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP D 219 " --> pdb=" O PHE D 263 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N LEU D 265 " --> pdb=" O ASP D 219 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU D 221 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N MET D 258 " --> pdb=" O MET D 251 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE D 238 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 204 through 205 removed outlier: 6.472A pdb=" N LEU D 164 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR D 242 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N CYS D 166 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ARG D 240 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU D 168 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE D 238 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE D 238 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 335 through 337 Processing sheet with id=AD1, first strand: chain 'D' and resid 387 through 389 removed outlier: 3.504A pdb=" N ALA D 557 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 10.479A pdb=" N TYR D 622 " --> pdb=" O VAL D 554 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU D 556 " --> pdb=" O TYR D 622 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ILE D 624 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TYR D 558 " --> pdb=" O ILE D 624 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE D 606 " --> pdb=" O PHE D 625 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 419 through 426 removed outlier: 3.656A pdb=" N ARG D 432 " --> pdb=" O THR D 426 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU D 452 " --> pdb=" O VAL D 439 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 493 through 495 removed outlier: 3.848A pdb=" N LEU D 493 " --> pdb=" O HIS D 500 " (cutoff:3.500A) 727 hydrogen bonds defined for protein. 1842 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: 10.26 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 18509 1.03 - 1.23: 407 1.23 - 1.43: 7519 1.43 - 1.63: 11036 1.63 - 1.82: 135 Bond restraints: 37606 Sorted by residual: bond pdb=" N LYS B 320 " pdb=" H LYS B 320 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CG LYS B 320 " pdb=" HG3 LYS B 320 " ideal model delta sigma weight residual 0.970 1.091 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" NZ LYS B 320 " pdb=" HZ1 LYS B 320 " ideal model delta sigma weight residual 0.890 1.010 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" NZ LYS B 320 " pdb=" HZ2 LYS B 320 " ideal model delta sigma weight residual 0.890 1.010 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" CB LYS B 320 " pdb=" HB3 LYS B 320 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 37601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.29: 68150 8.29 - 16.59: 1 16.59 - 24.88: 2 24.88 - 33.18: 4 33.18 - 41.47: 6 Bond angle restraints: 68163 Sorted by residual: angle pdb=" C PRO D 592 " pdb=" CA PRO D 592 " pdb=" HA PRO D 592 " ideal model delta sigma weight residual 109.00 67.53 41.47 3.00e+00 1.11e-01 1.91e+02 angle pdb=" CB PRO D 592 " pdb=" CA PRO D 592 " pdb=" HA PRO D 592 " ideal model delta sigma weight residual 109.00 73.62 35.38 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N PRO D 592 " pdb=" CA PRO D 592 " pdb=" HA PRO D 592 " ideal model delta sigma weight residual 110.00 74.82 35.18 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB GLU E 180 " pdb=" CA GLU E 180 " pdb=" HA GLU E 180 " ideal model delta sigma weight residual 109.00 73.89 35.11 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C GLU E 180 " pdb=" CA GLU E 180 " pdb=" HA GLU E 180 " ideal model delta sigma weight residual 109.00 74.33 34.67 3.00e+00 1.11e-01 1.34e+02 ... (remaining 68158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 17116 32.09 - 64.19: 559 64.19 - 96.28: 44 96.28 - 128.37: 0 128.37 - 160.46: 2 Dihedral angle restraints: 17721 sinusoidal: 9809 harmonic: 7912 Sorted by residual: dihedral pdb=" CA PHE A 158 " pdb=" C PHE A 158 " pdb=" N LEU A 159 " pdb=" CA LEU A 159 " ideal model delta harmonic sigma weight residual 180.00 151.64 28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA GLN A 387 " pdb=" C GLN A 387 " pdb=" N PHE A 388 " pdb=" CA PHE A 388 " ideal model delta harmonic sigma weight residual 180.00 152.57 27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA SER A1158 " pdb=" C SER A1158 " pdb=" N PHE A1159 " pdb=" CA PHE A1159 " ideal model delta harmonic sigma weight residual 180.00 -154.30 -25.70 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 17718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.853: 2951 0.853 - 1.707: 0 1.707 - 2.560: 0 2.560 - 3.414: 0 3.414 - 4.267: 1 Chirality restraints: 2952 Sorted by residual: chirality pdb=" C3' DA F 3 " pdb=" C4' DA F 3 " pdb=" O3' DA F 3 " pdb=" C2' DA F 3 " both_signs ideal model delta sigma weight residual False -2.66 1.61 -4.27 2.00e-01 2.50e+01 4.55e+02 chirality pdb=" CA GLU E 180 " pdb=" N GLU E 180 " pdb=" C GLU E 180 " pdb=" CB GLU E 180 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA PRO D 592 " pdb=" N PRO D 592 " pdb=" C PRO D 592 " pdb=" CB PRO D 592 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2949 not shown) Planarity restraints: 5476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 325 " 0.021 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" N VAL D 326 " -0.065 2.00e-02 2.50e+03 pdb=" CA VAL D 326 " 0.016 2.00e-02 2.50e+03 pdb=" H VAL D 326 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 325 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C GLU D 325 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU D 325 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL D 326 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 818 " -0.254 9.50e-02 1.11e+02 8.47e-02 7.76e+00 pdb=" NE ARG A 818 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 818 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 818 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 818 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 818 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 818 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 818 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 818 " -0.002 2.00e-02 2.50e+03 ... (remaining 5473 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1538 2.16 - 2.77: 73303 2.77 - 3.38: 103293 3.38 - 3.99: 130634 3.99 - 4.60: 202877 Nonbonded interactions: 511645 Sorted by model distance: nonbonded pdb=" HG SER A 730 " pdb=" O LEU A 819 " model vdw 1.550 2.450 nonbonded pdb=" O CYS A 424 " pdb=" H GLY A 427 " model vdw 1.556 2.450 nonbonded pdb=" OE1 GLU D 67 " pdb=" H GLU D 67 " model vdw 1.558 2.450 nonbonded pdb=" HG SER A1158 " pdb=" OG SER A1200 " model vdw 1.559 2.450 nonbonded pdb=" OD1 ASP D 163 " pdb=" H SER D 243 " model vdw 1.563 2.450 ... (remaining 511640 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 group one per residue 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.230 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 44.020 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 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 0.126 19026 Z= 0.237 Angle : 0.798 20.285 25906 Z= 0.426 Chirality : 0.090 4.267 2952 Planarity : 0.007 0.111 3287 Dihedral : 13.707 160.463 7092 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.79 % Favored : 89.65 % Rotamer: Outliers : 1.02 % Allowed : 4.89 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -3.40 (0.15), residues: 2319 helix: -2.16 (0.19), residues: 513 sheet: -2.51 (0.20), residues: 521 loop : -2.18 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 624 TYR 0.027 0.002 TYR B 30 PHE 0.020 0.002 PHE A 567 TRP 0.018 0.002 TRP A 781 HIS 0.012 0.001 HIS A 812 Details of bonding type rmsd covalent geometry : bond 0.00499 (19018) covalent geometry : angle 0.76240 (25894) hydrogen bonds : bond 0.18951 ( 703) hydrogen bonds : angle 8.73218 ( 1842) metal coordination : bond 0.01045 ( 8) metal coordination : angle 10.98401 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 229 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 PHE cc_start: 0.6668 (p90) cc_final: 0.6024 (p90) REVERT: A 272 HIS cc_start: 0.8462 (t70) cc_final: 0.8092 (t70) REVERT: A 448 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7264 (m-80) REVERT: B 240 ASN cc_start: 0.7707 (p0) cc_final: 0.7492 (p0) REVERT: B 320 LYS cc_start: 0.4468 (OUTLIER) cc_final: 0.4182 (tppt) REVERT: B 323 HIS cc_start: 0.7415 (t-90) cc_final: 0.6815 (t-90) REVERT: D 26 TYR cc_start: -0.0946 (OUTLIER) cc_final: -0.1730 (t80) outliers start: 21 outliers final: 7 residues processed: 249 average time/residue: 0.3642 time to fit residues: 134.9525 Evaluate side-chains 179 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 GLN ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 GLN ** 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 = 0.4519 r_free = 0.4519 target = 0.140845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.117326 restraints weight = 178867.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.120320 restraints weight = 251263.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.122256 restraints weight = 119493.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.122408 restraints weight = 93277.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.123277 restraints weight = 75314.639| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 19026 Z= 0.163 Angle : 0.694 21.660 25906 Z= 0.351 Chirality : 0.092 4.425 2952 Planarity : 0.005 0.054 3287 Dihedral : 9.921 160.243 2623 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.51 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.56 (0.16), residues: 2319 helix: -0.98 (0.21), residues: 522 sheet: -2.09 (0.20), residues: 519 loop : -1.82 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 251 TYR 0.025 0.002 TYR D 26 PHE 0.012 0.001 PHE A 680 TRP 0.013 0.001 TRP A 781 HIS 0.007 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00368 (19018) covalent geometry : angle 0.65549 (25894) hydrogen bonds : bond 0.05014 ( 703) hydrogen bonds : angle 6.75589 ( 1842) metal coordination : bond 0.00793 ( 8) metal coordination : angle 10.68151 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 240 ASN cc_start: 0.7637 (p0) cc_final: 0.7373 (p0) REVERT: B 318 MET cc_start: 0.6649 (mmp) cc_final: 0.6325 (mmp) REVERT: B 323 HIS cc_start: 0.6777 (t-90) cc_final: 0.6210 (t-90) REVERT: C 14 GLU cc_start: 0.6321 (mp0) cc_final: 0.5848 (mp0) REVERT: D 144 MET cc_start: 0.4534 (ttp) cc_final: 0.4106 (ttt) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.3312 time to fit residues: 107.0449 Evaluate side-chains 174 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 108 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 chunk 224 optimal weight: 9.9990 chunk 169 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 225 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 HIS ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** 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 = 0.4481 r_free = 0.4481 target = 0.137909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.117392 restraints weight = 178693.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.112899 restraints weight = 201441.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.110568 restraints weight = 158962.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.111757 restraints weight = 129518.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.111754 restraints weight = 92109.697| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.137 19026 Z= 0.276 Angle : 0.756 27.870 25906 Z= 0.379 Chirality : 0.092 4.429 2952 Planarity : 0.006 0.056 3287 Dihedral : 9.833 161.155 2623 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.48 % Favored : 89.44 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.57 (0.17), residues: 2319 helix: -0.75 (0.22), residues: 527 sheet: -2.16 (0.20), residues: 544 loop : -1.89 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 510 TYR 0.031 0.002 TYR A 467 PHE 0.017 0.002 PHE B 23 TRP 0.024 0.002 TRP A 594 HIS 0.007 0.001 HIS A 812 Details of bonding type rmsd covalent geometry : bond 0.00619 (19018) covalent geometry : angle 0.71604 (25894) hydrogen bonds : bond 0.05080 ( 703) hydrogen bonds : angle 6.61682 ( 1842) metal coordination : bond 0.01159 ( 8) metal coordination : angle 11.32981 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 240 ASN cc_start: 0.7656 (p0) cc_final: 0.7438 (p0) REVERT: B 318 MET cc_start: 0.6664 (mmp) cc_final: 0.6331 (mmp) REVERT: B 323 HIS cc_start: 0.6791 (t-90) cc_final: 0.6229 (t70) REVERT: C 14 GLU cc_start: 0.6608 (mp0) cc_final: 0.6117 (mp0) REVERT: D 144 MET cc_start: 0.4763 (ttp) cc_final: 0.4321 (ttt) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.3511 time to fit residues: 105.4485 Evaluate side-chains 167 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 29 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 45 optimal weight: 0.0870 chunk 56 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1017 GLN ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** 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 = 0.4528 r_free = 0.4528 target = 0.141153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.116692 restraints weight = 177649.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.118861 restraints weight = 244687.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.122000 restraints weight = 128875.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.121647 restraints weight = 95652.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.122974 restraints weight = 77087.911| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 19026 Z= 0.123 Angle : 0.622 23.479 25906 Z= 0.310 Chirality : 0.092 4.438 2952 Planarity : 0.005 0.127 3287 Dihedral : 9.442 159.499 2623 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.91 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.16 (0.17), residues: 2319 helix: -0.33 (0.22), residues: 527 sheet: -1.97 (0.21), residues: 547 loop : -1.64 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 510 TYR 0.017 0.001 TYR B 174 PHE 0.031 0.001 PHE A 986 TRP 0.014 0.001 TRP A 592 HIS 0.005 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00282 (19018) covalent geometry : angle 0.58607 (25894) hydrogen bonds : bond 0.03974 ( 703) hydrogen bonds : angle 6.04780 ( 1842) metal coordination : bond 0.00607 ( 8) metal coordination : angle 9.67147 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.7752 (p-90) cc_final: 0.7395 (p-90) REVERT: A 395 MET cc_start: 0.8196 (mmm) cc_final: 0.7657 (tpp) REVERT: B 240 ASN cc_start: 0.7595 (p0) cc_final: 0.7282 (p0) REVERT: B 318 MET cc_start: 0.6778 (mmp) cc_final: 0.6453 (mmp) REVERT: B 323 HIS cc_start: 0.6540 (t-90) cc_final: 0.6000 (t-90) REVERT: C 14 GLU cc_start: 0.6297 (mp0) cc_final: 0.5991 (mp0) REVERT: D 144 MET cc_start: 0.4648 (ttp) cc_final: 0.4077 (ttt) REVERT: D 251 MET cc_start: 0.6938 (mmm) cc_final: 0.6612 (mmm) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.3567 time to fit residues: 106.6025 Evaluate side-chains 169 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 215 optimal weight: 20.0000 chunk 216 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 225 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** 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 = 0.4519 r_free = 0.4519 target = 0.140621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.116761 restraints weight = 177580.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.120842 restraints weight = 248033.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.122550 restraints weight = 105275.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.123115 restraints weight = 76099.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.124001 restraints weight = 64278.691| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 19026 Z= 0.135 Angle : 0.596 20.725 25906 Z= 0.298 Chirality : 0.091 4.438 2952 Planarity : 0.005 0.084 3287 Dihedral : 9.290 159.204 2623 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.55 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.01 (0.17), residues: 2319 helix: -0.10 (0.23), residues: 529 sheet: -1.94 (0.21), residues: 558 loop : -1.56 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 731 TYR 0.014 0.001 TYR D 26 PHE 0.012 0.001 PHE B 267 TRP 0.015 0.001 TRP A 769 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00312 (19018) covalent geometry : angle 0.56568 (25894) hydrogen bonds : bond 0.03805 ( 703) hydrogen bonds : angle 5.88954 ( 1842) metal coordination : bond 0.00542 ( 8) metal coordination : angle 8.67870 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 MET cc_start: 0.8200 (mmm) cc_final: 0.7644 (tpp) REVERT: A 564 TRP cc_start: 0.6985 (m100) cc_final: 0.6502 (m100) REVERT: A 764 TYR cc_start: 0.6483 (p90) cc_final: 0.6066 (p90) REVERT: B 240 ASN cc_start: 0.7582 (p0) cc_final: 0.7276 (p0) REVERT: B 318 MET cc_start: 0.6758 (mmp) cc_final: 0.6452 (mmp) REVERT: B 323 HIS cc_start: 0.6485 (t-90) cc_final: 0.5958 (t-90) REVERT: C 14 GLU cc_start: 0.6121 (mp0) cc_final: 0.5820 (mp0) REVERT: D 144 MET cc_start: 0.4565 (ttp) cc_final: 0.3994 (ttt) REVERT: D 251 MET cc_start: 0.6942 (mmm) cc_final: 0.6705 (mmm) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.3561 time to fit residues: 99.4547 Evaluate side-chains 161 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 132 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 172 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** 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 = 0.4525 r_free = 0.4525 target = 0.140970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.117232 restraints weight = 177528.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.120617 restraints weight = 248675.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.122186 restraints weight = 116620.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.122474 restraints weight = 91158.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.123300 restraints weight = 75850.171| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 19026 Z= 0.127 Angle : 0.579 18.892 25906 Z= 0.290 Chirality : 0.091 4.441 2952 Planarity : 0.004 0.046 3287 Dihedral : 9.141 158.959 2623 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.17), residues: 2319 helix: 0.16 (0.23), residues: 529 sheet: -1.73 (0.22), residues: 529 loop : -1.50 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 372 TYR 0.013 0.001 TYR D 26 PHE 0.010 0.001 PHE A 158 TRP 0.019 0.001 TRP A 594 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00297 (19018) covalent geometry : angle 0.55255 (25894) hydrogen bonds : bond 0.03626 ( 703) hydrogen bonds : angle 5.69758 ( 1842) metal coordination : bond 0.00425 ( 8) metal coordination : angle 8.00163 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 LEU cc_start: 0.8317 (pt) cc_final: 0.8035 (pt) REVERT: A 395 MET cc_start: 0.8168 (mmm) cc_final: 0.7643 (tpp) REVERT: A 564 TRP cc_start: 0.6962 (m100) cc_final: 0.6462 (m100) REVERT: A 973 GLU cc_start: 0.7845 (tt0) cc_final: 0.7555 (tt0) REVERT: B 240 ASN cc_start: 0.7534 (p0) cc_final: 0.7198 (p0) REVERT: B 318 MET cc_start: 0.6782 (mmp) cc_final: 0.6504 (mmp) REVERT: B 323 HIS cc_start: 0.6558 (t-90) cc_final: 0.6024 (t-90) REVERT: C 14 GLU cc_start: 0.6041 (mp0) cc_final: 0.5773 (mp0) REVERT: D 144 MET cc_start: 0.4414 (ttp) cc_final: 0.3850 (ttt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.3429 time to fit residues: 99.0628 Evaluate side-chains 163 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 0.9990 chunk 95 optimal weight: 0.0670 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 15 optimal weight: 7.9990 chunk 51 optimal weight: 0.3980 chunk 197 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** 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 = 0.4574 r_free = 0.4574 target = 0.144980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.135261 restraints weight = 194199.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.135812 restraints weight = 283309.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.135792 restraints weight = 127468.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.136170 restraints weight = 98373.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.136248 restraints weight = 79993.520| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.139 19026 Z= 0.102 Angle : 0.558 20.222 25906 Z= 0.275 Chirality : 0.091 4.441 2952 Planarity : 0.004 0.043 3287 Dihedral : 8.949 158.219 2623 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.59 (0.17), residues: 2319 helix: 0.37 (0.23), residues: 530 sheet: -1.62 (0.21), residues: 548 loop : -1.38 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 731 TYR 0.011 0.001 TYR D 11 PHE 0.026 0.001 PHE A 800 TRP 0.013 0.001 TRP A 87 HIS 0.005 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00240 (19018) covalent geometry : angle 0.52567 (25894) hydrogen bonds : bond 0.03347 ( 703) hydrogen bonds : angle 5.44895 ( 1842) metal coordination : bond 0.00322 ( 8) metal coordination : angle 8.71305 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7354 (mt) cc_final: 0.7085 (mt) REVERT: A 395 MET cc_start: 0.8405 (mmm) cc_final: 0.7829 (tpp) REVERT: A 564 TRP cc_start: 0.7046 (m100) cc_final: 0.6602 (m100) REVERT: A 973 GLU cc_start: 0.7781 (tt0) cc_final: 0.7463 (tt0) REVERT: B 240 ASN cc_start: 0.7418 (p0) cc_final: 0.7104 (p0) REVERT: B 318 MET cc_start: 0.6613 (mmp) cc_final: 0.6308 (mmp) REVERT: B 323 HIS cc_start: 0.6438 (t-90) cc_final: 0.5902 (t-90) REVERT: C 14 GLU cc_start: 0.5914 (mp0) cc_final: 0.5680 (mp0) REVERT: D 144 MET cc_start: 0.4045 (ttp) cc_final: 0.3754 (ttt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3507 time to fit residues: 103.5493 Evaluate side-chains 167 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 96 optimal weight: 0.0570 chunk 185 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 196 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 201 optimal weight: 20.0000 overall best weight: 2.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.143672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.133456 restraints weight = 193889.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.131945 restraints weight = 178850.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.129516 restraints weight = 172917.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.129589 restraints weight = 161399.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.129219 restraints weight = 118799.618| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 19026 Z= 0.147 Angle : 0.581 19.253 25906 Z= 0.289 Chirality : 0.091 4.441 2952 Planarity : 0.004 0.042 3287 Dihedral : 8.974 158.777 2623 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.33 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.59 (0.17), residues: 2319 helix: 0.42 (0.23), residues: 530 sheet: -1.63 (0.21), residues: 557 loop : -1.40 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 119 TYR 0.017 0.001 TYR D 26 PHE 0.015 0.001 PHE A 986 TRP 0.029 0.001 TRP A 594 HIS 0.005 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00340 (19018) covalent geometry : angle 0.55253 (25894) hydrogen bonds : bond 0.03554 ( 703) hydrogen bonds : angle 5.50331 ( 1842) metal coordination : bond 0.00412 ( 8) metal coordination : angle 8.37627 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 MET cc_start: 0.8408 (mmm) cc_final: 0.7804 (tpp) REVERT: A 564 TRP cc_start: 0.7139 (m100) cc_final: 0.6641 (m100) REVERT: A 973 GLU cc_start: 0.7786 (tt0) cc_final: 0.7487 (tt0) REVERT: B 240 ASN cc_start: 0.7510 (p0) cc_final: 0.7175 (p0) REVERT: B 318 MET cc_start: 0.6680 (mmp) cc_final: 0.6382 (mmp) REVERT: C 14 GLU cc_start: 0.5948 (mp0) cc_final: 0.5685 (mp0) REVERT: D 251 MET cc_start: 0.7134 (mmm) cc_final: 0.6882 (mmm) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.3439 time to fit residues: 99.9961 Evaluate side-chains 168 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 56 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 chunk 187 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 GLN ** A1189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** 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 = 0.4541 r_free = 0.4541 target = 0.142778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.132244 restraints weight = 194294.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.131100 restraints weight = 182857.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.128677 restraints weight = 152959.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.128958 restraints weight = 158953.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.128600 restraints weight = 116808.950| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 19026 Z= 0.182 Angle : 0.609 19.828 25906 Z= 0.304 Chirality : 0.091 4.442 2952 Planarity : 0.005 0.081 3287 Dihedral : 9.072 159.548 2623 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.37 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.63 (0.17), residues: 2319 helix: 0.37 (0.23), residues: 529 sheet: -1.64 (0.21), residues: 546 loop : -1.44 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 251 TYR 0.021 0.001 TYR A 467 PHE 0.015 0.001 PHE A 986 TRP 0.049 0.001 TRP A 594 HIS 0.005 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00421 (19018) covalent geometry : angle 0.57992 (25894) hydrogen bonds : bond 0.03658 ( 703) hydrogen bonds : angle 5.57220 ( 1842) metal coordination : bond 0.00521 ( 8) metal coordination : angle 8.65644 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 HIS cc_start: 0.8354 (t70) cc_final: 0.8121 (t70) REVERT: A 395 MET cc_start: 0.8538 (mmm) cc_final: 0.7957 (tpp) REVERT: A 564 TRP cc_start: 0.7257 (m100) cc_final: 0.6686 (m100) REVERT: A 973 GLU cc_start: 0.7859 (tt0) cc_final: 0.7516 (tt0) REVERT: B 240 ASN cc_start: 0.7474 (p0) cc_final: 0.7134 (p0) REVERT: B 318 MET cc_start: 0.6774 (mmp) cc_final: 0.6469 (mmp) REVERT: C 14 GLU cc_start: 0.6089 (mp0) cc_final: 0.5831 (mp0) REVERT: D 251 MET cc_start: 0.7109 (mmm) cc_final: 0.6905 (mmm) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.3567 time to fit residues: 103.2060 Evaluate side-chains 163 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 109 optimal weight: 4.9990 chunk 225 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 151 optimal weight: 0.0370 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 0.1980 chunk 183 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 230 optimal weight: 20.0000 overall best weight: 2.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 GLN ** A1189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 HIS ** 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 = 0.4540 r_free = 0.4540 target = 0.142640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.131936 restraints weight = 193605.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.130509 restraints weight = 184706.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.128274 restraints weight = 153949.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.128560 restraints weight = 160085.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.128192 restraints weight = 120346.722| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 19026 Z= 0.171 Angle : 0.600 19.767 25906 Z= 0.299 Chirality : 0.091 4.442 2952 Planarity : 0.005 0.080 3287 Dihedral : 9.080 159.746 2623 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.37 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.18), residues: 2319 helix: 0.46 (0.23), residues: 523 sheet: -1.74 (0.21), residues: 547 loop : -1.40 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1089 TYR 0.019 0.001 TYR A 467 PHE 0.013 0.001 PHE A 986 TRP 0.055 0.001 TRP A 594 HIS 0.005 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00396 (19018) covalent geometry : angle 0.57037 (25894) hydrogen bonds : bond 0.03590 ( 703) hydrogen bonds : angle 5.54980 ( 1842) metal coordination : bond 0.00514 ( 8) metal coordination : angle 8.71886 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 TRP cc_start: 0.7270 (m100) cc_final: 0.6665 (m100) REVERT: A 973 GLU cc_start: 0.7870 (tt0) cc_final: 0.7536 (tt0) REVERT: B 240 ASN cc_start: 0.7449 (p0) cc_final: 0.7095 (p0) REVERT: B 318 MET cc_start: 0.6741 (mmp) cc_final: 0.6426 (mmp) REVERT: C 14 GLU cc_start: 0.5977 (mp0) cc_final: 0.5725 (mp0) REVERT: D 560 MET cc_start: 0.3686 (ppp) cc_final: 0.3018 (ppp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.3447 time to fit residues: 96.6471 Evaluate side-chains 163 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 213 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1017 GLN A1020 GLN ** A1189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 HIS ** 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 = 0.4566 r_free = 0.4566 target = 0.144414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.132293 restraints weight = 193700.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.131608 restraints weight = 188818.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.130069 restraints weight = 144659.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.130386 restraints weight = 133399.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.129890 restraints weight = 100569.727| |-----------------------------------------------------------------------------| r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.140 19026 Z= 0.104 Angle : 0.554 17.615 25906 Z= 0.275 Chirality : 0.091 4.442 2952 Planarity : 0.004 0.080 3287 Dihedral : 8.883 158.760 2623 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.21 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.18), residues: 2319 helix: 0.63 (0.23), residues: 525 sheet: -1.55 (0.22), residues: 529 loop : -1.27 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1153 TYR 0.012 0.001 TYR A 205 PHE 0.014 0.001 PHE D 191 TRP 0.026 0.001 TRP A 594 HIS 0.004 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00246 (19018) covalent geometry : angle 0.52724 (25894) hydrogen bonds : bond 0.03212 ( 703) hydrogen bonds : angle 5.28345 ( 1842) metal coordination : bond 0.00293 ( 8) metal coordination : angle 7.90266 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5398.28 seconds wall clock time: 93 minutes 22.34 seconds (5602.34 seconds total)