Starting phenix.real_space_refine on Mon Jul 6 18:15:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sok_40660/07_2026/8sok_40660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sok_40660/07_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_40660/07_2026/8sok_40660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sok_40660/07_2026/8sok_40660.map" model { file = "/net/cci-nas-00/data/ceres_data/8sok_40660/07_2026/8sok_40660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sok_40660/07_2026/8sok_40660.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8sok_40660/07_2026/8sok_40660.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sok_40660/07_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-dev-6108/lib/python3.11/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: 3.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.10 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: 11.65 Time building geometry restraints manager: 5.32 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=" C3' DA F 3 " pdb=" O3' DA F 3 " ideal model delta sigma weight residual 1.435 1.296 0.139 1.30e-02 5.92e+03 1.15e+02 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 ... (remaining 37601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.29: 68149 8.29 - 16.59: 2 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 - 0.867: 2951 0.867 - 1.735: 0 1.735 - 2.602: 0 2.602 - 3.470: 0 3.470 - 4.337: 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 -2.73 1.61 -4.34 2.00e-01 2.50e+01 4.70e+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=" C3' DT F 2 " pdb=" C4' DT F 2 " pdb=" O3' DT F 2 " pdb=" C2' DT F 2 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.61e+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: 0.010 Normalize map: mean=0, sd=1: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.260 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 50.240 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 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 0.139 19026 Z= 0.262 Angle : 0.804 20.285 25906 Z= 0.439 Chirality : 0.092 4.337 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/Z covalent geometry : bond 0.00503 / 0.26 (19018) covalent geometry : angle 0.76840 / 0.44 (25894) hydrogen bonds : bond 0.18951 / 12.70 ( 703) hydrogen bonds : angle 8.73218 / 6.03 ( 1842) metal coordination : bond 0.01045 / 0.66 ( 8) metal coordination : angle 10.98401 / 6.66 ( 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 : 1.121 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: 0.3578 time to fit residues: 134.6031 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 : 1.091 ------------------------------------------------------------------------------- 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... A 815 GLN ** 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** D 623 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.140890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.118531 restraints weight = 179370.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.121793 restraints weight = 258761.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.123429 restraints weight = 115868.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.123316 restraints weight = 102801.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.124303 restraints weight = 75079.641| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19026 Z= 0.173 Angle : 0.753 21.010 25906 Z= 0.387 Chirality : 0.060 2.199 2952 Planarity : 0.006 0.091 3287 Dihedral : 10.120 163.381 2623 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.47 % Favored : 93.45 % 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: -2.69 (0.16), residues: 2319 helix: -1.14 (0.21), residues: 521 sheet: -2.19 (0.20), residues: 534 loop : -1.85 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 436 TYR 0.026 0.002 TYR D 11 PHE 0.022 0.002 PHE C 29 TRP 0.020 0.002 TRP A 95 HIS 0.010 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (19018) covalent geometry : angle 0.71689 / 0.38 (25894) hydrogen bonds : bond 0.05822 / 3.79 ( 703) hydrogen bonds : angle 7.13852 / 4.94 ( 1842) metal coordination : bond 0.00813 / 0.54 ( 8) metal coordination : angle 10.70361 / 6.74 ( 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 204 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.906 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: B 240 ASN cc_start: 0.7545 (p0) cc_final: 0.7316 (p0) REVERT: B 318 MET cc_start: 0.6593 (mmp) cc_final: 0.6276 (mmp) REVERT: B 323 HIS cc_start: 0.6906 (t-90) cc_final: 0.6308 (t-90) REVERT: C 14 GLU cc_start: 0.6440 (mp0) cc_final: 0.5830 (mp0) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.3364 time to fit residues: 105.7882 Evaluate side-chains 171 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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: 8.9990 chunk 48 optimal weight: 5.9990 chunk 189 optimal weight: 0.5980 chunk 207 optimal weight: 20.0000 chunk 224 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 190 optimal weight: 0.6980 chunk 225 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4490 r_free = 0.4490 target = 0.138807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.120733 restraints weight = 175752.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.116338 restraints weight = 167326.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.114053 restraints weight = 146997.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.114695 restraints weight = 134986.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.114696 restraints weight = 91550.427| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 19026 Z= 0.266 Angle : 0.774 27.503 25906 Z= 0.389 Chirality : 0.060 2.241 2952 Planarity : 0.006 0.140 3287 Dihedral : 10.093 164.967 2623 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.87 % Favored : 90.04 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -2.66 (0.16), residues: 2319 helix: -0.91 (0.21), residues: 524 sheet: -2.19 (0.21), residues: 522 loop : -1.95 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG D 510 TYR 0.025 0.002 TYR A 467 PHE 0.017 0.002 PHE B 23 TRP 0.017 0.002 TRP A 916 HIS 0.007 0.001 HIS A 812 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.27 (19018) covalent geometry : angle 0.73278 / 0.39 (25894) hydrogen bonds : bond 0.05455 / 3.55 ( 703) hydrogen bonds : angle 6.90509 / 4.77 ( 1842) metal coordination : bond 0.01419 / 0.81 ( 8) metal coordination : angle 11.65479 / 7.40 ( 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 195 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.090 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: A 272 HIS cc_start: 0.8365 (t70) cc_final: 0.8104 (t70) REVERT: B 240 ASN cc_start: 0.7598 (p0) cc_final: 0.7371 (p0) REVERT: B 318 MET cc_start: 0.6631 (mmp) cc_final: 0.6382 (mmp) REVERT: B 323 HIS cc_start: 0.6708 (t-90) cc_final: 0.6142 (t-90) REVERT: C 14 GLU cc_start: 0.6458 (mp0) cc_final: 0.5982 (mp0) REVERT: D 144 MET cc_start: 0.4602 (ttp) cc_final: 0.4192 (ttt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3449 time to fit residues: 102.8872 Evaluate side-chains 164 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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: 10.0000 chunk 46 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4527 r_free = 0.4527 target = 0.141353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.119068 restraints weight = 175247.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.123201 restraints weight = 241359.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.124392 restraints weight = 93912.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.124869 restraints weight = 74449.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.125101 restraints weight = 61937.790| |-----------------------------------------------------------------------------| r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19026 Z= 0.124 Angle : 0.676 24.793 25906 Z= 0.335 Chirality : 0.058 2.143 2952 Planarity : 0.006 0.162 3287 Dihedral : 9.831 164.185 2623 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.74 % Favored : 94.18 % 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: -2.33 (0.17), residues: 2319 helix: -0.56 (0.22), residues: 521 sheet: -2.10 (0.20), residues: 541 loop : -1.69 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 510 TYR 0.034 0.001 TYR D 369 PHE 0.033 0.001 PHE A 986 TRP 0.013 0.001 TRP B 160 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (19018) covalent geometry : angle 0.63657 / 0.33 (25894) hydrogen bonds : bond 0.04525 / 2.96 ( 703) hydrogen bonds : angle 6.43408 / 4.44 ( 1842) metal coordination : bond 0.00721 / 0.47 ( 8) metal coordination : angle 10.58973 / 6.80 ( 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 197 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.982 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: 0.7624 (p0) cc_final: 0.7380 (p0) REVERT: B 318 MET cc_start: 0.6619 (mmp) cc_final: 0.6253 (mmp) REVERT: B 323 HIS cc_start: 0.6474 (t-90) cc_final: 0.5872 (t-90) REVERT: C 14 GLU cc_start: 0.6180 (mp0) cc_final: 0.5768 (mp0) REVERT: D 144 MET cc_start: 0.4527 (ttp) cc_final: 0.4119 (ttt) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.3089 time to fit residues: 94.0510 Evaluate side-chains 165 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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: 7.9990 chunk 134 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 0.0570 chunk 225 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4521 r_free = 0.4521 target = 0.140920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.116037 restraints weight = 174360.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.119187 restraints weight = 241835.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.120836 restraints weight = 119255.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.120840 restraints weight = 94307.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.121855 restraints weight = 77770.615| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19026 Z= 0.130 Angle : 0.645 22.458 25906 Z= 0.320 Chirality : 0.057 2.071 2952 Planarity : 0.005 0.133 3287 Dihedral : 9.706 163.755 2623 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: -0.37 (0.22), residues: 519 sheet: -2.00 (0.20), residues: 558 loop : -1.59 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 392 TYR 0.022 0.001 TYR D 369 PHE 0.037 0.001 PHE B 267 TRP 0.011 0.001 TRP A 781 HIS 0.004 0.001 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (19018) covalent geometry : angle 0.61061 / 0.32 (25894) hydrogen bonds : bond 0.04206 / 2.76 ( 703) hydrogen bonds : angle 6.22987 / 4.29 ( 1842) metal coordination : bond 0.00678 / 0.44 ( 8) metal coordination : angle 9.72954 / 6.33 ( 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 195 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.658 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: 0.7755 (p-90) cc_final: 0.7407 (p-90) REVERT: A 233 LEU cc_start: 0.8423 (pt) cc_final: 0.8133 (pt) REVERT: A 395 MET cc_start: 0.8180 (mmm) cc_final: 0.7642 (tpp) REVERT: B 240 ASN cc_start: 0.7698 (p0) cc_final: 0.7410 (p0) REVERT: B 318 MET cc_start: 0.6824 (mmp) cc_final: 0.6624 (mmp) REVERT: B 323 HIS cc_start: 0.6553 (t-90) cc_final: 0.5966 (t-90) REVERT: C 14 GLU cc_start: 0.6300 (mp0) cc_final: 0.5993 (mp0) REVERT: D 144 MET cc_start: 0.4635 (ttp) cc_final: 0.4196 (ttt) REVERT: D 251 MET cc_start: 0.6459 (mmm) cc_final: 0.6114 (mmm) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3088 time to fit residues: 92.3093 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 : 0.974 ------------------------------------------------------------------------------- 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: 5.9990 chunk 149 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 172 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1009 HIS ** 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 = 0.4512 r_free = 0.4512 target = 0.140295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.116736 restraints weight = 174922.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.119191 restraints weight = 263463.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.120405 restraints weight = 142703.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.121554 restraints weight = 96002.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.121928 restraints weight = 83899.804| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19026 Z= 0.144 Angle : 0.636 20.799 25906 Z= 0.316 Chirality : 0.055 1.990 2952 Planarity : 0.005 0.045 3287 Dihedral : 9.637 163.798 2623 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.81 % Favored : 92.11 % Rotamer: Outliers : 0.05 % Allowed : 0.97 % Favored : 98.98 % 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: -2.05 (0.17), residues: 2319 helix: -0.20 (0.22), residues: 525 sheet: -1.95 (0.21), residues: 555 loop : -1.55 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 624 TYR 0.014 0.001 TYR D 26 PHE 0.018 0.001 PHE A 986 TRP 0.013 0.001 TRP A 594 HIS 0.010 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (19018) covalent geometry : angle 0.60459 / 0.31 (25894) hydrogen bonds : bond 0.04061 / 2.67 ( 703) hydrogen bonds : angle 6.07582 / 4.18 ( 1842) metal coordination : bond 0.00638 / 0.39 ( 8) metal coordination : angle 9.12802 / 5.99 ( 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: 1 poor density : 188 time to evaluate : 0.638 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: A 233 LEU cc_start: 0.8405 (pt) cc_final: 0.8102 (pt) REVERT: A 395 MET cc_start: 0.8166 (mmm) cc_final: 0.7631 (tpp) REVERT: A 1009 HIS cc_start: 0.6602 (OUTLIER) cc_final: 0.6228 (t-170) REVERT: B 240 ASN cc_start: 0.7642 (p0) cc_final: 0.7357 (p0) REVERT: B 318 MET cc_start: 0.6797 (mmp) cc_final: 0.6589 (mmp) REVERT: B 323 HIS cc_start: 0.6480 (t-90) cc_final: 0.5940 (t-90) REVERT: C 14 GLU cc_start: 0.6215 (mp0) cc_final: 0.5948 (mp0) REVERT: D 144 MET cc_start: 0.4648 (ttp) cc_final: 0.4069 (ttt) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.2892 time to fit residues: 82.7495 Evaluate side-chains 165 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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: 0.4980 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4525 r_free = 0.4525 target = 0.141211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.117535 restraints weight = 175101.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.120206 restraints weight = 256002.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.121739 restraints weight = 129946.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.122029 restraints weight = 94659.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.122908 restraints weight = 80417.507| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19026 Z= 0.110 Angle : 0.620 25.899 25906 Z= 0.304 Chirality : 0.055 1.966 2952 Planarity : 0.004 0.047 3287 Dihedral : 9.538 163.474 2623 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.43 % Favored : 93.45 % 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: -1.93 (0.17), residues: 2319 helix: -0.06 (0.23), residues: 526 sheet: -1.87 (0.21), residues: 561 loop : -1.49 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 306 TYR 0.029 0.001 TYR D 9 PHE 0.035 0.001 PHE B 267 TRP 0.011 0.001 TRP E 207 HIS 0.004 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (19018) covalent geometry : angle 0.58281 / 0.30 (25894) hydrogen bonds : bond 0.03854 / 2.54 ( 703) hydrogen bonds : angle 5.90435 / 4.06 ( 1842) metal coordination : bond 0.00765 / 0.43 ( 8) metal coordination : angle 9.86543 / 6.31 ( 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 191 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.069 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: symmetry clash REVERT: A 171 TRP cc_start: 0.7739 (p-90) cc_final: 0.7377 (p-90) REVERT: A 233 LEU cc_start: 0.8379 (pt) cc_final: 0.8081 (pt) REVERT: A 395 MET cc_start: 0.8129 (mmm) cc_final: 0.7577 (tpp) REVERT: B 240 ASN cc_start: 0.7673 (p0) cc_final: 0.7355 (p0) REVERT: B 323 HIS cc_start: 0.6498 (t-90) cc_final: 0.5969 (t-90) REVERT: C 14 GLU cc_start: 0.6159 (mp0) cc_final: 0.5847 (mp0) REVERT: D 144 MET cc_start: 0.4609 (ttp) cc_final: 0.4036 (ttt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.3119 time to fit residues: 91.3153 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 : 1.014 ------------------------------------------------------------------------------- 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: 0.6980 chunk 185 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 165 optimal weight: 0.2980 chunk 136 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 196 optimal weight: 0.7980 chunk 216 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 overall best weight: 3.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4500 r_free = 0.4500 target = 0.139352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.119121 restraints weight = 176603.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.113648 restraints weight = 168535.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.111217 restraints weight = 155856.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.112435 restraints weight = 121687.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.112213 restraints weight = 84341.668| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 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 : 0.005 0.070 19026 Z= 0.227 Angle : 0.682 25.277 25906 Z= 0.339 Chirality : 0.055 1.925 2952 Planarity : 0.005 0.049 3287 Dihedral : 9.634 164.445 2623 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.01 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -2.06 (0.17), residues: 2319 helix: -0.10 (0.23), residues: 529 sheet: -1.96 (0.21), residues: 547 loop : -1.62 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 426 TYR 0.027 0.002 TYR A 467 PHE 0.026 0.002 PHE A 986 TRP 0.024 0.001 TRP A 594 HIS 0.008 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.23 (19018) covalent geometry : angle 0.65061 / 0.34 (25894) hydrogen bonds : bond 0.04151 / 2.72 ( 703) hydrogen bonds : angle 6.00797 / 4.13 ( 1842) metal coordination : bond 0.01137 / 0.58 ( 8) metal coordination : angle 9.57510 / 6.18 ( 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 188 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.054 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 233 LEU cc_start: 0.8554 (pt) cc_final: 0.8226 (pt) REVERT: A 245 PHE cc_start: 0.5896 (p90) cc_final: 0.5492 (p90) REVERT: A 272 HIS cc_start: 0.8112 (t70) cc_final: 0.7801 (t70) REVERT: A 395 MET cc_start: 0.8365 (mmm) cc_final: 0.7759 (tpp) REVERT: A 925 MET cc_start: 0.7170 (tpp) cc_final: 0.6545 (tpt) REVERT: B 240 ASN cc_start: 0.7566 (p0) cc_final: 0.7296 (p0) REVERT: B 323 HIS cc_start: 0.6587 (t-90) cc_final: 0.6039 (t-90) REVERT: C 14 GLU cc_start: 0.6330 (mp0) cc_final: 0.6046 (mp0) REVERT: D 144 MET cc_start: 0.4573 (ttp) cc_final: 0.4003 (ttt) REVERT: D 251 MET cc_start: 0.6785 (mmm) cc_final: 0.6436 (mmm) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3463 time to fit residues: 98.4614 Evaluate side-chains 160 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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: 0.5980 chunk 213 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 187 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4520 r_free = 0.4520 target = 0.140640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.116551 restraints weight = 177882.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.119010 restraints weight = 251462.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.121526 restraints weight = 126877.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.121467 restraints weight = 97273.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.122600 restraints weight = 77870.257| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19026 Z= 0.129 Angle : 0.616 23.728 25906 Z= 0.304 Chirality : 0.054 1.920 2952 Planarity : 0.004 0.044 3287 Dihedral : 9.545 164.210 2623 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.86 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -1.91 (0.17), residues: 2319 helix: 0.01 (0.23), residues: 529 sheet: -1.89 (0.20), residues: 563 loop : -1.50 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 306 TYR 0.010 0.001 TYR D 9 PHE 0.020 0.001 PHE A 763 TRP 0.024 0.001 TRP A 594 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (19018) covalent geometry : angle 0.58475 / 0.30 (25894) hydrogen bonds : bond 0.03786 / 2.48 ( 703) hydrogen bonds : angle 5.79717 / 3.97 ( 1842) metal coordination : bond 0.00695 / 0.38 ( 8) metal coordination : angle 9.08853 / 5.89 ( 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 190 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.003 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: A 233 LEU cc_start: 0.8394 (pt) cc_final: 0.8106 (pt) REVERT: A 395 MET cc_start: 0.8156 (mmm) cc_final: 0.7672 (tpp) REVERT: A 925 MET cc_start: 0.7207 (tpp) cc_final: 0.6671 (tpt) REVERT: B 240 ASN cc_start: 0.7553 (p0) cc_final: 0.7260 (p0) REVERT: B 323 HIS cc_start: 0.6549 (t-90) cc_final: 0.6014 (t-90) REVERT: C 14 GLU cc_start: 0.6159 (mp0) cc_final: 0.5872 (mp0) REVERT: D 144 MET cc_start: 0.4496 (ttp) cc_final: 0.3928 (ttt) REVERT: D 251 MET cc_start: 0.6904 (mmm) cc_final: 0.6378 (mmm) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3370 time to fit residues: 96.7744 Evaluate side-chains 164 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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: 3.9990 chunk 225 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 230 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 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 = 0.4513 r_free = 0.4513 target = 0.140198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.116404 restraints weight = 177927.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.119216 restraints weight = 251884.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.121754 restraints weight = 123169.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.121553 restraints weight = 97129.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.122822 restraints weight = 75825.532| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19026 Z= 0.148 Angle : 0.620 23.038 25906 Z= 0.307 Chirality : 0.054 1.899 2952 Planarity : 0.005 0.043 3287 Dihedral : 9.528 164.205 2623 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.89 % Favored : 92.02 % 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: -1.90 (0.17), residues: 2319 helix: 0.05 (0.23), residues: 529 sheet: -1.89 (0.21), residues: 563 loop : -1.50 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 216 TYR 0.016 0.001 TYR A 467 PHE 0.013 0.001 PHE C 29 TRP 0.028 0.001 TRP A 594 HIS 0.010 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (19018) covalent geometry : angle 0.58993 / 0.30 (25894) hydrogen bonds : bond 0.03781 / 2.47 ( 703) hydrogen bonds : angle 5.76359 / 3.95 ( 1842) metal coordination : bond 0.00713 / 0.39 ( 8) metal coordination : angle 8.82483 / 5.73 ( 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 188 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.157 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 233 LEU cc_start: 0.8407 (pt) cc_final: 0.8109 (pt) REVERT: A 395 MET cc_start: 0.8147 (mmm) cc_final: 0.7651 (tpp) REVERT: A 925 MET cc_start: 0.7225 (tpp) cc_final: 0.6690 (tpt) REVERT: B 240 ASN cc_start: 0.7569 (p0) cc_final: 0.7266 (p0) REVERT: B 323 HIS cc_start: 0.6585 (t-90) cc_final: 0.6032 (t-90) REVERT: C 14 GLU cc_start: 0.6173 (mp0) cc_final: 0.5880 (mp0) REVERT: D 144 MET cc_start: 0.4438 (ttp) cc_final: 0.3872 (ttt) REVERT: D 251 MET cc_start: 0.7009 (mmm) cc_final: 0.6524 (mmm) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3547 time to fit residues: 101.3047 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 : 1.051 ------------------------------------------------------------------------------- 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: 5.9990 chunk 65 optimal weight: 0.0770 chunk 50 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 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 = 0.4531 r_free = 0.4531 target = 0.141424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.123688 restraints weight = 177772.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.125572 restraints weight = 244443.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.125361 restraints weight = 100228.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.126146 restraints weight = 78193.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.126269 restraints weight = 63710.240| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 19026 Z= 0.103 Angle : 0.594 21.545 25906 Z= 0.294 Chirality : 0.054 1.888 2952 Planarity : 0.004 0.045 3287 Dihedral : 9.435 163.705 2623 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -1.75 (0.17), residues: 2319 helix: 0.17 (0.23), residues: 530 sheet: -1.81 (0.20), residues: 573 loop : -1.38 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 306 TYR 0.009 0.001 TYR D 26 PHE 0.021 0.001 PHE A 800 TRP 0.015 0.001 TRP A 594 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (19018) covalent geometry : angle 0.56711 / 0.29 (25894) hydrogen bonds : bond 0.03712 / 2.41 ( 703) hydrogen bonds : angle 5.62584 / 3.86 ( 1842) metal coordination : bond 0.00493 / 0.28 ( 8) metal coordination : angle 8.26052 / 5.38 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5195.06 seconds wall clock time: 89 minutes 50.87 seconds (5390.87 seconds total)