Starting phenix.real_space_refine on Sun Dec 29 18:58:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yix_33865/12_2024/7yix_33865.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yix_33865/12_2024/7yix_33865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yix_33865/12_2024/7yix_33865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yix_33865/12_2024/7yix_33865.map" model { file = "/net/cci-nas-00/data/ceres_data/7yix_33865/12_2024/7yix_33865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yix_33865/12_2024/7yix_33865.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.142 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 4 6.06 5 Mg 2 5.21 5 S 54 5.16 5 C 6928 2.51 5 N 1914 2.21 5 O 2176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11080 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3738 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 22, 'TRANS': 459} Chain: "B" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3738 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 22, 'TRANS': 459} Chain: "C" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1708 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 216} Chain breaks: 1 Chain: "D" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1720 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 218} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' CA': 1, ' MG': 1, ' ZN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' CA': 1, ' MG': 1, ' ZN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.29, per 1000 atoms: 0.66 Number of scatterers: 11080 At special positions: 0 Unit cell: (143, 84.7, 102.3, 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 4 29.99 Ca 2 19.99 S 54 16.00 Mg 2 11.99 O 2176 8.00 N 1914 7.00 C 6928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 497 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 489 " - pdb=" SG CYS B 497 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 251 " distance=2.04 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 123 " distance=2.03 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 251 " distance=2.04 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 601 " - " ASN A 140 " " NAG A 602 " - " ASN A 303 " " NAG B 601 " - " ASN B 140 " " NAG B 602 " - " ASN B 303 " " NAG E 1 " - " ASN A 271 " " NAG F 1 " - " ASN A 430 " " NAG G 1 " - " ASN B 271 " " NAG H 1 " - " ASN B 430 " Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 604 " pdb="ZN ZN A 604 " - pdb=" NE2 HIS A 454 " pdb="ZN ZN A 604 " - pdb=" NE2 HIS A 341 " pdb=" ZN A 606 " pdb="ZN ZN A 606 " - pdb=" NE2 HIS A 379 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 341 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 454 " pdb=" ZN B 606 " pdb="ZN ZN B 606 " - pdb=" ND1 HIS B 379 " 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2564 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 20 sheets defined 26.3% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 20 through 24 Processing helix chain 'A' and resid 25 through 43 removed outlier: 3.908A pdb=" N TRP A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.889A pdb=" N HIS A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.839A pdb=" N THR A 141 " --> pdb=" O ARG A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 157 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 193 through 199 Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.754A pdb=" N VAL A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 343 removed outlier: 4.278A pdb=" N HIS A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 366 removed outlier: 3.862A pdb=" N ALA A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 365 " --> pdb=" O GLN A 361 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 467 through 471 removed outlier: 4.082A pdb=" N LEU A 470 " --> pdb=" O MET A 467 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 471 " --> pdb=" O ALA A 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 467 through 471' Processing helix chain 'A' and resid 479 through 488 removed outlier: 3.587A pdb=" N VAL A 483 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 485 " --> pdb=" O PRO A 481 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 486 " --> pdb=" O HIS A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 25 through 43 removed outlier: 4.050A pdb=" N TRP B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.573A pdb=" N THR B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 120 removed outlier: 3.792A pdb=" N THR B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.864A pdb=" N THR B 141 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 142 " --> pdb=" O CYS B 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 142' Processing helix chain 'B' and resid 149 through 157 removed outlier: 3.599A pdb=" N TRP B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.580A pdb=" N MET B 192 " --> pdb=" O ASP B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.525A pdb=" N GLN B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.798A pdb=" N TYR B 225 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET B 226 " --> pdb=" O ARG B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 226' Processing helix chain 'B' and resid 251 through 257 removed outlier: 3.559A pdb=" N LYS B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 277 through 278 No H-bonds generated for 'chain 'B' and resid 277 through 278' Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.756A pdb=" N VAL B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 342 removed outlier: 4.195A pdb=" N HIS B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 342 " --> pdb=" O HIS B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 366 removed outlier: 3.717A pdb=" N ALA B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 467 through 471 removed outlier: 4.037A pdb=" N LEU B 470 " --> pdb=" O MET B 467 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 467 through 471' Processing helix chain 'B' and resid 478 through 488 removed outlier: 4.373A pdb=" N HIS B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 483 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET B 484 " --> pdb=" O VAL B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.648A pdb=" N TYR C 59 " --> pdb=" O PHE C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 removed outlier: 4.228A pdb=" N PHE C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.612A pdb=" N TYR D 59 " --> pdb=" O PHE D 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 286 through 289 removed outlier: 6.640A pdb=" N ILE A 218 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 217 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY A 221 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR A 167 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 54 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL A 331 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N MET A 56 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLY A 333 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU A 58 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 377 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA A 460 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N HIS A 475 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU A 97 " --> pdb=" O HIS A 475 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 381 removed outlier: 4.123A pdb=" N SER A 380 " --> pdb=" O GLY A 455 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 385 removed outlier: 7.319A pdb=" N SER A 445 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLY A 416 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 447 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.674A pdb=" N GLU A 427 " --> pdb=" O VAL A 424 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 289 removed outlier: 6.614A pdb=" N ILE B 218 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY B 221 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR B 167 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA B 377 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA B 460 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 94 " --> pdb=" O SER B 463 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N HIS B 475 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU B 97 " --> pdb=" O HIS B 475 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 383 through 385 Processing sheet with id=AA7, first strand: chain 'B' and resid 417 through 418 Processing sheet with id=AA8, first strand: chain 'B' and resid 423 through 424 removed outlier: 3.873A pdb=" N GLU B 427 " --> pdb=" O VAL B 424 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 30 through 33 Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 38 removed outlier: 6.743A pdb=" N ILE C 61 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TRP C 77 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TRP C 63 " --> pdb=" O MET C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 38 removed outlier: 3.639A pdb=" N TYR C 137 " --> pdb=" O ARG C 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 167 through 170 removed outlier: 3.824A pdb=" N ASP C 233 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.879A pdb=" N VAL C 174 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU C 196 " --> pdb=" O TYR C 212 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR C 212 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP C 198 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.879A pdb=" N VAL C 174 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR C 260 " --> pdb=" O GLN C 253 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 30 through 33 Processing sheet with id=AB7, first strand: chain 'D' and resid 37 through 39 removed outlier: 3.692A pdb=" N GLU D 37 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE D 61 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TRP D 77 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TRP D 63 " --> pdb=" O MET D 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 37 through 39 removed outlier: 3.692A pdb=" N GLU D 37 " --> pdb=" O LEU D 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 167 through 170 removed outlier: 4.208A pdb=" N ASP D 233 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 230 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 216 through 217 removed outlier: 6.631A pdb=" N TRP D 198 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR D 212 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU D 196 " --> pdb=" O TYR D 212 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR D 260 " --> pdb=" O GLN D 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 removed outlier: 6.631A pdb=" N TRP D 198 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR D 212 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU D 196 " --> pdb=" O TYR D 212 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1044 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: 3.77 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3646 1.34 - 1.46: 2639 1.46 - 1.58: 4945 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 11320 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 ... (remaining 11315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 15083 1.64 - 3.28: 252 3.28 - 4.92: 19 4.92 - 6.56: 3 6.56 - 8.20: 1 Bond angle restraints: 15358 Sorted by residual: angle pdb=" N GLU A 351 " pdb=" CA GLU A 351 " pdb=" CB GLU A 351 " ideal model delta sigma weight residual 110.28 114.61 -4.33 1.55e+00 4.16e-01 7.80e+00 angle pdb=" CA LEU A 43 " pdb=" CB LEU A 43 " pdb=" CG LEU A 43 " ideal model delta sigma weight residual 116.30 124.50 -8.20 3.50e+00 8.16e-02 5.49e+00 angle pdb=" C VAL A 447 " pdb=" CA VAL A 447 " pdb=" CB VAL A 447 " ideal model delta sigma weight residual 110.13 112.40 -2.27 9.70e-01 1.06e+00 5.47e+00 angle pdb=" C HIS A 350 " pdb=" N GLU A 351 " pdb=" CA GLU A 351 " ideal model delta sigma weight residual 120.31 116.96 3.35 1.52e+00 4.33e-01 4.85e+00 angle pdb=" C LEU A 18 " pdb=" N VAL A 19 " pdb=" CA VAL A 19 " ideal model delta sigma weight residual 122.13 126.12 -3.99 1.85e+00 2.92e-01 4.66e+00 ... (remaining 15353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6247 17.84 - 35.69: 489 35.69 - 53.53: 96 53.53 - 71.37: 18 71.37 - 89.22: 14 Dihedral angle restraints: 6864 sinusoidal: 2826 harmonic: 4038 Sorted by residual: dihedral pdb=" CB CYS B 489 " pdb=" SG CYS B 489 " pdb=" SG CYS B 497 " pdb=" CB CYS B 497 " ideal model delta sinusoidal sigma weight residual -86.00 -168.64 82.64 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS A 489 " pdb=" SG CYS A 489 " pdb=" SG CYS A 497 " pdb=" CB CYS A 497 " ideal model delta sinusoidal sigma weight residual -86.00 -158.57 72.57 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS A 139 " pdb=" SG CYS A 139 " pdb=" SG CYS A 201 " pdb=" CB CYS A 201 " ideal model delta sinusoidal sigma weight residual -86.00 -143.29 57.29 1 1.00e+01 1.00e-02 4.41e+01 ... (remaining 6861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1515 0.068 - 0.136: 190 0.136 - 0.204: 4 0.204 - 0.271: 0 0.271 - 0.339: 1 Chirality restraints: 1710 Sorted by residual: chirality pdb=" C1 NAG B 602 " pdb=" ND2 ASN B 303 " pdb=" C2 NAG B 602 " pdb=" O5 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA GLU A 351 " pdb=" N GLU A 351 " pdb=" C GLU A 351 " pdb=" CB GLU A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CB VAL A 19 " pdb=" CA VAL A 19 " pdb=" CG1 VAL A 19 " pdb=" CG2 VAL A 19 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1707 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 77 " -0.016 2.00e-02 2.50e+03 1.48e-02 5.47e+00 pdb=" CG TRP C 77 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 77 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP C 77 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 77 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 77 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 77 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 77 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 77 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 77 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 77 " 0.015 2.00e-02 2.50e+03 1.29e-02 4.14e+00 pdb=" CG TRP D 77 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP D 77 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 77 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 77 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 77 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 77 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 77 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 77 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 77 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 80 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO B 81 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 81 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 81 " 0.026 5.00e-02 4.00e+02 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 69 2.58 - 3.16: 8446 3.16 - 3.74: 15812 3.74 - 4.32: 22740 4.32 - 4.90: 40197 Nonbonded interactions: 87264 Sorted by model distance: nonbonded pdb=" OD2 ASP B 337 " pdb="ZN ZN B 604 " model vdw 2.001 2.230 nonbonded pdb=" OD1 ASP B 60 " pdb="ZN ZN B 606 " model vdw 2.088 2.230 nonbonded pdb=" OD1 ASP A 378 " pdb="ZN ZN A 606 " model vdw 2.119 2.230 nonbonded pdb=" OD2 ASP B 60 " pdb="MG MG B 603 " model vdw 2.147 2.170 nonbonded pdb=" OD2 ASP A 60 " pdb="MG MG A 603 " model vdw 2.155 2.170 ... (remaining 87259 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 28 through 146 or resid 164 through 269)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.970 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11320 Z= 0.206 Angle : 0.515 8.203 15358 Z= 0.272 Chirality : 0.044 0.339 1710 Planarity : 0.003 0.047 1980 Dihedral : 13.438 89.215 4276 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1404 helix: 0.54 (0.32), residues: 280 sheet: 0.61 (0.28), residues: 322 loop : -0.86 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 77 HIS 0.007 0.001 HIS A 379 PHE 0.012 0.001 PHE A 383 TYR 0.011 0.001 TYR A 117 ARG 0.003 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: A 195 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6580 (pt0) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 1.4831 time to fit residues: 228.0505 Evaluate side-chains 117 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 300 ASN B 282 ASN B 454 HIS D 33 GLN D 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11320 Z= 0.185 Angle : 0.498 5.710 15358 Z= 0.265 Chirality : 0.043 0.263 1710 Planarity : 0.004 0.048 1980 Dihedral : 5.943 55.332 1784 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.54 % Allowed : 7.53 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1404 helix: 0.53 (0.32), residues: 290 sheet: 0.79 (0.28), residues: 318 loop : -0.87 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 77 HIS 0.004 0.001 HIS A 379 PHE 0.012 0.001 PHE A 383 TYR 0.012 0.001 TYR A 206 ARG 0.004 0.000 ARG D 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: A 138 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6945 (mtm180) REVERT: A 199 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6871 (mt0) REVERT: A 240 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7172 (mp0) REVERT: A 433 MET cc_start: 0.7912 (mmm) cc_final: 0.7553 (mmt) REVERT: D 140 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7424 (pt0) outliers start: 18 outliers final: 6 residues processed: 129 average time/residue: 1.3333 time to fit residues: 186.2826 Evaluate side-chains 120 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11320 Z= 0.293 Angle : 0.548 7.392 15358 Z= 0.289 Chirality : 0.045 0.288 1710 Planarity : 0.004 0.049 1980 Dihedral : 5.795 57.349 1784 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.48 % Allowed : 10.02 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1404 helix: 0.28 (0.31), residues: 290 sheet: 0.68 (0.29), residues: 310 loop : -0.99 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 77 HIS 0.005 0.001 HIS B 454 PHE 0.018 0.002 PHE A 383 TYR 0.015 0.002 TYR B 206 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 199 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6743 (mt0) REVERT: A 351 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: A 433 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7510 (mmt) REVERT: D 140 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7537 (pt0) outliers start: 29 outliers final: 11 residues processed: 117 average time/residue: 1.4258 time to fit residues: 179.8748 Evaluate side-chains 119 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11320 Z= 0.246 Angle : 0.520 7.792 15358 Z= 0.275 Chirality : 0.044 0.294 1710 Planarity : 0.004 0.048 1980 Dihedral : 5.628 56.968 1784 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.91 % Allowed : 11.22 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.21), residues: 1404 helix: 0.32 (0.31), residues: 290 sheet: 0.72 (0.29), residues: 306 loop : -1.03 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 77 HIS 0.004 0.001 HIS A 341 PHE 0.015 0.002 PHE A 383 TYR 0.015 0.001 TYR B 206 ARG 0.002 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 138 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7073 (mtm180) REVERT: A 199 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6700 (mt0) REVERT: A 351 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6415 (mp0) REVERT: A 433 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7497 (mmt) REVERT: B 240 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7384 (mp0) REVERT: B 427 GLU cc_start: 0.7348 (mp0) cc_final: 0.6956 (pm20) REVERT: C 70 GLN cc_start: 0.6638 (mp10) cc_final: 0.6355 (mp10) REVERT: D 70 GLN cc_start: 0.6416 (mp10) cc_final: 0.6140 (mp10) REVERT: D 140 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7528 (pt0) outliers start: 34 outliers final: 17 residues processed: 124 average time/residue: 1.4224 time to fit residues: 190.1934 Evaluate side-chains 126 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 233 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11320 Z= 0.166 Angle : 0.483 8.484 15358 Z= 0.253 Chirality : 0.043 0.279 1710 Planarity : 0.003 0.047 1980 Dihedral : 5.368 55.282 1784 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.74 % Allowed : 11.99 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1404 helix: 0.59 (0.31), residues: 290 sheet: 0.42 (0.28), residues: 328 loop : -0.86 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 77 HIS 0.003 0.001 HIS A 341 PHE 0.010 0.001 PHE A 94 TYR 0.013 0.001 TYR A 117 ARG 0.002 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: A 199 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6729 (mt0) REVERT: A 240 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7139 (mp0) REVERT: A 351 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6432 (mp0) REVERT: A 433 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7453 (mmt) REVERT: B 56 MET cc_start: 0.7815 (ttt) cc_final: 0.7609 (ttt) REVERT: B 427 GLU cc_start: 0.7203 (mp0) cc_final: 0.6835 (pm20) REVERT: C 70 GLN cc_start: 0.6570 (mp10) cc_final: 0.6311 (mp10) REVERT: D 70 GLN cc_start: 0.6348 (mp10) cc_final: 0.6128 (mp10) outliers start: 32 outliers final: 18 residues processed: 126 average time/residue: 1.3801 time to fit residues: 187.3183 Evaluate side-chains 128 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 233 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11320 Z= 0.327 Angle : 0.563 8.631 15358 Z= 0.294 Chirality : 0.046 0.296 1710 Planarity : 0.004 0.049 1980 Dihedral : 5.566 57.867 1784 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.00 % Allowed : 13.27 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1404 helix: 0.32 (0.31), residues: 288 sheet: 0.53 (0.28), residues: 316 loop : -1.07 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 77 HIS 0.004 0.001 HIS A 341 PHE 0.018 0.002 PHE A 383 TYR 0.017 0.002 TYR B 206 ARG 0.003 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6558 (mt0) REVERT: A 433 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7439 (mmt) REVERT: B 240 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7322 (mp0) REVERT: B 427 GLU cc_start: 0.7275 (mp0) cc_final: 0.6881 (pm20) REVERT: C 70 GLN cc_start: 0.6594 (mp10) cc_final: 0.6352 (mp10) REVERT: C 224 ARG cc_start: 0.7745 (mtm110) cc_final: 0.7539 (mtm110) REVERT: D 140 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7481 (pt0) outliers start: 35 outliers final: 19 residues processed: 127 average time/residue: 1.3900 time to fit residues: 190.3547 Evaluate side-chains 127 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11320 Z= 0.171 Angle : 0.490 8.308 15358 Z= 0.257 Chirality : 0.043 0.286 1710 Planarity : 0.003 0.048 1980 Dihedral : 5.346 55.762 1784 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.40 % Allowed : 14.47 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1404 helix: 0.57 (0.31), residues: 290 sheet: 0.36 (0.28), residues: 328 loop : -0.92 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 77 HIS 0.003 0.001 HIS A 341 PHE 0.010 0.001 PHE A 94 TYR 0.013 0.001 TYR B 206 ARG 0.002 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 351 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6393 (mp0) REVERT: A 433 MET cc_start: 0.7713 (mmm) cc_final: 0.7457 (mmt) REVERT: B 427 GLU cc_start: 0.7240 (mp0) cc_final: 0.6832 (pm20) outliers start: 28 outliers final: 17 residues processed: 127 average time/residue: 1.3508 time to fit residues: 185.2144 Evaluate side-chains 125 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11320 Z= 0.196 Angle : 0.505 8.054 15358 Z= 0.264 Chirality : 0.043 0.277 1710 Planarity : 0.004 0.047 1980 Dihedral : 5.301 55.803 1784 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.40 % Allowed : 14.73 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1404 helix: 0.57 (0.31), residues: 290 sheet: 0.34 (0.28), residues: 328 loop : -0.90 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 77 HIS 0.006 0.001 HIS A 267 PHE 0.011 0.001 PHE A 383 TYR 0.013 0.001 TYR B 206 ARG 0.002 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.284 Fit side-chains REVERT: A 240 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7167 (mp0) REVERT: A 351 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6408 (mp0) REVERT: A 433 MET cc_start: 0.7698 (mmm) cc_final: 0.7437 (mmt) REVERT: B 240 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7187 (mp0) REVERT: B 427 GLU cc_start: 0.7279 (mp0) cc_final: 0.6854 (pm20) REVERT: C 70 GLN cc_start: 0.6359 (mp10) cc_final: 0.6055 (mp10) outliers start: 28 outliers final: 20 residues processed: 127 average time/residue: 1.3863 time to fit residues: 190.3402 Evaluate side-chains 129 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11320 Z= 0.168 Angle : 0.495 8.004 15358 Z= 0.259 Chirality : 0.043 0.270 1710 Planarity : 0.003 0.047 1980 Dihedral : 5.222 55.290 1784 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.23 % Allowed : 14.90 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.22), residues: 1404 helix: 0.68 (0.31), residues: 290 sheet: 0.37 (0.28), residues: 328 loop : -0.85 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 77 HIS 0.003 0.001 HIS A 341 PHE 0.010 0.001 PHE A 268 TYR 0.013 0.001 TYR B 206 ARG 0.002 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.292 Fit side-chains REVERT: A 240 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7183 (mp0) REVERT: A 351 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: A 433 MET cc_start: 0.7673 (mmm) cc_final: 0.7427 (mmt) REVERT: B 240 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7134 (mp0) REVERT: B 427 GLU cc_start: 0.7253 (mp0) cc_final: 0.6839 (pm20) REVERT: C 70 GLN cc_start: 0.6346 (mp10) cc_final: 0.6019 (mp10) outliers start: 26 outliers final: 22 residues processed: 127 average time/residue: 1.3718 time to fit residues: 187.8643 Evaluate side-chains 130 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 233 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 139 optimal weight: 0.0770 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 496 HIS D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11320 Z= 0.157 Angle : 0.491 10.766 15358 Z= 0.256 Chirality : 0.042 0.260 1710 Planarity : 0.003 0.047 1980 Dihedral : 5.138 54.893 1784 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.88 % Allowed : 15.07 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1404 helix: 0.76 (0.32), residues: 290 sheet: 0.38 (0.28), residues: 328 loop : -0.83 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 77 HIS 0.004 0.001 HIS B 496 PHE 0.010 0.001 PHE A 94 TYR 0.013 0.001 TYR B 117 ARG 0.002 0.000 ARG B 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.303 Fit side-chains REVERT: A 240 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7145 (mp0) REVERT: A 351 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: A 433 MET cc_start: 0.7647 (mmm) cc_final: 0.7401 (mmt) REVERT: B 240 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7179 (mp0) REVERT: B 427 GLU cc_start: 0.7223 (mp0) cc_final: 0.6807 (pm20) REVERT: C 70 GLN cc_start: 0.6344 (mp10) cc_final: 0.6012 (mp10) outliers start: 22 outliers final: 19 residues processed: 126 average time/residue: 1.4052 time to fit residues: 191.2693 Evaluate side-chains 130 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.3980 chunk 102 optimal weight: 0.0470 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 6 optimal weight: 0.0570 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.159125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.126066 restraints weight = 11784.914| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.20 r_work: 0.3523 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11320 Z= 0.123 Angle : 0.463 9.995 15358 Z= 0.241 Chirality : 0.041 0.241 1710 Planarity : 0.003 0.046 1980 Dihedral : 4.926 54.237 1784 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.71 % Allowed : 15.50 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.22), residues: 1404 helix: 0.93 (0.32), residues: 290 sheet: 0.45 (0.28), residues: 328 loop : -0.73 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 77 HIS 0.002 0.000 HIS B 267 PHE 0.008 0.001 PHE A 94 TYR 0.018 0.001 TYR B 117 ARG 0.002 0.000 ARG B 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3781.51 seconds wall clock time: 69 minutes 37.12 seconds (4177.12 seconds total)