Starting phenix.real_space_refine on Tue Sep 15 12:24:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6smq_10245/09_2026/6smq_10245.cif Found real_map, /net/cci-nas-00/data/ceres_data/6smq_10245/09_2026/6smq_10245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6smq_10245/09_2026/6smq_10245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6smq_10245/09_2026/6smq_10245.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6smq_10245/09_2026/6smq_10245.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6smq_10245/09_2026/6smq_10245.cif" model { file = "/net/cci-nas-00/data/ceres_data/6smq_10245/09_2026/6smq_10245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6smq_10245/09_2026/6smq_10245.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 21504 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: 4 Type Number sf(0) Gaussians S 82 5.16 5 C 14061 2.51 5 N 3702 2.21 5 O 4291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22136 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3843 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 460} Chain: "B" Number of atoms: 7076 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 903, 7068 Classifications: {'peptide': 903} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 871} Conformer: "B" Number of residues, atoms: 903, 7068 Classifications: {'peptide': 903} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 871} bond proxies already assigned to first conformer: 7222 Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 82 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "D" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3843 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 460} Chain: "E" Number of atoms: 7138 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 911, 7130 Classifications: {'peptide': 911} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 879} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 911, 7130 Classifications: {'peptide': 911} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 879} Chain breaks: 1 bond proxies already assigned to first conformer: 7284 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'5PL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'5PL:plan-1': 1, '5PL:plan-2': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'C8E': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'5PL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'5PL:plan-1': 1, '5PL:plan-2': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'C8E': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 6.52, per 1000 atoms: 0.29 Number of scatterers: 22136 At special positions: 0 Unit cell: (134.82, 149.8, 150.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 82 16.00 O 4291 8.00 N 3702 7.00 C 14061 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.3 seconds 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5136 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 27 sheets defined 23.3% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 removed outlier: 3.925A pdb=" N THR A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.533A pdb=" N GLN A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 105 through 133 removed outlier: 3.685A pdb=" N TYR A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 167 removed outlier: 3.660A pdb=" N LEU A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 218 removed outlier: 3.867A pdb=" N GLU A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 247 Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.585A pdb=" N ALA A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.502A pdb=" N VAL A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.551A pdb=" N LYS A 338 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 339 " --> pdb=" O PHE A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 339' Processing helix chain 'A' and resid 381 through 395 removed outlier: 4.060A pdb=" N LEU A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 412 removed outlier: 3.901A pdb=" N ALA A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 432 Processing helix chain 'A' and resid 437 through 445 Processing helix chain 'A' and resid 457 through 461 removed outlier: 4.089A pdb=" N GLU A 461 " --> pdb=" O PRO A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.783A pdb=" N TYR A 480 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 removed outlier: 3.535A pdb=" N GLN B 143 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 removed outlier: 3.544A pdb=" N VAL B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 195 No H-bonds generated for 'chain 'B' and resid 194 through 195' Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.967A pdb=" N ASN B 258 " --> pdb=" O PRO B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 299 through 304 removed outlier: 4.715A pdb=" N ASP B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 326 removed outlier: 3.570A pdb=" N ALA B 324 " --> pdb=" O ASP B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 removed outlier: 3.508A pdb=" N MET B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.555A pdb=" N LYS B 451 " --> pdb=" O PRO B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 715 Processing helix chain 'B' and resid 737 through 741 Processing helix chain 'B' and resid 849 through 853 removed outlier: 3.780A pdb=" N GLU B 853 " --> pdb=" O ALA B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 898 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.636A pdb=" N LEU B 915 " --> pdb=" O LYS B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 939 No H-bonds generated for 'chain 'B' and resid 937 through 939' Processing helix chain 'D' and resid 37 through 56 removed outlier: 3.633A pdb=" N THR D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 removed outlier: 3.586A pdb=" N MET D 60 " --> pdb=" O ASN D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 67 Processing helix chain 'D' and resid 81 through 86 removed outlier: 3.657A pdb=" N VAL D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 133 Processing helix chain 'D' and resid 138 through 168 removed outlier: 3.955A pdb=" N ILE D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER D 168 " --> pdb=" O MET D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 218 removed outlier: 3.971A pdb=" N GLU D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 247 removed outlier: 3.577A pdb=" N ALA D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY D 247 " --> pdb=" O TYR D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 257 removed outlier: 3.574A pdb=" N ALA D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA D 253 " --> pdb=" O TYR D 249 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 279 removed outlier: 3.890A pdb=" N ARG D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.790A pdb=" N VAL D 328 " --> pdb=" O PHE D 324 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR D 331 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 removed outlier: 3.501A pdb=" N VAL D 340 " --> pdb=" O PHE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.748A pdb=" N LYS D 348 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP D 349 " --> pdb=" O VAL D 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 345 through 349' Processing helix chain 'D' and resid 360 through 364 removed outlier: 3.824A pdb=" N ARG D 364 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 395 Processing helix chain 'D' and resid 397 through 400 removed outlier: 4.084A pdb=" N THR D 400 " --> pdb=" O ASP D 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 397 through 400' Processing helix chain 'D' and resid 401 through 412 Processing helix chain 'D' and resid 421 through 432 removed outlier: 3.581A pdb=" N GLN D 425 " --> pdb=" O MET D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 445 removed outlier: 3.922A pdb=" N VAL D 443 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 481 removed outlier: 3.794A pdb=" N TYR D 480 " --> pdb=" O PHE D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 130 Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 188 through 193 Processing helix chain 'E' and resid 194 through 195 No H-bonds generated for 'chain 'E' and resid 194 through 195' Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 254 through 258 removed outlier: 3.850A pdb=" N ASN E 258 " --> pdb=" O PRO E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 272 Processing helix chain 'E' and resid 409 through 417 removed outlier: 3.681A pdb=" N MET E 417 " --> pdb=" O GLY E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 453 Processing helix chain 'E' and resid 573 through 577 removed outlier: 3.672A pdb=" N SER E 576 " --> pdb=" O THR E 573 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU E 577 " --> pdb=" O GLY E 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 573 through 577' Processing helix chain 'E' and resid 712 through 715 Processing helix chain 'E' and resid 737 through 741 removed outlier: 3.561A pdb=" N GLY E 741 " --> pdb=" O TYR E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 849 through 853 removed outlier: 4.015A pdb=" N GLU E 853 " --> pdb=" O ALA E 850 " (cutoff:3.500A) Processing helix chain 'E' and resid 895 through 900 removed outlier: 3.751A pdb=" N GLU E 900 " --> pdb=" O ARG E 896 " (cutoff:3.500A) Processing helix chain 'E' and resid 911 through 915 Processing helix chain 'E' and resid 959 through 963 removed outlier: 3.597A pdb=" N PHE E 963 " --> pdb=" O ASN E 960 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 73 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 287 through 290 removed outlier: 6.793A pdb=" N ILE A 287 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER A 380 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE A 289 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 346 removed outlier: 5.608A pdb=" N LYS A 344 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU A 353 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 125 removed outlier: 6.891A pdb=" N GLN B 227 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET B 203 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE B 225 " --> pdb=" O MET B 203 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL B 205 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 223 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 179 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE B 226 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 181 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR B 228 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 152 Processing sheet with id=AA9, first strand: chain 'B' and resid 238 through 250 removed outlier: 3.604A pdb=" N SER B 370 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 465 " --> pdb=" O ASN B 388 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG B 396 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER B 457 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 526 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ARG B 509 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LYS B 558 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLU B 511 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N SER B 556 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA B 513 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N GLY B 554 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ARG B 515 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL B 552 " --> pdb=" O ARG B 515 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL B 517 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLY B 550 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LYS B 519 " --> pdb=" O TYR B 548 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N TYR B 548 " --> pdb=" O LYS B 519 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N PHE B 521 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE B 546 " --> pdb=" O PHE B 521 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN B 523 " --> pdb=" O GLU B 544 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLU B 544 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA B 525 " --> pdb=" O GLY B 542 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLY B 542 " --> pdb=" O ALA B 525 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N TYR B 527 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU B 540 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE B 529 " --> pdb=" O THR B 538 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N THR B 538 " --> pdb=" O PHE B 529 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N TRP B 626 " --> pdb=" O GLY B 660 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLY B 660 " --> pdb=" O TRP B 626 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR B 628 " --> pdb=" O THR B 658 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N SER B 751 " --> pdb=" O THR B 787 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 775 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY B 867 " --> pdb=" O ASN B 778 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 951 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 884 " --> pdb=" O LEU B 949 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU B 949 " --> pdb=" O ALA B 884 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE B 886 " --> pdb=" O LEU B 947 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 947 " --> pdb=" O ILE B 886 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE B 946 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 984 " --> pdb=" O PHE B 946 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG B 948 " --> pdb=" O LEU B 982 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU B 982 " --> pdb=" O ARG B 948 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LYS B 950 " --> pdb=" O ASN B 980 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU B 981 " --> pdb=" O SER B1006 " (cutoff:3.500A) removed outlier: 11.375A pdb=" N SER B1006 " --> pdb=" O LEU B 981 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 245 " --> pdb=" O ALA B1011 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 433 through 434 Processing sheet with id=AB2, first strand: chain 'B' and resid 731 through 734 Processing sheet with id=AB3, first strand: chain 'B' and resid 795 through 797 removed outlier: 4.067A pdb=" N PHE B 813 " --> pdb=" O ILE B 856 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 818 through 821 removed outlier: 7.060A pdb=" N LEU B 829 " --> pdb=" O ALA B 819 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL B 843 " --> pdb=" O VAL B 832 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 941 through 943 removed outlier: 7.668A pdb=" N GLY B 999 " --> pdb=" O TRP B 890 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE B 892 " --> pdb=" O GLY B 999 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.546A pdb=" N ASP D 30 " --> pdb=" O VAL E 673 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 72 through 73 Processing sheet with id=AB8, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AB9, first strand: chain 'D' and resid 287 through 290 removed outlier: 6.730A pdb=" N ILE D 287 " --> pdb=" O SER D 380 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER D 380 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE D 289 " --> pdb=" O TYR D 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 308 through 311 Processing sheet with id=AC2, first strand: chain 'D' and resid 342 through 343 Processing sheet with id=AC3, first strand: chain 'E' and resid 122 through 125 removed outlier: 6.143A pdb=" N LEU E 179 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE E 226 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE E 181 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N THR E 228 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET E 185 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 149 through 152 Processing sheet with id=AC5, first strand: chain 'E' and resid 238 through 250 removed outlier: 3.713A pdb=" N SER E 244 " --> pdb=" O GLN E 333 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY E 340 " --> pdb=" O TYR E 347 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR E 347 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG E 396 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER E 457 " --> pdb=" O ARG E 396 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N GLY E 507 " --> pdb=" O GLY E 559 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N TRP E 626 " --> pdb=" O GLY E 660 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLY E 660 " --> pdb=" O TRP E 626 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR E 628 " --> pdb=" O THR E 658 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY E 867 " --> pdb=" O ASN E 778 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR E 885 " --> pdb=" O GLY E 866 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA E 881 " --> pdb=" O LEU E 870 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN E 951 " --> pdb=" O ASP E 882 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA E 884 " --> pdb=" O LEU E 949 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEU E 949 " --> pdb=" O ALA E 884 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE E 886 " --> pdb=" O LEU E 947 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU E 947 " --> pdb=" O ILE E 886 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE E 241 " --> pdb=" O LEU E1015 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 731 through 732 Processing sheet with id=AC7, first strand: chain 'E' and resid 795 through 796 removed outlier: 3.778A pdb=" N PHE E 813 " --> pdb=" O ILE E 856 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 818 through 821 removed outlier: 6.646A pdb=" N TYR E 818 " --> pdb=" O TYR E 831 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR E 831 " --> pdb=" O TYR E 818 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY E 820 " --> pdb=" O LEU E 829 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 941 through 943 removed outlier: 7.877A pdb=" N GLY E 999 " --> pdb=" O TRP E 890 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE E 892 " --> pdb=" O GLY E 999 " (cutoff:3.500A) 917 hydrogen bonds defined for protein. 2533 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: 4.79 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3729 1.30 - 1.43: 6182 1.43 - 1.55: 12541 1.55 - 1.68: 20 1.68 - 1.81: 158 Bond restraints: 22630 Sorted by residual: bond pdb=" CBU 5PL A 601 " pdb=" OCK 5PL A 601 " ideal model delta sigma weight residual 1.328 1.410 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" CBU 5PL D 601 " pdb=" OCK 5PL D 601 " ideal model delta sigma weight residual 1.328 1.407 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" CBL 5PL D 601 " pdb=" OCL 5PL D 601 " ideal model delta sigma weight residual 1.329 1.407 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" CBL 5PL A 601 " pdb=" OCL 5PL A 601 " ideal model delta sigma weight residual 1.329 1.404 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" CB THR E 212 " pdb=" CG2 THR E 212 " ideal model delta sigma weight residual 1.521 1.420 0.101 3.30e-02 9.18e+02 9.37e+00 ... (remaining 22625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 30083 3.26 - 6.52: 449 6.52 - 9.79: 57 9.79 - 13.05: 11 13.05 - 16.31: 1 Bond angle restraints: 30601 Sorted by residual: angle pdb=" C ALA E 131 " pdb=" N GLU E 132 " pdb=" CA GLU E 132 " ideal model delta sigma weight residual 121.54 132.38 -10.84 1.91e+00 2.74e-01 3.22e+01 angle pdb=" CA GLY B 276 " pdb=" C GLY B 276 " pdb=" O GLY B 276 " ideal model delta sigma weight residual 122.37 118.26 4.11 7.30e-01 1.88e+00 3.18e+01 angle pdb=" C LYS A 347 " pdb=" N LYS A 348 " pdb=" CA LYS A 348 " ideal model delta sigma weight residual 121.54 132.12 -10.58 1.91e+00 2.74e-01 3.07e+01 angle pdb=" C GLY B 989 " pdb=" N PHE B 990 " pdb=" CA PHE B 990 " ideal model delta sigma weight residual 121.54 131.74 -10.20 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C THR E 689 " pdb=" N ALA E 690 " pdb=" CA ALA E 690 " ideal model delta sigma weight residual 121.54 131.60 -10.06 1.91e+00 2.74e-01 2.78e+01 ... (remaining 30596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11941 17.92 - 35.84: 1206 35.84 - 53.76: 227 53.76 - 71.68: 39 71.68 - 89.59: 19 Dihedral angle restraints: 13432 sinusoidal: 5344 harmonic: 8088 Sorted by residual: dihedral pdb=" CA ASP B 601 " pdb=" C ASP B 601 " pdb=" N LYS B 602 " pdb=" CA LYS B 602 " ideal model delta harmonic sigma weight residual 180.00 126.61 53.39 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA GLU E 132 " pdb=" C GLU E 132 " pdb=" N LYS E 133 " pdb=" CA LYS E 133 " ideal model delta harmonic sigma weight residual 180.00 132.14 47.86 0 5.00e+00 4.00e-02 9.16e+01 dihedral pdb=" CA PHE E 790 " pdb=" C PHE E 790 " pdb=" N PHE E 791 " pdb=" CA PHE E 791 " ideal model delta harmonic sigma weight residual -180.00 -141.49 -38.51 0 5.00e+00 4.00e-02 5.93e+01 ... (remaining 13429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2361 0.063 - 0.126: 728 0.126 - 0.188: 126 0.188 - 0.251: 12 0.251 - 0.314: 12 Chirality restraints: 3239 Sorted by residual: chirality pdb=" CB ILE E 473 " pdb=" CA ILE E 473 " pdb=" CG1 ILE E 473 " pdb=" CG2 ILE E 473 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA PHE B 790 " pdb=" N PHE B 790 " pdb=" C PHE B 790 " pdb=" CB PHE B 790 " 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=" CB VAL E 433 " pdb=" CA VAL E 433 " pdb=" CG1 VAL E 433 " pdb=" CG2 VAL E 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 3236 not shown) Planarity restraints: 3999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 329 " 0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 330 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1003 " 0.013 2.00e-02 2.50e+03 2.05e-02 8.37e+00 pdb=" CG TYR B1003 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B1003 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B1003 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR B1003 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B1003 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B1003 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B1003 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 157 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO E 158 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 158 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 158 " -0.039 5.00e-02 4.00e+02 ... (remaining 3996 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5565 2.79 - 3.32: 16987 3.32 - 3.84: 34655 3.84 - 4.37: 41514 4.37 - 4.90: 77751 Nonbonded interactions: 176472 Sorted by model distance: nonbonded pdb=" O PRO E 737 " pdb=" OG SER E 740 " model vdw 2.261 3.040 nonbonded pdb=" O SER A 294 " pdb=" OG SER A 299 " model vdw 2.267 3.040 nonbonded pdb=" O SER E 662 " pdb=" OG SER E 662 " model vdw 2.269 3.040 nonbonded pdb=" OD2 ASP E 183 " pdb=" OG1 THR E 228 " model vdw 2.270 3.040 nonbonded pdb=" OD2 ASP D 233 " pdb=" OH TYR D 263 " model vdw 2.283 3.040 ... (remaining 176467 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' and (resid 20 through 501 or (resid 601 and (name CAA or name CAE or \ name CAF or name CAG or name CAK or name CAW or name CBH or name CBI or name CBL \ or name CBM or name CBN or name CBO or name CBP or name CBR or name CBS or name \ CBT or name CBU or name CBV or name CBW or name CBX or name CBY or name CBZ or \ name OCK or name OCL or name OCN or name OCO)) or (resid 602 and (name C1 or nam \ e C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name O2 )))) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 115 through 721 or resid 723 through 837 or resid 842 thro \ ugh 1017 or (resid 1101 through 1102 and (name C10 or name C11 or name C13 or na \ me C14 or name C6 or name C7 or name C8 or name O12 or name O9 )))) selection = (chain 'E' and (resid 115 through 721 or resid 723 through 1017 or (resid 1101 t \ hrough 1102 and (name C10 or name C11 or name C13 or name C14 or name C6 or name \ C7 or name C8 or name O12 or name O9 )))) } 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=0.50 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.190 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 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 : 0.011 0.168 22634 Z= 0.457 Angle : 1.042 16.311 30601 Z= 0.559 Chirality : 0.062 0.314 3239 Planarity : 0.006 0.086 3999 Dihedral : 14.862 89.595 8296 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.41 % Favored : 92.41 % Rotamer: Outliers : 0.43 % Allowed : 8.28 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -3.34 (0.13), residues: 2781 helix: -2.89 (0.15), residues: 561 sheet: -0.76 (0.18), residues: 796 loop : -2.85 (0.13), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 515 TYR 0.048 0.003 TYR B1003 PHE 0.028 0.003 PHE B 790 TRP 0.019 0.002 TRP B 874 HIS 0.019 0.003 HIS E 582 Details of bonding type rmsd/Z covalent geometry : bond 0.01061 / 0.44 (22630) covalent geometry : angle 1.04211 / 0.56 (30601) hydrogen bonds : bond 0.16073 / 10.78 ( 917) hydrogen bonds : angle 6.67487 / 4.69 ( 2533) Misc. bond : bond 0.08400 / 4.20 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 329 time to evaluate : 0.889 Fit side-chains REVERT: A 101 ASP cc_start: 0.7657 (m-30) cc_final: 0.7305 (m-30) REVERT: A 403 LYS cc_start: 0.8784 (tmtt) cc_final: 0.8559 (tttp) REVERT: A 494 GLN cc_start: 0.8870 (pt0) cc_final: 0.8647 (pt0) REVERT: B 140 ASP cc_start: 0.8706 (t0) cc_final: 0.8463 (t0) REVERT: B 417 MET cc_start: 0.8964 (mmm) cc_final: 0.8492 (mmt) REVERT: B 436 MET cc_start: 0.8463 (mtm) cc_final: 0.8183 (mtp) REVERT: B 573 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8508 (t) REVERT: B 776 SER cc_start: 0.8918 (p) cc_final: 0.8701 (t) REVERT: B 788 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8646 (tttm) REVERT: B 854 THR cc_start: 0.8615 (m) cc_final: 0.8095 (p) REVERT: D 22 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8638 (pp) REVERT: D 398 THR cc_start: 0.8327 (t) cc_final: 0.7965 (m) REVERT: E 232 LYS cc_start: 0.7965 (ptmm) cc_final: 0.7554 (mmtp) REVERT: E 1013 ILE cc_start: 0.9263 (tp) cc_final: 0.9054 (tp) outliers start: 10 outliers final: 6 residues processed: 336 average time/residue: 0.1684 time to fit residues: 87.5893 Evaluate side-chains 266 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 258 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 516 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 145 GLN B 150 GLN B 374 ASN B 463 ASN B 469 GLN B 498 ASN B 638 ASN B 702 GLN B 713 ASN B 748 ASN B 754 ASN B 782 ASN B 894 ASN B 932 GLN B 935 GLN B 951 ASN B1005 ASN D 86 ASN D 449 ASN D 457 GLN D 490 GLN E 103 GLN E 269 GLN E 278 ASN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 ASN E 748 ASN E 754 ASN E 800 ASN E 828 GLN E 932 GLN E 980 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.117138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.091831 restraints weight = 37680.336| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.58 r_work: 0.2526 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22634 Z= 0.165 Angle : 0.611 10.950 30601 Z= 0.327 Chirality : 0.045 0.171 3239 Planarity : 0.005 0.068 3999 Dihedral : 7.196 83.646 3196 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.54 % Favored : 94.31 % Rotamer: Outliers : 1.37 % Allowed : 11.63 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.17 (0.15), residues: 2781 helix: -1.11 (0.20), residues: 575 sheet: -0.34 (0.18), residues: 811 loop : -2.30 (0.14), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 238 TYR 0.021 0.001 TYR B 514 PHE 0.021 0.001 PHE B 712 TRP 0.016 0.001 TRP E 697 HIS 0.007 0.001 HIS E 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (22630) covalent geometry : angle 0.61085 / 0.33 (30601) hydrogen bonds : bond 0.04232 / 2.78 ( 917) hydrogen bonds : angle 5.05545 / 3.54 ( 2533) Misc. bond : bond 0.00037 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 0.855 Fit side-chains REVERT: A 94 ASP cc_start: 0.8063 (t0) cc_final: 0.7417 (p0) REVERT: A 101 ASP cc_start: 0.8010 (m-30) cc_final: 0.7742 (m-30) REVERT: A 214 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8439 (m) REVERT: A 421 MET cc_start: 0.8538 (tpp) cc_final: 0.8228 (tpt) REVERT: B 140 ASP cc_start: 0.9031 (t70) cc_final: 0.8829 (t0) REVERT: B 417 MET cc_start: 0.9100 (mmm) cc_final: 0.8701 (mmt) REVERT: B 436 MET cc_start: 0.8963 (mtm) cc_final: 0.8659 (mtp) REVERT: B 707 LEU cc_start: 0.8545 (tt) cc_final: 0.8254 (tp) REVERT: B 788 LYS cc_start: 0.9051 (ttmt) cc_final: 0.8830 (mtpp) REVERT: B 854 THR cc_start: 0.8339 (m) cc_final: 0.7849 (p) REVERT: D 22 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8623 (pp) REVERT: D 336 PHE cc_start: 0.8576 (m-80) cc_final: 0.8331 (m-80) REVERT: D 449 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.7923 (t0) REVERT: E 232 LYS cc_start: 0.8200 (ptmm) cc_final: 0.7507 (mmtp) REVERT: E 238 ARG cc_start: 0.8451 (ptm-80) cc_final: 0.8215 (ptm160) REVERT: E 271 LYS cc_start: 0.8863 (mtpp) cc_final: 0.8586 (mttm) REVERT: E 713 ASN cc_start: 0.8493 (t0) cc_final: 0.8087 (t0) REVERT: E 1013 ILE cc_start: 0.9051 (tp) cc_final: 0.8832 (tt) outliers start: 32 outliers final: 18 residues processed: 316 average time/residue: 0.1597 time to fit residues: 80.6691 Evaluate side-chains 285 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 264 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 982 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 180 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 145 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 145 GLN B 894 ASN D 449 ASN D 450 ASN D 490 GLN E 186 GLN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 997 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.114888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.088252 restraints weight = 33044.027| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.57 r_work: 0.2534 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2388 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2366 r_free = 0.2366 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2366 r_free = 0.2366 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 22634 Z= 0.238 Angle : 0.654 10.705 30601 Z= 0.347 Chirality : 0.047 0.186 3239 Planarity : 0.005 0.075 3999 Dihedral : 7.080 82.817 3188 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.62 % Favored : 93.27 % Rotamer: Outliers : 2.19 % Allowed : 13.47 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.77 (0.15), residues: 2781 helix: -0.39 (0.22), residues: 563 sheet: -0.23 (0.18), residues: 815 loop : -2.14 (0.15), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 444 TYR 0.026 0.002 TYR E 637 PHE 0.021 0.002 PHE E 791 TRP 0.015 0.001 TRP E 697 HIS 0.009 0.001 HIS E 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 (22630) covalent geometry : angle 0.65424 / 0.35 (30601) hydrogen bonds : bond 0.04674 / 3.07 ( 917) hydrogen bonds : angle 4.97931 / 3.47 ( 2533) Misc. bond : bond 0.00026 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 0.867 Fit side-chains REVERT: A 101 ASP cc_start: 0.8066 (m-30) cc_final: 0.7827 (m-30) REVERT: A 214 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8383 (m) REVERT: B 417 MET cc_start: 0.9132 (mmm) cc_final: 0.8698 (mmt) REVERT: B 436 MET cc_start: 0.8986 (mtm) cc_final: 0.8708 (mtp) REVERT: B 638 ASN cc_start: 0.8977 (m-40) cc_final: 0.8155 (t0) REVERT: B 788 LYS cc_start: 0.9101 (ttmt) cc_final: 0.8760 (mtpp) REVERT: B 854 THR cc_start: 0.8340 (m) cc_final: 0.7822 (p) REVERT: D 22 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8710 (pp) REVERT: D 276 ASN cc_start: 0.8421 (m110) cc_final: 0.8099 (m-40) REVERT: D 336 PHE cc_start: 0.8468 (m-80) cc_final: 0.8230 (m-80) REVERT: D 449 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8164 (t0) REVERT: E 232 LYS cc_start: 0.8240 (ptmm) cc_final: 0.7452 (mmtp) REVERT: E 271 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8595 (mttm) REVERT: E 283 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8372 (tttt) REVERT: E 922 ASN cc_start: 0.7587 (t0) cc_final: 0.6506 (p0) REVERT: E 1013 ILE cc_start: 0.9129 (tp) cc_final: 0.8900 (tt) outliers start: 51 outliers final: 39 residues processed: 291 average time/residue: 0.1552 time to fit residues: 72.6470 Evaluate side-chains 298 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 878 SER Chi-restraints excluded: chain B residue 894 ASN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 746 TYR Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 982 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 144 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 chunk 216 optimal weight: 6.9990 chunk 273 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 145 GLN B 252 ASN B 894 ASN B 932 GLN E 198 ASN E 365 ASN E 463 ASN E 481 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.117459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.090649 restraints weight = 37998.043| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.85 r_work: 0.2555 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22634 Z= 0.136 Angle : 0.563 10.407 30601 Z= 0.300 Chirality : 0.043 0.166 3239 Planarity : 0.004 0.065 3999 Dihedral : 6.569 83.201 3188 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 2.06 % Allowed : 14.54 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.36 (0.15), residues: 2781 helix: -0.00 (0.22), residues: 577 sheet: 0.09 (0.18), residues: 781 loop : -1.92 (0.15), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 444 TYR 0.017 0.001 TYR B 514 PHE 0.017 0.001 PHE B 712 TRP 0.014 0.001 TRP E 697 HIS 0.005 0.001 HIS B 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (22630) covalent geometry : angle 0.56316 / 0.30 (30601) hydrogen bonds : bond 0.03659 / 2.39 ( 917) hydrogen bonds : angle 4.72929 / 3.29 ( 2533) Misc. bond : bond 0.00020 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 281 time to evaluate : 0.871 Fit side-chains REVERT: A 94 ASP cc_start: 0.7983 (t0) cc_final: 0.7315 (p0) REVERT: A 214 SER cc_start: 0.8613 (OUTLIER) cc_final: 0.8370 (m) REVERT: A 348 LYS cc_start: 0.7965 (mtpt) cc_final: 0.7394 (tttm) REVERT: B 417 MET cc_start: 0.9016 (mmm) cc_final: 0.8683 (mmt) REVERT: B 436 MET cc_start: 0.8854 (mtm) cc_final: 0.8442 (mtp) REVERT: B 602 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7373 (mmtp) REVERT: B 638 ASN cc_start: 0.8821 (m-40) cc_final: 0.8081 (t0) REVERT: B 788 LYS cc_start: 0.9035 (ttmt) cc_final: 0.8764 (mtpp) REVERT: B 906 MET cc_start: 0.9466 (mmm) cc_final: 0.9179 (mmm) REVERT: B 1008 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8358 (mt0) REVERT: D 22 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8626 (pp) REVERT: D 334 GLU cc_start: 0.7506 (pm20) cc_final: 0.7263 (pm20) REVERT: D 336 PHE cc_start: 0.8432 (m-80) cc_final: 0.8143 (m-80) REVERT: E 232 LYS cc_start: 0.8084 (ptmm) cc_final: 0.7388 (mmtp) REVERT: E 283 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8373 (tttt) REVERT: E 922 ASN cc_start: 0.7810 (t0) cc_final: 0.6538 (p0) REVERT: E 960 ASN cc_start: 0.8596 (t0) cc_final: 0.8205 (t0) REVERT: E 1013 ILE cc_start: 0.9029 (tp) cc_final: 0.8820 (tt) outliers start: 48 outliers final: 29 residues processed: 307 average time/residue: 0.1543 time to fit residues: 75.7151 Evaluate side-chains 292 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 259 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 878 SER Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 1008 GLN Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 746 TYR Chi-restraints excluded: chain E residue 962 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 30 optimal weight: 0.1980 chunk 151 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN B 145 GLN B 894 ASN B 932 GLN E 535 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.115357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.088370 restraints weight = 35932.193| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.73 r_work: 0.2527 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2508 r_free = 0.2508 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2508 r_free = 0.2508 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22634 Z= 0.205 Angle : 0.615 10.840 30601 Z= 0.326 Chirality : 0.045 0.175 3239 Planarity : 0.004 0.070 3999 Dihedral : 6.704 81.547 3188 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.55 % Favored : 93.38 % Rotamer: Outliers : 2.36 % Allowed : 15.02 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.15), residues: 2781 helix: 0.22 (0.23), residues: 570 sheet: 0.03 (0.18), residues: 801 loop : -1.86 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 238 TYR 0.030 0.002 TYR E 637 PHE 0.022 0.001 PHE E 791 TRP 0.014 0.001 TRP E 697 HIS 0.009 0.001 HIS E 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (22630) covalent geometry : angle 0.61465 / 0.33 (30601) hydrogen bonds : bond 0.04257 / 2.79 ( 917) hydrogen bonds : angle 4.79172 / 3.33 ( 2533) Misc. bond : bond 0.00025 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 263 time to evaluate : 0.891 Fit side-chains REVERT: A 214 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8399 (m) REVERT: A 348 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7428 (tttm) REVERT: B 417 MET cc_start: 0.9058 (mmm) cc_final: 0.8639 (mmt) REVERT: B 436 MET cc_start: 0.8865 (mtm) cc_final: 0.8464 (mtp) REVERT: B 602 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7528 (mmtp) REVERT: B 638 ASN cc_start: 0.8816 (m-40) cc_final: 0.8057 (t0) REVERT: B 788 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8718 (mtpp) REVERT: B 861 THR cc_start: 0.9118 (t) cc_final: 0.8770 (m) REVERT: B 906 MET cc_start: 0.9484 (mmm) cc_final: 0.9199 (mmm) REVERT: B 1008 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8342 (mt0) REVERT: D 22 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8645 (pp) REVERT: D 336 PHE cc_start: 0.8452 (m-80) cc_final: 0.8094 (m-80) REVERT: E 232 LYS cc_start: 0.8121 (ptmm) cc_final: 0.7399 (mmtp) REVERT: E 283 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8324 (tttt) REVERT: E 922 ASN cc_start: 0.7847 (t0) cc_final: 0.6575 (p0) REVERT: E 960 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8229 (t0) REVERT: E 1013 ILE cc_start: 0.9033 (tp) cc_final: 0.8809 (tt) outliers start: 55 outliers final: 41 residues processed: 295 average time/residue: 0.1536 time to fit residues: 73.4405 Evaluate side-chains 298 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 878 SER Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 894 ASN Chi-restraints excluded: chain B residue 1008 GLN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 746 TYR Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 960 ASN Chi-restraints excluded: chain E residue 962 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 204 optimal weight: 7.9990 chunk 178 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 145 GLN B 835 GLN B 894 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.114735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.087712 restraints weight = 37962.398| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.82 r_work: 0.2491 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22634 Z= 0.243 Angle : 0.643 10.919 30601 Z= 0.341 Chirality : 0.047 0.178 3239 Planarity : 0.005 0.079 3999 Dihedral : 6.780 80.999 3188 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.51 % Favored : 93.45 % Rotamer: Outliers : 3.05 % Allowed : 15.32 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.28 (0.16), residues: 2781 helix: 0.23 (0.23), residues: 570 sheet: -0.08 (0.18), residues: 825 loop : -1.83 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 238 TYR 0.022 0.002 TYR B 514 PHE 0.020 0.002 PHE E 791 TRP 0.014 0.001 TRP E 697 HIS 0.008 0.001 HIS E 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.24 (22630) covalent geometry : angle 0.64336 / 0.34 (30601) hydrogen bonds : bond 0.04513 / 2.96 ( 917) hydrogen bonds : angle 4.82615 / 3.35 ( 2533) Misc. bond : bond 0.00027 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 264 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7687 (m-30) cc_final: 0.7366 (m-30) REVERT: A 214 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8389 (m) REVERT: A 348 LYS cc_start: 0.7947 (mtpt) cc_final: 0.7348 (ttpt) REVERT: B 233 MET cc_start: 0.8653 (mtm) cc_final: 0.8384 (mtm) REVERT: B 417 MET cc_start: 0.9079 (mmm) cc_final: 0.8656 (mmt) REVERT: B 436 MET cc_start: 0.8894 (mtm) cc_final: 0.8495 (mtp) REVERT: B 602 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7504 (mmtp) REVERT: B 638 ASN cc_start: 0.8848 (m-40) cc_final: 0.8080 (t0) REVERT: B 788 LYS cc_start: 0.9008 (ttmt) cc_final: 0.8727 (mtpp) REVERT: B 854 THR cc_start: 0.8306 (m) cc_final: 0.7843 (p) REVERT: B 906 MET cc_start: 0.9469 (mmm) cc_final: 0.9174 (mmm) REVERT: B 1008 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.8362 (mt0) REVERT: D 22 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8630 (pp) REVERT: D 276 ASN cc_start: 0.8431 (m110) cc_final: 0.8097 (m-40) REVERT: D 336 PHE cc_start: 0.8502 (m-80) cc_final: 0.8171 (m-80) REVERT: E 232 LYS cc_start: 0.8159 (ptmm) cc_final: 0.7417 (mmtp) REVERT: E 283 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8266 (tttt) REVERT: E 960 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8229 (t0) REVERT: E 1013 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8856 (tt) outliers start: 71 outliers final: 58 residues processed: 301 average time/residue: 0.1519 time to fit residues: 73.9049 Evaluate side-chains 324 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 260 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 878 SER Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 1008 GLN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 695 LEU Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 746 TYR Chi-restraints excluded: chain E residue 790 PHE Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain E residue 960 ASN Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 1013 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 166 optimal weight: 0.8980 chunk 265 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 275 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 145 GLN B 835 GLN B 894 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.116404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.089596 restraints weight = 44014.394| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.24 r_work: 0.2497 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22634 Z= 0.160 Angle : 0.573 10.533 30601 Z= 0.305 Chirality : 0.044 0.170 3239 Planarity : 0.004 0.066 3999 Dihedral : 6.413 81.257 3188 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.65 % Favored : 94.31 % Rotamer: Outliers : 2.79 % Allowed : 15.74 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.07 (0.16), residues: 2781 helix: 0.30 (0.23), residues: 584 sheet: 0.15 (0.18), residues: 790 loop : -1.70 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 238 TYR 0.018 0.001 TYR B 514 PHE 0.016 0.001 PHE B 990 TRP 0.013 0.001 TRP E 697 HIS 0.006 0.001 HIS E 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (22630) covalent geometry : angle 0.57319 / 0.31 (30601) hydrogen bonds : bond 0.03789 / 2.48 ( 917) hydrogen bonds : angle 4.67106 / 3.24 ( 2533) Misc. bond : bond 0.00021 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 260 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.8161 (t0) cc_final: 0.7554 (p0) REVERT: A 214 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8381 (m) REVERT: A 348 LYS cc_start: 0.7762 (mtpt) cc_final: 0.7321 (tttm) REVERT: A 422 GLU cc_start: 0.8228 (mm-30) cc_final: 0.8009 (mt-10) REVERT: B 417 MET cc_start: 0.9050 (mmm) cc_final: 0.8712 (mmt) REVERT: B 436 MET cc_start: 0.8898 (mtm) cc_final: 0.8514 (mtp) REVERT: B 602 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7526 (mmtp) REVERT: B 604 MET cc_start: 0.8549 (ttp) cc_final: 0.8158 (ttp) REVERT: B 638 ASN cc_start: 0.8792 (m-40) cc_final: 0.8049 (t0) REVERT: B 788 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8748 (mtpp) REVERT: B 790 PHE cc_start: 0.9346 (OUTLIER) cc_final: 0.8895 (p90) REVERT: B 861 THR cc_start: 0.9070 (t) cc_final: 0.8788 (m) REVERT: B 906 MET cc_start: 0.9481 (mmm) cc_final: 0.9203 (mmm) REVERT: B 1008 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.8427 (mt0) REVERT: D 22 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8656 (pp) REVERT: D 276 ASN cc_start: 0.8434 (m110) cc_final: 0.8099 (m-40) REVERT: D 334 GLU cc_start: 0.7317 (pm20) cc_final: 0.7075 (pm20) REVERT: D 336 PHE cc_start: 0.8446 (m-80) cc_final: 0.8106 (m-80) REVERT: E 232 LYS cc_start: 0.8148 (ptmm) cc_final: 0.7425 (mmtp) REVERT: E 282 GLN cc_start: 0.9056 (tp-100) cc_final: 0.8815 (tp-100) REVERT: E 283 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8339 (tttt) REVERT: E 960 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8213 (t0) REVERT: E 1013 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8876 (tt) outliers start: 65 outliers final: 53 residues processed: 298 average time/residue: 0.1480 time to fit residues: 71.4907 Evaluate side-chains 317 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 257 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 790 PHE Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 878 SER Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 894 ASN Chi-restraints excluded: chain B residue 1008 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 695 LEU Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 746 TYR Chi-restraints excluded: chain E residue 790 PHE Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain E residue 960 ASN Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 1013 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 41 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 145 GLN B 748 ASN B 835 GLN B 894 ASN B 932 GLN E 481 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.113493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.086627 restraints weight = 33004.993| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.56 r_work: 0.2505 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2363 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2340 r_free = 0.2340 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2340 r_free = 0.2340 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 22634 Z= 0.317 Angle : 0.696 11.307 30601 Z= 0.369 Chirality : 0.049 0.188 3239 Planarity : 0.005 0.101 3999 Dihedral : 6.928 80.214 3186 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.27 % Favored : 92.70 % Rotamer: Outliers : 3.17 % Allowed : 15.57 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.28 (0.16), residues: 2781 helix: 0.22 (0.22), residues: 569 sheet: -0.09 (0.18), residues: 824 loop : -1.82 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 490 TYR 0.022 0.002 TYR B 514 PHE 0.022 0.002 PHE E 791 TRP 0.013 0.001 TRP E 697 HIS 0.009 0.002 HIS E 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00776 / 0.32 (22630) covalent geometry : angle 0.69630 / 0.37 (30601) hydrogen bonds : bond 0.05021 / 3.30 ( 917) hydrogen bonds : angle 4.91469 / 3.41 ( 2533) Misc. bond : bond 0.00029 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 261 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 214 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8391 (m) REVERT: A 348 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7382 (ttpt) REVERT: A 422 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8124 (mt-10) REVERT: B 417 MET cc_start: 0.9156 (mmm) cc_final: 0.8720 (mmt) REVERT: B 436 MET cc_start: 0.8987 (mtm) cc_final: 0.8693 (mtp) REVERT: B 602 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7679 (mmtp) REVERT: B 638 ASN cc_start: 0.8921 (m-40) cc_final: 0.8100 (t0) REVERT: B 788 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8794 (mtpp) REVERT: B 790 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9153 (p90) REVERT: B 854 THR cc_start: 0.8391 (m) cc_final: 0.7924 (p) REVERT: B 906 MET cc_start: 0.9513 (mmm) cc_final: 0.9240 (mmm) REVERT: B 1008 GLN cc_start: 0.9434 (OUTLIER) cc_final: 0.8458 (mt0) REVERT: D 22 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8695 (pp) REVERT: D 276 ASN cc_start: 0.8514 (m110) cc_final: 0.8179 (m-40) REVERT: D 334 GLU cc_start: 0.7293 (pm20) cc_final: 0.7049 (pm20) REVERT: D 336 PHE cc_start: 0.8543 (m-80) cc_final: 0.8246 (m-80) REVERT: E 232 LYS cc_start: 0.8343 (ptmm) cc_final: 0.7498 (mmtp) REVERT: E 282 GLN cc_start: 0.9082 (tp-100) cc_final: 0.8842 (tp-100) REVERT: E 283 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8422 (tttt) REVERT: E 960 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8220 (t0) REVERT: E 1013 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8976 (tt) outliers start: 74 outliers final: 63 residues processed: 303 average time/residue: 0.1469 time to fit residues: 71.7452 Evaluate side-chains 330 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 260 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 790 PHE Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 878 SER Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 894 ASN Chi-restraints excluded: chain B residue 1008 GLN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 695 LEU Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 790 PHE Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain E residue 960 ASN Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 1013 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 199 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 chunk 227 optimal weight: 0.7980 chunk 224 optimal weight: 0.9980 chunk 251 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 chunk 217 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 145 GLN B 748 ASN B 778 ASN B 835 GLN B 894 ASN E 481 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.119071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.092303 restraints weight = 36055.604| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.77 r_work: 0.2587 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22634 Z= 0.098 Angle : 0.530 10.500 30601 Z= 0.283 Chirality : 0.042 0.161 3239 Planarity : 0.004 0.062 3999 Dihedral : 6.056 81.766 3186 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.15 % Favored : 94.82 % Rotamer: Outliers : 2.36 % Allowed : 16.39 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.89 (0.16), residues: 2781 helix: 0.53 (0.23), residues: 580 sheet: 0.20 (0.18), residues: 792 loop : -1.57 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 238 TYR 0.045 0.001 TYR E 637 PHE 0.014 0.001 PHE B 712 TRP 0.016 0.001 TRP A 161 HIS 0.004 0.001 HIS B 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (22630) covalent geometry : angle 0.52977 / 0.28 (30601) hydrogen bonds : bond 0.03092 / 2.02 ( 917) hydrogen bonds : angle 4.52634 / 3.14 ( 2533) Misc. bond : bond 0.00016 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 280 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.8044 (t0) cc_final: 0.7548 (p0) REVERT: A 348 LYS cc_start: 0.7707 (mtpt) cc_final: 0.7302 (tttm) REVERT: B 232 LYS cc_start: 0.8542 (mttm) cc_final: 0.8196 (mmtp) REVERT: B 417 MET cc_start: 0.8945 (mmm) cc_final: 0.8725 (mmt) REVERT: B 604 MET cc_start: 0.8427 (ttp) cc_final: 0.8029 (ttp) REVERT: B 638 ASN cc_start: 0.8715 (m-40) cc_final: 0.7977 (t0) REVERT: B 788 LYS cc_start: 0.8937 (ttmt) cc_final: 0.8681 (mtpp) REVERT: B 861 THR cc_start: 0.8886 (t) cc_final: 0.8625 (m) REVERT: B 906 MET cc_start: 0.9438 (mmm) cc_final: 0.9158 (mmm) REVERT: B 1008 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8392 (mt0) REVERT: D 22 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8599 (pp) REVERT: D 276 ASN cc_start: 0.8369 (m110) cc_final: 0.8039 (m-40) REVERT: D 316 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7503 (pttt) REVERT: D 334 GLU cc_start: 0.7279 (pm20) cc_final: 0.7018 (pm20) REVERT: D 336 PHE cc_start: 0.8429 (m-80) cc_final: 0.8077 (m-80) REVERT: E 232 LYS cc_start: 0.8116 (ptmm) cc_final: 0.7450 (mmtp) REVERT: E 283 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8454 (tttt) REVERT: E 765 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7364 (mp) REVERT: E 960 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8283 (t0) REVERT: E 1013 ILE cc_start: 0.9058 (tp) cc_final: 0.8826 (tt) outliers start: 55 outliers final: 40 residues processed: 310 average time/residue: 0.1505 time to fit residues: 74.8010 Evaluate side-chains 311 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 1008 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 746 TYR Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 790 PHE Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain E residue 960 ASN Chi-restraints excluded: chain E residue 962 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 189 optimal weight: 0.9990 chunk 204 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 250 optimal weight: 0.0170 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 266 optimal weight: 8.9990 chunk 228 optimal weight: 4.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 835 GLN B 894 ASN ** E 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 704 ASN E 997 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.114916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.088237 restraints weight = 39727.588| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.93 r_work: 0.2489 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22634 Z= 0.236 Angle : 0.634 11.300 30601 Z= 0.336 Chirality : 0.046 0.181 3239 Planarity : 0.005 0.079 3999 Dihedral : 6.438 80.003 3185 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.51 % Favored : 93.45 % Rotamer: Outliers : 2.23 % Allowed : 16.65 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.00 (0.16), residues: 2781 helix: 0.33 (0.23), residues: 585 sheet: 0.17 (0.18), residues: 793 loop : -1.63 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 238 TYR 0.022 0.002 TYR B 514 PHE 0.019 0.002 PHE B 990 TRP 0.009 0.001 TRP E 697 HIS 0.009 0.001 HIS E 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (22630) covalent geometry : angle 0.63388 / 0.34 (30601) hydrogen bonds : bond 0.04360 / 2.86 ( 917) hydrogen bonds : angle 4.70253 / 3.26 ( 2533) Misc. bond : bond 0.00022 / 0.01 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 256 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.8144 (t0) cc_final: 0.7521 (p0) REVERT: A 348 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7327 (ttpt) REVERT: B 417 MET cc_start: 0.9072 (mmm) cc_final: 0.8678 (mmt) REVERT: B 436 MET cc_start: 0.8934 (mtm) cc_final: 0.8466 (mtp) REVERT: B 602 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7395 (mmtm) REVERT: B 604 MET cc_start: 0.8527 (ttp) cc_final: 0.8069 (ttp) REVERT: B 638 ASN cc_start: 0.8790 (m-40) cc_final: 0.8031 (t0) REVERT: B 788 LYS cc_start: 0.9011 (ttmt) cc_final: 0.8738 (mtpp) REVERT: B 906 MET cc_start: 0.9473 (mmm) cc_final: 0.9185 (mmm) REVERT: B 1008 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.8375 (mt0) REVERT: D 22 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8654 (pp) REVERT: D 276 ASN cc_start: 0.8400 (m110) cc_final: 0.8067 (m-40) REVERT: D 334 GLU cc_start: 0.7334 (pm20) cc_final: 0.7065 (pm20) REVERT: D 336 PHE cc_start: 0.8464 (m-80) cc_final: 0.8096 (m-80) REVERT: E 232 LYS cc_start: 0.8125 (ptmm) cc_final: 0.7419 (mmtp) REVERT: E 283 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8499 (tttt) REVERT: E 922 ASN cc_start: 0.7869 (t0) cc_final: 0.7536 (t0) REVERT: E 960 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8237 (t0) REVERT: E 1013 ILE cc_start: 0.9068 (tp) cc_final: 0.8852 (tt) outliers start: 52 outliers final: 46 residues processed: 286 average time/residue: 0.1513 time to fit residues: 70.2086 Evaluate side-chains 305 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 894 ASN Chi-restraints excluded: chain B residue 1008 GLN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 790 PHE Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain E residue 960 ASN Chi-restraints excluded: chain E residue 962 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 185 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 145 GLN B 835 GLN B 894 ASN B 932 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.115800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.090289 restraints weight = 28785.468| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.16 r_work: 0.2588 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2429 r_free = 0.2429 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2429 r_free = 0.2429 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22634 Z= 0.186 Angle : 0.604 10.951 30601 Z= 0.321 Chirality : 0.045 0.174 3239 Planarity : 0.004 0.068 3999 Dihedral : 6.376 80.396 3185 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.83 % Favored : 94.13 % Rotamer: Outliers : 2.49 % Allowed : 16.65 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.96 (0.16), residues: 2781 helix: 0.38 (0.23), residues: 583 sheet: 0.19 (0.18), residues: 794 loop : -1.60 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 238 TYR 0.020 0.002 TYR B 514 PHE 0.018 0.001 PHE B 990 TRP 0.012 0.001 TRP E 697 HIS 0.006 0.001 HIS E 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (22630) covalent geometry : angle 0.60444 / 0.32 (30601) hydrogen bonds : bond 0.04027 / 2.64 ( 917) hydrogen bonds : angle 4.67998 / 3.25 ( 2533) Misc. bond : bond 0.00020 / 0.01 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5618.37 seconds wall clock time: 96 minutes 49.16 seconds (5809.16 seconds total)