Starting phenix.real_space_refine on Fri Mar 6 01:27:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ole_12979/03_2026/7ole_12979_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ole_12979/03_2026/7ole_12979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ole_12979/03_2026/7ole_12979_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ole_12979/03_2026/7ole_12979_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ole_12979/03_2026/7ole_12979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ole_12979/03_2026/7ole_12979.map" } resolution = 3.41 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 88 5.16 5 C 16678 2.51 5 N 4879 2.21 5 O 5340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26995 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3328 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3209 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3281 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3224 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3156 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3232 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 3208 Classifications: {'peptide': 644} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 632} Link IDs: {'CIS': 1, 'TRANS': 642} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1282 Unresolved non-hydrogen angles: 1924 Unresolved non-hydrogen dihedrals: 638 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 638} Unresolved non-hydrogen planarities: 640 Chain: "J" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 2273 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 449} Link IDs: {'CIS': 2, 'TRANS': 453} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 901 Unresolved non-hydrogen angles: 1351 Unresolved non-hydrogen dihedrals: 450 Planarities with less than four sites: {'UNK:plan-1': 450} Unresolved non-hydrogen planarities: 451 Chain: "K" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 138 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "K" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 25} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'UNK:plan-1': 10, 'ARG:plan': 2, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 355 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 3, 'TRANS': 68} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'UNK:plan-1': 8, 'ASP:plan': 1, 'GLN:plan1': 5, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 110 Chain: "K" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1316 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 231} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 253} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 759 Unresolved non-hydrogen angles: 975 Unresolved non-hydrogen dihedrals: 595 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'UNK:plan-1': 18, 'ASN:plan1': 5, 'ARG:plan': 19, 'GLN:plan1': 20, 'GLU:plan': 15, 'PHE:plan': 6, 'TYR:plan': 2, 'ASP:plan': 7, 'HIS:plan': 5, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.07, per 1000 atoms: 0.26 Number of scatterers: 26995 At special positions: 0 Unit cell: (199.02, 190.46, 154.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 10 15.00 O 5340 8.00 N 4879 7.00 C 16678 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 Atom "HETATM26882 O3A ADP B 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=8, symmetry=0 Links applied TRANS " UNK K 39 " - " TYR K 38 " " UNK K 67 " - " LEU K 66 " " UNK K 139 " - " GLY K 138 " Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 834.4 milliseconds 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7584 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 32 sheets defined 80.5% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 145 through 150 removed outlier: 4.151A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.851A pdb=" N SER A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.543A pdb=" N LEU A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.625A pdb=" N LYS A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 414 through 417 removed outlier: 3.581A pdb=" N LEU A 417 " --> pdb=" O HIS A 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 417' Processing helix chain 'A' and resid 445 through 448 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 485 through 499 removed outlier: 4.426A pdb=" N GLU A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 507 through 518 Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.793A pdb=" N VAL A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 550 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 49 through 65 removed outlier: 3.518A pdb=" N GLU B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 95 Processing helix chain 'B' and resid 104 through 109 removed outlier: 3.868A pdb=" N ILE B 108 " --> pdb=" O GLY B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 175 through 182 removed outlier: 3.739A pdb=" N GLU B 180 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 269 through 284 removed outlier: 3.792A pdb=" N ARG B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 305 through 318 removed outlier: 4.142A pdb=" N SER B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 373 through 376 Processing helix chain 'B' and resid 384 through 397 removed outlier: 3.572A pdb=" N ILE B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 435 through 452 removed outlier: 3.571A pdb=" N GLN B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N MET B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR B 446 " --> pdb=" O TYR B 442 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 450 " --> pdb=" O TYR B 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.609A pdb=" N ALA C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.552A pdb=" N VAL C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 removed outlier: 4.145A pdb=" N LYS C 182 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU C 183 " --> pdb=" O LEU C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 183' Processing helix chain 'C' and resid 240 through 249 removed outlier: 4.249A pdb=" N ARG C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 290 removed outlier: 3.543A pdb=" N ARG C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 308 through 315 removed outlier: 3.821A pdb=" N PHE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 321 removed outlier: 4.017A pdb=" N SER C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 383 removed outlier: 4.160A pdb=" N GLN C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 removed outlier: 3.907A pdb=" N HIS C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 394 " --> pdb=" O ALA C 390 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 409 through 421 removed outlier: 3.601A pdb=" N ASN C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 434 removed outlier: 3.857A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 451 Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 49 through 65 Processing helix chain 'D' and resid 83 through 95 removed outlier: 3.586A pdb=" N ALA D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.627A pdb=" N PHE D 109 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 114 through 125 Processing helix chain 'D' and resid 177 through 185 removed outlier: 4.757A pdb=" N SER D 181 " --> pdb=" O LYS D 177 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D 182 " --> pdb=" O MET D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 251 removed outlier: 3.898A pdb=" N ASP D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.595A pdb=" N GLU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.585A pdb=" N PHE D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 353 removed outlier: 3.830A pdb=" N ARG D 353 " --> pdb=" O ASP D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 379 removed outlier: 3.921A pdb=" N THR D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 390 removed outlier: 3.539A pdb=" N VAL D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 395 Processing helix chain 'D' and resid 398 through 417 removed outlier: 3.894A pdb=" N GLN D 404 " --> pdb=" O ARG D 400 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 411 " --> pdb=" O THR D 407 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 440 Processing helix chain 'D' and resid 440 through 451 Processing helix chain 'E' and resid 11 through 15 Processing helix chain 'E' and resid 16 through 21 removed outlier: 4.123A pdb=" N HIS E 20 " --> pdb=" O SER E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 58 Processing helix chain 'E' and resid 75 through 88 Processing helix chain 'E' and resid 99 through 102 Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.636A pdb=" N VAL E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 184 Processing helix chain 'E' and resid 239 through 247 removed outlier: 3.849A pdb=" N LEU E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 289 removed outlier: 3.715A pdb=" N ARG E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN E 280 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS E 281 " --> pdb=" O GLY E 277 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 308 through 320 removed outlier: 3.550A pdb=" N PHE E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 357 removed outlier: 4.091A pdb=" N ARG E 357 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 383 removed outlier: 4.522A pdb=" N GLN E 373 " --> pdb=" O GLN E 369 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN E 380 " --> pdb=" O LYS E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 401 removed outlier: 4.198A pdb=" N LEU E 391 " --> pdb=" O SER E 387 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU E 396 " --> pdb=" O ASN E 392 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE E 397 " --> pdb=" O HIS E 393 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 407 Processing helix chain 'E' and resid 409 through 420 removed outlier: 3.956A pdb=" N LEU E 416 " --> pdb=" O PRO E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 437 removed outlier: 3.657A pdb=" N VAL E 430 " --> pdb=" O GLU E 426 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE E 433 " --> pdb=" O HIS E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 451 Processing helix chain 'F' and resid 49 through 65 Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.674A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 109 Processing helix chain 'F' and resid 114 through 126 Processing helix chain 'F' and resid 178 through 185 removed outlier: 4.107A pdb=" N ASP F 185 " --> pdb=" O SER F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 251 removed outlier: 3.648A pdb=" N ASN F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 287 removed outlier: 3.935A pdb=" N ARG F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA F 281 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU F 282 " --> pdb=" O ALA F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 378 removed outlier: 3.977A pdb=" N THR F 367 " --> pdb=" O SER F 363 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 removed outlier: 3.544A pdb=" N ILE F 393 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 396 " --> pdb=" O ARG F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 416 removed outlier: 4.031A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 435 through 452 Processing helix chain 'H' and resid 40 through 55 Processing helix chain 'H' and resid 63 through 82 Processing helix chain 'H' and resid 87 through 111 Processing helix chain 'H' and resid 113 through 135 removed outlier: 3.768A pdb=" N UNK H 133 " --> pdb=" O UNK H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 156 Processing helix chain 'H' and resid 156 through 161 Processing helix chain 'H' and resid 161 through 176 removed outlier: 4.160A pdb=" N UNK H 166 " --> pdb=" O UNK H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 191 Processing helix chain 'H' and resid 192 through 197 Processing helix chain 'H' and resid 198 through 219 removed outlier: 3.732A pdb=" N UNK H 218 " --> pdb=" O UNK H 214 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N UNK H 219 " --> pdb=" O UNK H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 239 Processing helix chain 'H' and resid 240 through 245 Processing helix chain 'H' and resid 245 through 256 Processing helix chain 'H' and resid 263 through 277 Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 296 through 309 Processing helix chain 'H' and resid 313 through 333 Processing helix chain 'H' and resid 339 through 360 removed outlier: 3.813A pdb=" N UNK H 343 " --> pdb=" O UNK H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 376 removed outlier: 3.590A pdb=" N UNK H 376 " --> pdb=" O UNK H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 390 removed outlier: 3.723A pdb=" N GLY H 383 " --> pdb=" O UNK H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 391 through 400 Processing helix chain 'H' and resid 401 through 414 Processing helix chain 'H' and resid 416 through 429 Processing helix chain 'H' and resid 434 through 450 Processing helix chain 'H' and resid 453 through 472 Processing helix chain 'H' and resid 473 through 475 No H-bonds generated for 'chain 'H' and resid 473 through 475' Processing helix chain 'H' and resid 476 through 495 removed outlier: 3.684A pdb=" N UNK H 495 " --> pdb=" O UNK H 491 " (cutoff:3.500A) Processing helix chain 'H' and resid 497 through 516 removed outlier: 3.827A pdb=" N UNK H 502 " --> pdb=" O UNK H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 520 through 540 Processing helix chain 'H' and resid 541 through 554 Processing helix chain 'H' and resid 560 through 572 Processing helix chain 'H' and resid 582 through 598 removed outlier: 4.388A pdb=" N UNK H 593 " --> pdb=" O UNK H 589 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N UNK H 594 " --> pdb=" O UNK H 590 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK H 598 " --> pdb=" O UNK H 594 " (cutoff:3.500A) Processing helix chain 'H' and resid 601 through 618 Processing helix chain 'H' and resid 621 through 636 removed outlier: 3.557A pdb=" N UNK H 635 " --> pdb=" O UNK H 631 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N UNK H 636 " --> pdb=" O UNK H 632 " (cutoff:3.500A) Processing helix chain 'H' and resid 637 through 647 Processing helix chain 'H' and resid 650 through 660 Processing helix chain 'H' and resid 669 through 682 Processing helix chain 'J' and resid 45 through 60 Processing helix chain 'J' and resid 71 through 83 Processing helix chain 'J' and resid 87 through 101 removed outlier: 3.590A pdb=" N UNK J 101 " --> pdb=" O UNK J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 122 Processing helix chain 'J' and resid 126 through 147 Processing helix chain 'J' and resid 152 through 170 WARNING: missing atoms! removed outlier: 4.277A pdb=" N UNK J 170 " --> pdb=" O GLY J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 191 removed outlier: 4.405A pdb=" N UNK J 191 " --> pdb=" O UNK J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 211 removed outlier: 3.672A pdb=" N UNK J 200 " --> pdb=" O UNK J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 231 Processing helix chain 'J' and resid 233 through 239 Processing helix chain 'J' and resid 243 through 263 Processing helix chain 'J' and resid 266 through 280 Processing helix chain 'J' and resid 287 through 304 removed outlier: 3.820A pdb=" N UNK J 295 " --> pdb=" O UNK J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 329 Processing helix chain 'J' and resid 331 through 349 Processing helix chain 'J' and resid 352 through 376 removed outlier: 4.016A pdb=" N UNK J 371 " --> pdb=" O UNK J 367 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N UNK J 374 " --> pdb=" O UNK J 370 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 395 removed outlier: 4.098A pdb=" N UNK J 381 " --> pdb=" O UNK J 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 396 through 420 Processing helix chain 'J' and resid 424 through 445 removed outlier: 4.037A pdb=" N UNK J 428 " --> pdb=" O UNK J 424 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N UNK J 429 " --> pdb=" O UNK J 425 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N UNK J 430 " --> pdb=" O UNK J 426 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N UNK J 433 " --> pdb=" O UNK J 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 451 Processing helix chain 'J' and resid 457 through 475 Processing helix chain 'J' and resid 479 through 494 Processing helix chain 'J' and resid 496 through 508 Processing helix chain 'K' and resid 12 through 22 Processing helix chain 'K' and resid 24 through 38 removed outlier: 4.054A pdb=" N LEU K 35 " --> pdb=" O THR K 31 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS K 36 " --> pdb=" O LEU K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 58 removed outlier: 3.970A pdb=" N UNK K 45 " --> pdb=" O UNK K 41 " (cutoff:3.500A) Proline residue: K 50 - end of helix Processing helix chain 'K' and resid 58 through 67 removed outlier: 3.823A pdb=" N LEU K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 86 removed outlier: 3.786A pdb=" N GLN K 78 " --> pdb=" O UNK K 74 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA K 79 " --> pdb=" O PRO K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 103 Processing helix chain 'K' and resid 105 through 137 Proline residue: K 127 - end of helix Processing helix chain 'K' and resid 142 through 163 removed outlier: 4.388A pdb=" N UNK K 156 " --> pdb=" O UNK K 152 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY K 157 " --> pdb=" O UNK K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 190 Processing helix chain 'K' and resid 197 through 214 Processing helix chain 'K' and resid 215 through 233 removed outlier: 3.822A pdb=" N ILE K 219 " --> pdb=" O ARG K 215 " (cutoff:3.500A) Proline residue: K 225 - end of helix Processing helix chain 'K' and resid 235 through 245 Processing helix chain 'K' and resid 248 through 264 Processing helix chain 'K' and resid 264 through 277 Processing helix chain 'K' and resid 282 through 295 Processing helix chain 'K' and resid 299 through 317 Processing helix chain 'K' and resid 319 through 333 removed outlier: 3.812A pdb=" N GLU K 330 " --> pdb=" O LYS K 326 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY K 333 " --> pdb=" O LEU K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 340 Processing helix chain 'K' and resid 343 through 359 Processing helix chain 'K' and resid 363 through 385 Processing helix chain 'K' and resid 388 through 403 Processing sheet with id=AA1, first strand: chain 'A' and resid 222 through 229 Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 259 Processing sheet with id=AA3, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.331A pdb=" N GLY A 395 " --> pdb=" O ILE A 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 434 through 435 removed outlier: 4.222A pdb=" N CYS A 434 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 444 " --> pdb=" O CYS A 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 484 removed outlier: 7.282A pdb=" N ASN A 483 " --> pdb=" O ILE A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.738A pdb=" N SER B 43 " --> pdb=" O MET B 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 72 through 76 removed outlier: 6.925A pdb=" N ALA B 72 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL B 357 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 74 " --> pdb=" O VAL B 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.585A pdb=" N THR B 101 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 243 Processing sheet with id=AB1, first strand: chain 'B' and resid 132 through 138 Processing sheet with id=AB2, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AB3, first strand: chain 'B' and resid 332 through 334 Processing sheet with id=AB4, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.612A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 236 through 239 Processing sheet with id=AB6, first strand: chain 'C' and resid 202 through 204 removed outlier: 4.682A pdb=" N ARG C 202 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR C 192 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY C 204 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 157 through 162 Processing sheet with id=AB8, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AB9, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.405A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AC2, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AC3, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AC4, first strand: chain 'E' and resid 96 through 97 removed outlier: 6.868A pdb=" N MET E 96 " --> pdb=" O ASP E 302 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL E 66 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N SER E 331 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU E 68 " --> pdb=" O SER E 331 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 230 through 237 Processing sheet with id=AC6, first strand: chain 'E' and resid 157 through 159 Processing sheet with id=AC7, first strand: chain 'E' and resid 162 through 163 Processing sheet with id=AC8, first strand: chain 'E' and resid 335 through 337 Processing sheet with id=AC9, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.188A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 239 through 243 Processing sheet with id=AD2, first strand: chain 'F' and resid 135 through 136 Processing sheet with id=AD3, first strand: chain 'F' and resid 141 through 142 Processing sheet with id=AD4, first strand: chain 'F' and resid 193 through 194 Processing sheet with id=AD5, first strand: chain 'F' and resid 332 through 334 1638 hydrogen bonds defined for protein. 4764 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: 4.67 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 4832 1.26 - 1.40: 5695 1.40 - 1.54: 16338 1.54 - 1.68: 214 1.68 - 1.83: 151 Bond restraints: 27230 Sorted by residual: bond pdb=" C GLU K 268 " pdb=" O GLU K 268 " ideal model delta sigma weight residual 1.236 1.126 0.110 1.15e-02 7.56e+03 9.17e+01 bond pdb=" C GLN K 120 " pdb=" O GLN K 120 " ideal model delta sigma weight residual 1.236 1.118 0.118 1.29e-02 6.01e+03 8.33e+01 bond pdb=" CA VAL K 380 " pdb=" C VAL K 380 " ideal model delta sigma weight residual 1.524 1.421 0.103 1.16e-02 7.43e+03 7.92e+01 bond pdb=" C LYS K 280 " pdb=" O LYS K 280 " ideal model delta sigma weight residual 1.232 1.351 -0.118 1.38e-02 5.25e+03 7.33e+01 bond pdb=" C VAL K 380 " pdb=" O VAL K 380 " ideal model delta sigma weight residual 1.237 1.142 0.095 1.12e-02 7.97e+03 7.20e+01 ... (remaining 27225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.72: 36907 8.72 - 17.43: 155 17.43 - 26.15: 23 26.15 - 34.87: 3 34.87 - 43.58: 1 Bond angle restraints: 37089 Sorted by residual: angle pdb=" C ARG K 318 " pdb=" N PRO K 319 " pdb=" CA PRO K 319 " ideal model delta sigma weight residual 119.84 154.17 -34.33 1.25e+00 6.40e-01 7.54e+02 angle pdb=" N LEU K 273 " pdb=" CA LEU K 273 " pdb=" C LEU K 273 " ideal model delta sigma weight residual 111.03 91.22 19.81 1.11e+00 8.12e-01 3.18e+02 angle pdb=" C PHE K 169 " pdb=" N PRO K 170 " pdb=" CA PRO K 170 " ideal model delta sigma weight residual 119.19 134.97 -15.78 1.06e+00 8.90e-01 2.22e+02 angle pdb=" N VAL K 279 " pdb=" CA VAL K 279 " pdb=" C VAL K 279 " ideal model delta sigma weight residual 108.27 128.46 -20.19 1.37e+00 5.33e-01 2.17e+02 angle pdb=" N UNK H 311 " pdb=" CA UNK H 311 " pdb=" C UNK H 311 " ideal model delta sigma weight residual 110.74 154.32 -43.58 3.00e+00 1.11e-01 2.11e+02 ... (remaining 37084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 16321 35.01 - 70.03: 274 70.03 - 105.04: 31 105.04 - 140.05: 6 140.05 - 175.07: 2 Dihedral angle restraints: 16634 sinusoidal: 4984 harmonic: 11650 Sorted by residual: dihedral pdb=" CA UNK J 242 " pdb=" C UNK J 242 " pdb=" N UNK J 243 " pdb=" CA UNK J 243 " ideal model delta harmonic sigma weight residual 180.00 64.65 115.35 0 5.00e+00 4.00e-02 5.32e+02 dihedral pdb=" CA UNK J 349 " pdb=" C UNK J 349 " pdb=" N UNK J 350 " pdb=" CA UNK J 350 " ideal model delta harmonic sigma weight residual 180.00 87.76 92.24 0 5.00e+00 4.00e-02 3.40e+02 dihedral pdb=" CA UNK H 177 " pdb=" C UNK H 177 " pdb=" N UNK H 178 " pdb=" CA UNK H 178 " ideal model delta harmonic sigma weight residual 180.00 89.23 90.77 0 5.00e+00 4.00e-02 3.30e+02 ... (remaining 16631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.337: 4556 0.337 - 0.675: 40 0.675 - 1.012: 12 1.012 - 1.350: 1 1.350 - 1.687: 1 Chirality restraints: 4610 Sorted by residual: chirality pdb=" CA UNK J 241 " pdb=" N UNK J 241 " pdb=" C UNK J 241 " pdb=" CB UNK J 241 " both_signs ideal model delta sigma weight residual False 2.52 0.83 1.69 2.00e-01 2.50e+01 7.12e+01 chirality pdb=" CA UNK H 311 " pdb=" N UNK H 311 " pdb=" C UNK H 311 " pdb=" CB UNK H 311 " both_signs ideal model delta sigma weight residual False 2.52 1.21 1.32 2.00e-01 2.50e+01 4.32e+01 chirality pdb=" CA UNK J 287 " pdb=" N UNK J 287 " pdb=" C UNK J 287 " pdb=" CB UNK J 287 " both_signs ideal model delta sigma weight residual False 2.52 1.54 0.98 2.00e-01 2.50e+01 2.40e+01 ... (remaining 4607 not shown) Planarity restraints: 4906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY K 214 " -0.075 2.00e-02 2.50e+03 1.39e-01 1.94e+02 pdb=" C GLY K 214 " 0.241 2.00e-02 2.50e+03 pdb=" O GLY K 214 " -0.089 2.00e-02 2.50e+03 pdb=" N ARG K 215 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK J 59 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C UNK J 59 " 0.216 2.00e-02 2.50e+03 pdb=" O UNK J 59 " -0.080 2.00e-02 2.50e+03 pdb=" N UNK J 60 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK H 497 " -0.063 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C UNK H 497 " 0.193 2.00e-02 2.50e+03 pdb=" O UNK H 497 " -0.067 2.00e-02 2.50e+03 pdb=" N UNK H 498 " -0.063 2.00e-02 2.50e+03 ... (remaining 4903 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 56 2.14 - 2.83: 10784 2.83 - 3.52: 46019 3.52 - 4.21: 64236 4.21 - 4.90: 104019 Nonbonded interactions: 225114 Sorted by model distance: nonbonded pdb=" O UNK H 376 " pdb=" CB UNK H 381 " model vdw 1.448 3.440 nonbonded pdb=" CB UNK J 393 " pdb=" O GLY J 400 " model vdw 1.456 3.440 nonbonded pdb=" O GLN K 171 " pdb=" CB PHE K 174 " model vdw 1.614 3.440 nonbonded pdb=" O ALA K 91 " pdb=" CB SER K 94 " model vdw 1.699 3.440 nonbonded pdb=" O LEU A 124 " pdb=" OG SER B 410 " model vdw 1.781 3.040 ... (remaining 225109 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 103 through 238 or resid 254 through 346 or (resid 369 thr \ ough 370 and (name N or name CA or name C or name O or name CB )) or resid 371 o \ r (resid 372 through 374 and (name N or name CA or name C or name O or name CB ) \ ) or resid 375 through 501 or (resid 502 and (name N or name CA or name C or nam \ e O or name CB )) or resid 503 through 550)) selection = (chain 'C' and (resid 5 through 140 or resid 156 through 248 or (resid 271 throu \ gh 272 and (name N or name CA or name C or name O or name CB )) or resid 273 or \ (resid 274 through 276 and (name N or name CA or name C or name O or name CB )) \ or resid 277 through 403 or (resid 404 and (name N or name CA or name C or name \ O or name CB )) or resid 405 through 452)) selection = (chain 'E' and (resid 5 through 248 or resid 271 through 452)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 23 through 253 or resid 267 through 269 or (resid 270 and \ (name N or name CA or name C or name O or name CB )) or resid 271 through 451 or \ (resid 452 through 453 and (name N or name CA or name C or name O or name CB )) \ or resid 501)) selection = (chain 'F' and (resid 23 through 252 or (resid 253 through 267 and (name N or na \ me CA or name C or name O or name CB )) or resid 268 through 451 or (resid 452 t \ hrough 453 and (name N or name CA or name C or name O or name CB )) or resid 501 \ )) } 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=0.01 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.640 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2731 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 : 0.013 0.274 27241 Z= 0.803 Angle : 1.742 43.583 37098 Z= 0.969 Chirality : 0.099 1.687 4610 Planarity : 0.009 0.139 4903 Dihedral : 15.119 175.065 9041 Min Nonbonded Distance : 1.448 Molprobity Statistics. All-atom Clashscore : 42.01 Ramachandran Plot: Outliers : 0.84 % Allowed : 17.25 % Favored : 81.91 % Rotamer: Outliers : 0.38 % Allowed : 13.07 % Favored : 86.55 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.68 % 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: -5.68 (0.11), residues: 2853 helix: -3.72 (0.10), residues: 1119 sheet: -2.69 (0.28), residues: 258 loop : -4.12 (0.13), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 144 TYR 0.023 0.003 TYR E 209 PHE 0.033 0.002 PHE A 398 TRP 0.024 0.002 TRP D 283 HIS 0.012 0.002 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.01295 (27230) covalent geometry : angle 1.74181 (37089) hydrogen bonds : bond 0.23310 ( 1638) hydrogen bonds : angle 8.90173 ( 4764) Misc. bond : bond 0.14898 ( 8) link_TRANS : bond 0.00850 ( 3) link_TRANS : angle 1.09155 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 349 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6714 (tp30) cc_final: 0.6307 (tp30) REVERT: A 216 ARG cc_start: 0.4324 (tpm170) cc_final: 0.3246 (ptm160) REVERT: A 330 LYS cc_start: 0.7812 (tptp) cc_final: 0.7592 (ptpt) REVERT: A 392 LEU cc_start: 0.8792 (pp) cc_final: 0.8579 (mt) REVERT: A 403 HIS cc_start: 0.3952 (t70) cc_final: 0.3139 (t-90) REVERT: A 404 MET cc_start: 0.4137 (ttm) cc_final: 0.3929 (ttp) REVERT: A 425 VAL cc_start: 0.1041 (p) cc_final: 0.0769 (p) REVERT: A 448 ILE cc_start: 0.2709 (pt) cc_final: 0.2277 (pt) REVERT: A 456 VAL cc_start: 0.3238 (m) cc_final: 0.2193 (m) REVERT: A 469 MET cc_start: 0.7468 (mtp) cc_final: 0.6772 (mmm) REVERT: A 473 ILE cc_start: 0.7302 (mp) cc_final: 0.6926 (mt) REVERT: A 476 ARG cc_start: 0.2922 (mmt180) cc_final: 0.1892 (ptp-170) REVERT: B 46 MET cc_start: -0.2700 (ptt) cc_final: -0.2952 (ptt) REVERT: B 62 MET cc_start: 0.5981 (mtp) cc_final: 0.5711 (mmt) REVERT: B 67 LYS cc_start: 0.5770 (mttt) cc_final: 0.5429 (ttpt) REVERT: B 94 LEU cc_start: 0.3009 (tp) cc_final: 0.2559 (tt) REVERT: B 168 MET cc_start: 0.2637 (ptp) cc_final: 0.2427 (ttp) REVERT: B 250 ILE cc_start: 0.5199 (mt) cc_final: 0.4409 (mt) REVERT: C 315 LEU cc_start: 0.7484 (mt) cc_final: 0.7216 (mt) REVERT: D 382 MET cc_start: 0.7197 (ttt) cc_final: 0.6974 (ttt) REVERT: F 297 PHE cc_start: 0.5288 (t80) cc_final: 0.4972 (t80) outliers start: 8 outliers final: 1 residues processed: 356 average time/residue: 0.1694 time to fit residues: 94.5861 Evaluate side-chains 212 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN A 491 HIS A 548 GLN B 121 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 251 ASN B 313 ASN B 341 GLN B 422 GLN B 441 GLN C 18 HIS ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 284 ASN C 305 HIS C 316 HIS C 451 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 302 HIS D 341 GLN D 369 GLN E 34 GLN E 42 GLN E 156 HIS E 181 GLN E 289 GLN F 92 GLN ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN F 341 GLN F 447 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.112774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.090768 restraints weight = 199120.581| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 7.45 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27241 Z= 0.205 Angle : 0.916 14.777 37098 Z= 0.449 Chirality : 0.046 0.311 4610 Planarity : 0.005 0.084 4903 Dihedral : 8.833 156.602 4257 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.38 % Favored : 89.24 % Rotamer: Outliers : 3.37 % Allowed : 18.25 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.43 % 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: -3.55 (0.14), residues: 2853 helix: -1.24 (0.14), residues: 1242 sheet: -2.15 (0.27), residues: 295 loop : -3.59 (0.14), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 144 TYR 0.030 0.002 TYR E 192 PHE 0.023 0.002 PHE F 297 TRP 0.015 0.001 TRP D 283 HIS 0.013 0.002 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00412 (27230) covalent geometry : angle 0.91587 (37089) hydrogen bonds : bond 0.05658 ( 1638) hydrogen bonds : angle 6.17365 ( 4764) Misc. bond : bond 0.00143 ( 8) link_TRANS : bond 0.00253 ( 3) link_TRANS : angle 0.66755 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 233 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.5940 (tp30) cc_final: 0.5531 (mt-10) REVERT: A 216 ARG cc_start: 0.4917 (tpm170) cc_final: 0.3704 (ptm160) REVERT: A 304 CYS cc_start: 0.7968 (m) cc_final: 0.7606 (p) REVERT: A 330 LYS cc_start: 0.8634 (tptp) cc_final: 0.8383 (ptpt) REVERT: A 407 ILE cc_start: 0.5013 (mp) cc_final: 0.4709 (mp) REVERT: A 450 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6736 (pp) REVERT: A 473 ILE cc_start: 0.5110 (OUTLIER) cc_final: 0.4428 (mt) REVERT: B 125 ARG cc_start: 0.5725 (tpp80) cc_final: 0.5512 (tpt90) REVERT: B 168 MET cc_start: 0.2462 (ptp) cc_final: 0.2194 (ttp) REVERT: B 170 THR cc_start: 0.4142 (OUTLIER) cc_final: 0.3783 (p) REVERT: B 250 ILE cc_start: 0.5775 (mt) cc_final: 0.5518 (mt) REVERT: B 325 ILE cc_start: 0.6305 (OUTLIER) cc_final: 0.6083 (pt) REVERT: D 243 SER cc_start: 0.7573 (OUTLIER) cc_final: 0.7182 (p) REVERT: D 382 MET cc_start: 0.6164 (ttt) cc_final: 0.5753 (ttt) outliers start: 71 outliers final: 24 residues processed: 288 average time/residue: 0.1538 time to fit residues: 72.5029 Evaluate side-chains 212 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 344 HIS Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 431 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 20.0000 chunk 252 optimal weight: 50.0000 chunk 188 optimal weight: 20.0000 chunk 259 optimal weight: 50.0000 chunk 80 optimal weight: 7.9990 chunk 254 optimal weight: 50.0000 chunk 247 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 44 optimal weight: 0.5980 chunk 219 optimal weight: 8.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS E 42 GLN E 229 HIS F 25 HIS F 226 GLN F 341 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.104529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.080382 restraints weight = 196528.265| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 7.71 r_work: 0.3750 rms_B_bonded: 7.45 restraints_weight: 2.0000 r_work: 0.3840 rms_B_bonded: 5.39 restraints_weight: 4.0000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.8295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 27241 Z= 0.278 Angle : 0.985 15.719 37098 Z= 0.487 Chirality : 0.049 0.383 4610 Planarity : 0.006 0.075 4903 Dihedral : 8.307 170.936 4255 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.65 % Favored : 87.10 % Rotamer: Outliers : 6.27 % Allowed : 20.58 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.25 % 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: -3.24 (0.14), residues: 2853 helix: -0.98 (0.14), residues: 1245 sheet: -1.87 (0.29), residues: 297 loop : -3.47 (0.15), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 276 TYR 0.024 0.003 TYR C 366 PHE 0.026 0.003 PHE A 535 TRP 0.020 0.002 TRP D 283 HIS 0.010 0.002 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00597 (27230) covalent geometry : angle 0.98503 (37089) hydrogen bonds : bond 0.05298 ( 1638) hydrogen bonds : angle 5.81054 ( 4764) Misc. bond : bond 0.00137 ( 8) link_TRANS : bond 0.00226 ( 3) link_TRANS : angle 0.74693 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 194 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6892 (tp30) cc_final: 0.6074 (tp30) REVERT: A 384 TYR cc_start: 0.6068 (OUTLIER) cc_final: 0.5608 (m-10) REVERT: A 402 VAL cc_start: 0.0870 (OUTLIER) cc_final: 0.0539 (t) REVERT: A 463 LEU cc_start: 0.3273 (OUTLIER) cc_final: 0.2927 (pp) REVERT: A 507 LEU cc_start: 0.8065 (mt) cc_final: 0.7565 (tt) REVERT: A 526 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6929 (pm20) REVERT: B 168 MET cc_start: 0.2445 (ptp) cc_final: 0.2111 (ttp) REVERT: B 232 LEU cc_start: 0.0163 (OUTLIER) cc_final: -0.0419 (mt) REVERT: B 250 ILE cc_start: 0.6155 (OUTLIER) cc_final: 0.5912 (mt) REVERT: B 382 MET cc_start: 0.1041 (tpt) cc_final: -0.0828 (ttm) REVERT: C 52 ILE cc_start: 0.1146 (OUTLIER) cc_final: 0.0923 (tt) REVERT: C 310 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8581 (mm-30) REVERT: D 204 LYS cc_start: 0.4831 (tmtt) cc_final: 0.4628 (tptp) REVERT: E 316 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.8246 (t70) REVERT: E 359 MET cc_start: 0.8956 (mpp) cc_final: 0.8463 (mtt) REVERT: F 86 ILE cc_start: 0.8912 (mt) cc_final: 0.8614 (mm) outliers start: 132 outliers final: 45 residues processed: 305 average time/residue: 0.1452 time to fit residues: 73.8334 Evaluate side-chains 192 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 138 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 189 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 chunk 77 optimal weight: 0.1980 chunk 198 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.104965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.080443 restraints weight = 193268.598| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 7.99 r_work: 0.3729 rms_B_bonded: 7.84 restraints_weight: 2.0000 r_work: 0.3803 rms_B_bonded: 6.29 restraints_weight: 4.0000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.8785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27241 Z= 0.156 Angle : 0.776 14.652 37098 Z= 0.375 Chirality : 0.042 0.264 4610 Planarity : 0.004 0.079 4903 Dihedral : 7.533 172.180 4255 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.78 % Favored : 89.98 % Rotamer: Outliers : 3.47 % Allowed : 22.62 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.22 % 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: -2.58 (0.15), residues: 2853 helix: -0.37 (0.14), residues: 1258 sheet: -1.51 (0.29), residues: 296 loop : -3.22 (0.15), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 273 TYR 0.019 0.001 TYR F 172 PHE 0.018 0.002 PHE D 433 TRP 0.014 0.001 TRP D 283 HIS 0.008 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00320 (27230) covalent geometry : angle 0.77578 (37089) hydrogen bonds : bond 0.04179 ( 1638) hydrogen bonds : angle 5.16596 ( 4764) Misc. bond : bond 0.00058 ( 8) link_TRANS : bond 0.00174 ( 3) link_TRANS : angle 0.69733 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 156 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.6708 (tpp) cc_final: 0.6491 (mmp) REVERT: A 212 GLU cc_start: 0.7185 (tp30) cc_final: 0.6317 (tp30) REVERT: A 384 TYR cc_start: 0.6074 (OUTLIER) cc_final: 0.5693 (m-10) REVERT: A 469 MET cc_start: 0.8235 (mtp) cc_final: 0.7571 (mtm) REVERT: A 473 ILE cc_start: 0.6312 (OUTLIER) cc_final: 0.5603 (mt) REVERT: A 507 LEU cc_start: 0.8309 (mt) cc_final: 0.7707 (tt) REVERT: A 526 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: B 168 MET cc_start: 0.2541 (ptp) cc_final: 0.2216 (ttp) REVERT: B 170 THR cc_start: 0.4713 (OUTLIER) cc_final: 0.4354 (p) REVERT: B 250 ILE cc_start: 0.6344 (mt) cc_final: 0.6062 (mt) REVERT: B 382 MET cc_start: 0.0457 (tpt) cc_final: -0.1489 (ttm) REVERT: C 371 MET cc_start: 0.9105 (tpp) cc_final: 0.8573 (mpp) REVERT: E 359 MET cc_start: 0.8959 (mpp) cc_final: 0.8515 (mtt) outliers start: 73 outliers final: 35 residues processed: 222 average time/residue: 0.1498 time to fit residues: 54.8463 Evaluate side-chains 165 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 32 optimal weight: 0.6980 chunk 262 optimal weight: 40.0000 chunk 58 optimal weight: 8.9990 chunk 108 optimal weight: 0.2980 chunk 255 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 267 optimal weight: 8.9990 chunk 57 optimal weight: 40.0000 chunk 248 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN B 369 GLN C 369 GLN ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.100440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.078633 restraints weight = 189618.501| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 8.78 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 1.0371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27241 Z= 0.209 Angle : 0.843 16.054 37098 Z= 0.413 Chirality : 0.045 0.254 4610 Planarity : 0.005 0.105 4903 Dihedral : 7.557 167.762 4255 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.94 % Favored : 88.85 % Rotamer: Outliers : 4.80 % Allowed : 23.15 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.25 % 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: -2.41 (0.15), residues: 2853 helix: -0.23 (0.14), residues: 1255 sheet: -1.39 (0.30), residues: 285 loop : -3.12 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 124 TYR 0.023 0.002 TYR B 442 PHE 0.022 0.002 PHE F 100 TRP 0.015 0.002 TRP D 283 HIS 0.009 0.002 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00446 (27230) covalent geometry : angle 0.84351 (37089) hydrogen bonds : bond 0.04441 ( 1638) hydrogen bonds : angle 5.13082 ( 4764) Misc. bond : bond 0.00142 ( 8) link_TRANS : bond 0.00205 ( 3) link_TRANS : angle 0.72444 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 134 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.4787 (OUTLIER) cc_final: 0.3148 (mt) REVERT: A 145 GLU cc_start: 0.3608 (OUTLIER) cc_final: 0.1760 (tm-30) REVERT: A 211 MET cc_start: 0.7626 (tpp) cc_final: 0.7372 (mmp) REVERT: A 216 ARG cc_start: 0.7648 (tpm170) cc_final: 0.7179 (ttp-170) REVERT: A 337 THR cc_start: 0.7134 (p) cc_final: 0.6485 (t) REVERT: A 429 SER cc_start: 0.6671 (m) cc_final: 0.6183 (t) REVERT: A 469 MET cc_start: 0.8659 (mtp) cc_final: 0.8254 (mtp) REVERT: A 507 LEU cc_start: 0.8977 (mt) cc_final: 0.8506 (tt) REVERT: A 526 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: B 113 MET cc_start: 0.8003 (mmm) cc_final: 0.7532 (mmp) REVERT: B 250 ILE cc_start: 0.7237 (OUTLIER) cc_final: 0.6937 (mt) REVERT: B 368 LYS cc_start: 0.9317 (tttm) cc_final: 0.9021 (tptp) REVERT: B 382 MET cc_start: 0.1774 (tpt) cc_final: 0.0215 (tmm) REVERT: B 404 GLN cc_start: 0.3220 (OUTLIER) cc_final: 0.2439 (mm-40) REVERT: B 435 ASP cc_start: 0.7402 (m-30) cc_final: 0.6957 (p0) REVERT: E 371 MET cc_start: 0.8684 (mtp) cc_final: 0.8383 (mtp) REVERT: F 304 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8685 (tt) outliers start: 101 outliers final: 51 residues processed: 226 average time/residue: 0.1476 time to fit residues: 55.8482 Evaluate side-chains 172 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 115 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 404 GLN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 101 optimal weight: 50.0000 chunk 251 optimal weight: 30.0000 chunk 212 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN C 156 HIS ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.097156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.074153 restraints weight = 188234.183| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 8.34 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 1.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 27241 Z= 0.260 Angle : 0.889 16.107 37098 Z= 0.434 Chirality : 0.046 0.290 4610 Planarity : 0.005 0.061 4903 Dihedral : 7.658 143.305 4255 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.25 % Favored : 88.54 % Rotamer: Outliers : 4.13 % Allowed : 23.91 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.29 % 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: -2.43 (0.15), residues: 2853 helix: -0.29 (0.14), residues: 1251 sheet: -1.24 (0.31), residues: 288 loop : -3.13 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 53 TYR 0.035 0.002 TYR F 387 PHE 0.049 0.002 PHE F 100 TRP 0.024 0.002 TRP D 283 HIS 0.012 0.002 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00568 (27230) covalent geometry : angle 0.88859 (37089) hydrogen bonds : bond 0.04431 ( 1638) hydrogen bonds : angle 5.31528 ( 4764) Misc. bond : bond 0.00139 ( 8) link_TRANS : bond 0.00250 ( 3) link_TRANS : angle 0.74612 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 113 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 SER cc_start: 0.7098 (m) cc_final: 0.6590 (t) REVERT: A 463 LEU cc_start: 0.2409 (OUTLIER) cc_final: 0.2123 (tp) REVERT: B 88 MET cc_start: 0.9102 (tpt) cc_final: 0.8759 (tpp) REVERT: C 358 VAL cc_start: 0.8708 (m) cc_final: 0.8474 (m) REVERT: D 193 ILE cc_start: 0.0221 (OUTLIER) cc_final: -0.1139 (mp) REVERT: D 204 LYS cc_start: 0.4517 (tptp) cc_final: 0.4106 (mmtt) REVERT: D 231 GLU cc_start: 0.5661 (OUTLIER) cc_final: 0.5423 (pm20) REVERT: D 450 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7988 (p90) REVERT: E 371 MET cc_start: 0.8657 (mtp) cc_final: 0.8365 (mtp) REVERT: F 304 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8745 (tt) outliers start: 87 outliers final: 48 residues processed: 194 average time/residue: 0.1388 time to fit residues: 45.2302 Evaluate side-chains 158 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 105 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 204 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 262 optimal weight: 30.0000 chunk 181 optimal weight: 30.0000 chunk 208 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 231 optimal weight: 3.9990 chunk 220 optimal weight: 0.5980 chunk 267 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN B 44 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 GLN F 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.098334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.075572 restraints weight = 188116.447| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 8.24 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 1.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27241 Z= 0.157 Angle : 0.756 15.463 37098 Z= 0.366 Chirality : 0.042 0.318 4610 Planarity : 0.004 0.059 4903 Dihedral : 7.152 132.235 4255 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.23 % Favored : 89.55 % Rotamer: Outliers : 3.37 % Allowed : 25.19 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.25 % 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: -2.10 (0.16), residues: 2853 helix: 0.02 (0.15), residues: 1265 sheet: -0.96 (0.32), residues: 271 loop : -3.03 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 372 TYR 0.019 0.001 TYR A 318 PHE 0.040 0.002 PHE D 452 TRP 0.014 0.001 TRP D 283 HIS 0.008 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00334 (27230) covalent geometry : angle 0.75597 (37089) hydrogen bonds : bond 0.03948 ( 1638) hydrogen bonds : angle 4.89548 ( 4764) Misc. bond : bond 0.00103 ( 8) link_TRANS : bond 0.00190 ( 3) link_TRANS : angle 0.70469 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 118 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7172 (tppt) REVERT: A 124 LEU cc_start: 0.8559 (pt) cc_final: 0.7419 (tt) REVERT: A 141 GLU cc_start: 0.8678 (tt0) cc_final: 0.8347 (mm-30) REVERT: A 159 MET cc_start: 0.5520 (ppp) cc_final: 0.5063 (ppp) REVERT: A 429 SER cc_start: 0.6804 (m) cc_final: 0.6291 (t) REVERT: B 88 MET cc_start: 0.9138 (tpt) cc_final: 0.8765 (tpp) REVERT: B 320 MET cc_start: 0.7965 (tpp) cc_final: 0.7504 (tpt) REVERT: C 371 MET cc_start: 0.9137 (mmm) cc_final: 0.8766 (mmt) REVERT: D 193 ILE cc_start: -0.0911 (OUTLIER) cc_final: -0.1885 (mp) REVERT: D 231 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.5659 (pm20) REVERT: D 450 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8106 (p90) REVERT: E 371 MET cc_start: 0.8609 (mtp) cc_final: 0.8357 (mtp) REVERT: F 304 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8815 (tt) outliers start: 71 outliers final: 43 residues processed: 184 average time/residue: 0.1400 time to fit residues: 43.6517 Evaluate side-chains 157 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 109 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 27 optimal weight: 6.9990 chunk 144 optimal weight: 0.1980 chunk 106 optimal weight: 9.9990 chunk 228 optimal weight: 0.0870 chunk 248 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 264 optimal weight: 40.0000 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.099184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.076957 restraints weight = 189329.123| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 8.03 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 1.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27241 Z= 0.137 Angle : 0.738 14.958 37098 Z= 0.358 Chirality : 0.042 0.316 4610 Planarity : 0.004 0.059 4903 Dihedral : 6.771 112.934 4255 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.74 % Favored : 90.08 % Rotamer: Outliers : 2.66 % Allowed : 25.62 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.16), residues: 2853 helix: 0.24 (0.15), residues: 1262 sheet: -0.86 (0.32), residues: 276 loop : -2.86 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.014 0.001 TYR F 387 PHE 0.057 0.002 PHE F 309 TRP 0.010 0.001 TRP D 283 HIS 0.008 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00284 (27230) covalent geometry : angle 0.73849 (37089) hydrogen bonds : bond 0.03718 ( 1638) hydrogen bonds : angle 4.65116 ( 4764) Misc. bond : bond 0.00100 ( 8) link_TRANS : bond 0.00187 ( 3) link_TRANS : angle 0.68414 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 112 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.8479 (pt) cc_final: 0.8029 (mp) REVERT: A 159 MET cc_start: 0.4949 (ppp) cc_final: 0.4390 (ppp) REVERT: A 429 SER cc_start: 0.6820 (m) cc_final: 0.5600 (t) REVERT: B 88 MET cc_start: 0.9360 (tpt) cc_final: 0.8839 (tpp) REVERT: B 320 MET cc_start: 0.8200 (tpp) cc_final: 0.7745 (tpt) REVERT: B 382 MET cc_start: 0.1525 (tpt) cc_final: -0.1014 (tmm) REVERT: B 406 ILE cc_start: 0.8094 (tt) cc_final: 0.7875 (tt) REVERT: C 371 MET cc_start: 0.9137 (mmm) cc_final: 0.8889 (mmt) REVERT: D 450 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8060 (p90) REVERT: E 61 MET cc_start: 0.8299 (tpp) cc_final: 0.7893 (mpp) REVERT: E 371 MET cc_start: 0.8662 (mtp) cc_final: 0.8415 (mtp) REVERT: F 49 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8843 (mm-40) outliers start: 56 outliers final: 36 residues processed: 164 average time/residue: 0.1504 time to fit residues: 41.2167 Evaluate side-chains 143 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 154 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 256 optimal weight: 50.0000 chunk 79 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 HIS ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 GLN E 236 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.097972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.075080 restraints weight = 188151.453| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 8.11 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 1.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27241 Z= 0.159 Angle : 0.746 14.885 37098 Z= 0.361 Chirality : 0.042 0.316 4610 Planarity : 0.004 0.059 4903 Dihedral : 6.746 113.041 4255 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.30 % Favored : 89.52 % Rotamer: Outliers : 2.57 % Allowed : 25.81 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.16), residues: 2853 helix: 0.29 (0.15), residues: 1263 sheet: -0.88 (0.32), residues: 276 loop : -2.83 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 357 TYR 0.017 0.002 TYR A 464 PHE 0.016 0.002 PHE F 100 TRP 0.011 0.001 TRP D 283 HIS 0.011 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00343 (27230) covalent geometry : angle 0.74563 (37089) hydrogen bonds : bond 0.03745 ( 1638) hydrogen bonds : angle 4.66414 ( 4764) Misc. bond : bond 0.00112 ( 8) link_TRANS : bond 0.00201 ( 3) link_TRANS : angle 0.69587 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 107 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.5297 (ppp) cc_final: 0.4739 (ppp) REVERT: A 429 SER cc_start: 0.6963 (m) cc_final: 0.6353 (t) REVERT: B 88 MET cc_start: 0.9313 (tpt) cc_final: 0.8895 (tpp) REVERT: C 371 MET cc_start: 0.9118 (mmm) cc_final: 0.8872 (mmt) REVERT: D 450 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8147 (p90) REVERT: E 61 MET cc_start: 0.8425 (tpp) cc_final: 0.8061 (mpp) REVERT: E 371 MET cc_start: 0.8675 (mtp) cc_final: 0.8427 (mtp) REVERT: F 49 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8820 (mm-40) REVERT: F 443 MET cc_start: 0.9078 (tpp) cc_final: 0.8713 (ttm) outliers start: 54 outliers final: 41 residues processed: 157 average time/residue: 0.1524 time to fit residues: 40.3249 Evaluate side-chains 146 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 HIS Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 217 optimal weight: 4.9990 chunk 181 optimal weight: 0.5980 chunk 278 optimal weight: 30.0000 chunk 53 optimal weight: 0.9980 chunk 250 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 273 optimal weight: 40.0000 chunk 266 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.098039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.075098 restraints weight = 187230.649| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 7.65 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 1.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27241 Z= 0.148 Angle : 0.748 14.754 37098 Z= 0.362 Chirality : 0.042 0.297 4610 Planarity : 0.004 0.072 4903 Dihedral : 6.657 111.909 4255 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.71 % Favored : 90.12 % Rotamer: Outliers : 2.09 % Allowed : 26.43 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.14 % 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: -1.71 (0.16), residues: 2853 helix: 0.31 (0.15), residues: 1273 sheet: -0.83 (0.32), residues: 274 loop : -2.78 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 357 TYR 0.019 0.001 TYR C 314 PHE 0.034 0.002 PHE D 452 TRP 0.010 0.001 TRP D 283 HIS 0.023 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00317 (27230) covalent geometry : angle 0.74797 (37089) hydrogen bonds : bond 0.03669 ( 1638) hydrogen bonds : angle 4.61647 ( 4764) Misc. bond : bond 0.00106 ( 8) link_TRANS : bond 0.00194 ( 3) link_TRANS : angle 0.68279 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.8308 (pt) cc_final: 0.8044 (mp) REVERT: A 220 LEU cc_start: 0.7492 (mp) cc_final: 0.7195 (mt) REVERT: A 429 SER cc_start: 0.6679 (m) cc_final: 0.5702 (t) REVERT: B 88 MET cc_start: 0.9321 (tpt) cc_final: 0.8923 (tpp) REVERT: B 320 MET cc_start: 0.8231 (tpp) cc_final: 0.7805 (tpt) REVERT: C 359 MET cc_start: 0.6417 (mmm) cc_final: 0.6139 (mmm) REVERT: C 371 MET cc_start: 0.9098 (mmm) cc_final: 0.8858 (mmt) REVERT: D 123 PHE cc_start: 0.9545 (OUTLIER) cc_final: 0.9198 (t80) REVERT: D 450 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8065 (p90) REVERT: D 452 PHE cc_start: 0.8238 (m-80) cc_final: 0.8038 (m-80) REVERT: E 61 MET cc_start: 0.8447 (tpp) cc_final: 0.8112 (mpp) REVERT: E 371 MET cc_start: 0.8628 (mtp) cc_final: 0.8384 (mtp) REVERT: F 49 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8781 (mm-40) REVERT: F 326 MET cc_start: 0.8926 (mpp) cc_final: 0.8571 (mtm) REVERT: F 443 MET cc_start: 0.9048 (tpp) cc_final: 0.8572 (ttm) outliers start: 44 outliers final: 37 residues processed: 150 average time/residue: 0.1474 time to fit residues: 37.1444 Evaluate side-chains 147 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 51 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 256 optimal weight: 30.0000 chunk 250 optimal weight: 8.9990 chunk 262 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 234 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 HIS D 44 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 GLN E 236 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.095703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.073027 restraints weight = 185763.191| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 8.04 r_work: 0.3437 rms_B_bonded: 7.87 restraints_weight: 2.0000 r_work: 0.3530 rms_B_bonded: 5.26 restraints_weight: 4.0000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 1.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27241 Z= 0.202 Angle : 0.807 15.271 37098 Z= 0.395 Chirality : 0.044 0.301 4610 Planarity : 0.005 0.076 4903 Dihedral : 6.953 114.615 4255 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.08 % Favored : 88.75 % Rotamer: Outliers : 2.38 % Allowed : 25.95 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.88 (0.16), residues: 2853 helix: 0.16 (0.15), residues: 1268 sheet: -1.05 (0.31), residues: 279 loop : -2.83 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 357 TYR 0.023 0.002 TYR A 464 PHE 0.059 0.002 PHE F 309 TRP 0.017 0.002 TRP D 283 HIS 0.007 0.002 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00440 (27230) covalent geometry : angle 0.80678 (37089) hydrogen bonds : bond 0.03945 ( 1638) hydrogen bonds : angle 4.85786 ( 4764) Misc. bond : bond 0.00136 ( 8) link_TRANS : bond 0.00231 ( 3) link_TRANS : angle 0.71130 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9418.72 seconds wall clock time: 160 minutes 48.01 seconds (9648.01 seconds total)