Starting phenix.real_space_refine on Mon Jun 23 08:49:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ole_12979/06_2025/7ole_12979_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ole_12979/06_2025/7ole_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ole_12979/06_2025/7ole_12979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ole_12979/06_2025/7ole_12979.map" model { file = "/net/cci-nas-00/data/ceres_data/7ole_12979/06_2025/7ole_12979_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ole_12979/06_2025/7ole_12979_neut.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 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: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS: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: {'GLU:plan': 1, 'HIS: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: {'HIS:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} 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: {'GLU:plan': 1, 'UNK:plan-1': 10, 'TRP:plan': 1, 'ARG:plan': 2} 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: {'GLN:plan1': 5, 'UNK:plan-1': 8, 'ASP:plan': 1, '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: {'GLN:plan1': 20, 'HIS:plan': 5, 'ASN:plan1': 5, 'TYR:plan': 2, 'UNK:plan-1': 18, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 15, 'ARG:plan': 19} 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: 15.79, per 1000 atoms: 0.58 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: 7.80 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.98 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: 9.68 Time building geometry restraints manager: 9.01 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: 1.110 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: 1.070 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 59.450 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.120 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.400 ------------------------------------------------------------------------------- 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 : 42.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.024 0.002 TRP D 283 HIS 0.012 0.002 HIS B 27 PHE 0.033 0.002 PHE A 398 TYR 0.023 0.003 TYR E 209 ARG 0.009 0.001 ARG A 144 Details of bonding type rmsd link_TRANS : bond 0.00850 ( 3) link_TRANS : angle 1.09155 ( 9) hydrogen bonds : bond 0.23310 ( 1638) hydrogen bonds : angle 8.90173 ( 4764) covalent geometry : bond 0.01295 (27230) covalent geometry : angle 1.74181 (37089) Misc. bond : bond 0.14898 ( 8) *********************** 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 : 2.762 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: A 212 GLU cc_start: 0.6714 (tp30) cc_final: 0.6310 (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: 0.8580 (mt) REVERT: A 403 HIS cc_start: 0.3952 (t70) cc_final: 0.3138 (t-90) REVERT: A 404 MET cc_start: 0.4137 (ttm) cc_final: 0.3930 (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: 0.2195 (m) REVERT: A 469 MET cc_start: 0.7468 (mtp) cc_final: 0.6773 (mmm) REVERT: A 473 ILE cc_start: 0.7302 (mp) cc_final: 0.6938 (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: -0.2953 (ptt) REVERT: B 62 MET cc_start: 0.5981 (mtp) cc_final: 0.5713 (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: 0.2429 (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: 0.7226 (mt) REVERT: D 382 MET cc_start: 0.7197 (ttt) cc_final: 0.6975 (ttt) REVERT: F 297 PHE cc_start: 0.5288 (t80) cc_final: 0.4974 (t80) outliers start: 8 outliers final: 1 residues processed: 356 average time/residue: 0.4915 time to fit residues: 277.9440 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 : 3.871 ------------------------------------------------------------------------------- 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 239 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 257 optimal weight: 50.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 548 GLN B 121 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 251 ASN B 313 ASN 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 188 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 HIS F 447 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.113375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.093059 restraints weight = 198635.415| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 7.56 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4073 r_free = 0.4073 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 = 0.4073 r_free = 0.4073 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27241 Z= 0.202 Angle : 0.911 15.165 37098 Z= 0.446 Chirality : 0.045 0.315 4610 Planarity : 0.005 0.083 4903 Dihedral : 8.848 157.788 4257 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.45 % Favored : 89.17 % Rotamer: Outliers : 3.18 % Allowed : 18.01 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.14), residues: 2853 helix: -1.23 (0.14), residues: 1238 sheet: -2.13 (0.27), residues: 294 loop : -3.57 (0.14), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 283 HIS 0.014 0.002 HIS B 27 PHE 0.022 0.002 PHE E 300 TYR 0.036 0.002 TYR E 192 ARG 0.014 0.001 ARG A 144 Details of bonding type rmsd link_TRANS : bond 0.00204 ( 3) link_TRANS : angle 0.69159 ( 9) hydrogen bonds : bond 0.05747 ( 1638) hydrogen bonds : angle 6.18131 ( 4764) covalent geometry : bond 0.00405 (27230) covalent geometry : angle 0.91057 (37089) Misc. bond : bond 0.00144 ( 8) *********************** 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 301 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 234 time to evaluate : 3.143 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: A 159 MET cc_start: 0.6722 (ptm) cc_final: 0.6280 (ppp) REVERT: A 212 GLU cc_start: 0.6217 (tp30) cc_final: 0.5626 (tp30) REVERT: A 216 ARG cc_start: 0.4878 (tpm170) cc_final: 0.4070 (ptm160) REVERT: A 304 CYS cc_start: 0.7930 (m) cc_final: 0.7257 (p) REVERT: A 330 LYS cc_start: 0.8625 (tptp) cc_final: 0.8399 (ttmt) REVERT: A 450 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6775 (pp) REVERT: A 473 ILE cc_start: 0.5568 (OUTLIER) cc_final: 0.5037 (mt) REVERT: B 168 MET cc_start: 0.1333 (ptp) cc_final: 0.0897 (ttp) REVERT: B 170 THR cc_start: -0.1489 (OUTLIER) cc_final: -0.1732 (p) REVERT: B 250 ILE cc_start: 0.5744 (mt) cc_final: 0.5491 (mt) REVERT: C 97 VAL cc_start: 0.6110 (m) cc_final: 0.5550 (m) REVERT: D 218 MET cc_start: 0.0097 (tmm) cc_final: -0.0158 (tpt) REVERT: D 382 MET cc_start: 0.6311 (ttt) cc_final: 0.5812 (ttt) REVERT: D 430 TYR cc_start: 0.8116 (t80) cc_final: 0.7912 (t80) REVERT: E 47 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: F 62 MET cc_start: 0.5827 (tpp) cc_final: 0.5352 (tpp) outliers start: 67 outliers final: 20 residues processed: 286 average time/residue: 0.3628 time to fit residues: 170.6479 Evaluate side-chains 211 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 389 ILE 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 473 ILE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 536 TYR 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 323 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 52 ILE 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 E residue 47 GLU 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 50 LEU 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 152 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 265 optimal weight: 40.0000 chunk 58 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 210 optimal weight: 0.8980 chunk 272 optimal weight: 40.0000 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 19 optimal weight: 30.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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** A 382 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 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 ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS E 42 GLN E 229 HIS F 25 HIS ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.107352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.083377 restraints weight = 195230.699| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 8.17 r_work: 0.3816 rms_B_bonded: 8.00 restraints_weight: 2.0000 r_work: 0.3894 rms_B_bonded: 6.21 restraints_weight: 4.0000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.7177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 27241 Z= 0.231 Angle : 0.906 13.355 37098 Z= 0.446 Chirality : 0.047 0.398 4610 Planarity : 0.005 0.089 4903 Dihedral : 7.921 154.800 4255 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.46 % Favored : 88.29 % Rotamer: Outliers : 5.42 % Allowed : 20.34 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.15), residues: 2853 helix: -0.55 (0.14), residues: 1203 sheet: -1.80 (0.29), residues: 302 loop : -3.21 (0.15), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 283 HIS 0.013 0.002 HIS A 118 PHE 0.026 0.003 PHE A 535 TYR 0.023 0.002 TYR A 384 ARG 0.021 0.001 ARG B 125 Details of bonding type rmsd link_TRANS : bond 0.00193 ( 3) link_TRANS : angle 0.72164 ( 9) hydrogen bonds : bond 0.04920 ( 1638) hydrogen bonds : angle 5.57538 ( 4764) covalent geometry : bond 0.00487 (27230) covalent geometry : angle 0.90572 (37089) Misc. bond : bond 0.00149 ( 8) *********************** 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 320 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 206 time to evaluate : 2.783 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: A 212 GLU cc_start: 0.6975 (tp30) cc_final: 0.6333 (tp30) REVERT: A 216 ARG cc_start: 0.6749 (tpm170) cc_final: 0.5703 (ptm160) REVERT: A 330 LYS cc_start: 0.8486 (tptp) cc_final: 0.8165 (ptpt) REVERT: A 410 PHE cc_start: 0.7310 (m-10) cc_final: 0.7015 (m-80) REVERT: A 458 ILE cc_start: 0.3436 (OUTLIER) cc_final: 0.3231 (tt) REVERT: A 526 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6554 (pm20) REVERT: B 50 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6715 (tt) REVERT: B 168 MET cc_start: 0.2665 (ptp) cc_final: 0.2381 (ttp) REVERT: B 232 LEU cc_start: 0.1189 (OUTLIER) cc_final: 0.0621 (mt) REVERT: B 250 ILE cc_start: 0.6078 (OUTLIER) cc_final: 0.5855 (mt) REVERT: B 382 MET cc_start: 0.1250 (tpt) cc_final: -0.1467 (ttm) REVERT: C 42 GLN cc_start: 0.0459 (OUTLIER) cc_final: -0.0637 (pp30) REVERT: C 52 ILE cc_start: 0.0338 (OUTLIER) cc_final: 0.0063 (tt) REVERT: C 310 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8548 (mm-30) REVERT: C 315 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8396 (mm) REVERT: C 386 ILE cc_start: 0.7032 (OUTLIER) cc_final: 0.6827 (pt) REVERT: D 178 MET cc_start: 0.5241 (tpp) cc_final: 0.4966 (tpp) REVERT: D 218 MET cc_start: -0.0192 (tmm) cc_final: -0.0510 (tpt) REVERT: E 359 MET cc_start: 0.8836 (mpp) cc_final: 0.8570 (mtm) REVERT: F 98 THR cc_start: 0.6057 (m) cc_final: 0.5764 (p) outliers start: 114 outliers final: 40 residues processed: 303 average time/residue: 0.3443 time to fit residues: 172.0412 Evaluate side-chains 208 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 384 TYR 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 458 ILE Chi-restraints excluded: chain A residue 465 THR 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 73 VAL Chi-restraints excluded: chain B residue 81 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 355 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 67 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 396 GLU 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 154 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 chunk 262 optimal weight: 50.0000 chunk 24 optimal weight: 1.9990 chunk 265 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 225 optimal weight: 40.0000 chunk 126 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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** B 313 ASN C 145 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN F 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.104683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.083260 restraints weight = 192918.284| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 7.82 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.8512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27241 Z= 0.203 Angle : 0.801 15.036 37098 Z= 0.390 Chirality : 0.044 0.280 4610 Planarity : 0.004 0.060 4903 Dihedral : 7.509 176.899 4255 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.57 % Favored : 90.22 % Rotamer: Outliers : 4.28 % Allowed : 22.10 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.15), residues: 2853 helix: -0.27 (0.14), residues: 1262 sheet: -1.65 (0.28), residues: 293 loop : -3.12 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 283 HIS 0.009 0.002 HIS A 118 PHE 0.018 0.002 PHE D 452 TYR 0.022 0.002 TYR F 387 ARG 0.007 0.001 ARG F 124 Details of bonding type rmsd link_TRANS : bond 0.00197 ( 3) link_TRANS : angle 0.73189 ( 9) hydrogen bonds : bond 0.04246 ( 1638) hydrogen bonds : angle 5.13813 ( 4764) covalent geometry : bond 0.00392 (27230) covalent geometry : angle 0.80079 (37089) Misc. bond : bond 0.00120 ( 8) *********************** 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 242 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 152 time to evaluate : 3.571 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 159 MET cc_start: 0.5596 (ppp) cc_final: 0.5359 (ppp) REVERT: A 211 MET cc_start: 0.6641 (tpp) cc_final: 0.6195 (mmp) REVERT: A 212 GLU cc_start: 0.7045 (tp30) cc_final: 0.6177 (tp30) REVERT: A 330 LYS cc_start: 0.8690 (tptp) cc_final: 0.8315 (ptpt) REVERT: A 384 TYR cc_start: 0.6115 (OUTLIER) cc_final: 0.5696 (m-10) REVERT: A 473 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6908 (mt) REVERT: A 507 LEU cc_start: 0.8049 (mt) cc_final: 0.7408 (tt) REVERT: A 526 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: A 529 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7995 (mm-30) REVERT: B 168 MET cc_start: 0.0886 (ptp) cc_final: 0.0204 (ttp) REVERT: B 250 ILE cc_start: 0.6112 (mt) cc_final: 0.5828 (mt) REVERT: B 360 THR cc_start: 0.7009 (OUTLIER) cc_final: 0.6784 (p) REVERT: B 382 MET cc_start: 0.1788 (tpt) cc_final: -0.0402 (ttm) REVERT: C 116 PHE cc_start: 0.9448 (OUTLIER) cc_final: 0.8931 (t80) REVERT: D 193 ILE cc_start: -0.0293 (OUTLIER) cc_final: -0.0638 (pt) REVERT: D 218 MET cc_start: -0.0259 (tmm) cc_final: -0.0556 (tpt) REVERT: E 359 MET cc_start: 0.9041 (mpp) cc_final: 0.8656 (mtt) outliers start: 90 outliers final: 36 residues processed: 233 average time/residue: 0.4438 time to fit residues: 176.9423 Evaluate side-chains 168 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 4.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 473 ILE 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 81 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 431 SER 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 192 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 31 optimal weight: 0.0000 chunk 202 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 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 42 GLN E 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.104372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.082910 restraints weight = 192037.007| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 7.77 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.9211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27241 Z= 0.147 Angle : 0.737 14.013 37098 Z= 0.356 Chirality : 0.042 0.278 4610 Planarity : 0.004 0.061 4903 Dihedral : 7.098 163.818 4255 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.13 % Favored : 89.66 % Rotamer: Outliers : 3.85 % Allowed : 23.19 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.15), residues: 2853 helix: 0.13 (0.15), residues: 1248 sheet: -1.43 (0.28), residues: 304 loop : -2.93 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 283 HIS 0.011 0.001 HIS A 446 PHE 0.015 0.001 PHE F 123 TYR 0.017 0.001 TYR F 442 ARG 0.010 0.001 ARG B 372 Details of bonding type rmsd link_TRANS : bond 0.00173 ( 3) link_TRANS : angle 0.66580 ( 9) hydrogen bonds : bond 0.03934 ( 1638) hydrogen bonds : angle 4.83332 ( 4764) covalent geometry : bond 0.00307 (27230) covalent geometry : angle 0.73701 (37089) Misc. bond : bond 0.00075 ( 8) *********************** 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 221 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 140 time to evaluate : 2.590 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: A 122 LEU cc_start: 0.3698 (OUTLIER) cc_final: 0.1264 (mt) REVERT: A 159 MET cc_start: 0.6000 (ppp) cc_final: 0.5680 (ppp) REVERT: A 211 MET cc_start: 0.7150 (tpp) cc_final: 0.6728 (mmp) REVERT: A 212 GLU cc_start: 0.6975 (tp30) cc_final: 0.6106 (tp30) REVERT: A 316 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5474 (mt-10) REVERT: A 318 TYR cc_start: 0.3322 (m-80) cc_final: 0.3042 (m-10) REVERT: A 330 LYS cc_start: 0.8597 (tptp) cc_final: 0.8201 (ptpt) REVERT: A 429 SER cc_start: 0.5684 (m) cc_final: 0.5409 (t) REVERT: A 469 MET cc_start: 0.8491 (mtp) cc_final: 0.8264 (tmm) REVERT: A 473 ILE cc_start: 0.6533 (OUTLIER) cc_final: 0.5242 (mt) REVERT: A 507 LEU cc_start: 0.8399 (mt) cc_final: 0.7770 (tt) REVERT: A 526 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: A 529 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8194 (mm-30) REVERT: B 113 MET cc_start: 0.7244 (mmm) cc_final: 0.6584 (mmp) REVERT: B 168 MET cc_start: -0.0535 (ptp) cc_final: -0.1307 (ttp) REVERT: B 250 ILE cc_start: 0.6396 (OUTLIER) cc_final: 0.6063 (mt) REVERT: B 382 MET cc_start: 0.1834 (tpt) cc_final: -0.0343 (tmm) REVERT: C 359 MET cc_start: 0.6686 (mtm) cc_final: 0.6248 (mpp) REVERT: C 371 MET cc_start: 0.9095 (tpp) cc_final: 0.8636 (mpp) REVERT: D 204 LYS cc_start: 0.4487 (tptt) cc_final: 0.4042 (tptt) REVERT: E 61 MET cc_start: 0.8317 (tpp) cc_final: 0.7990 (mpp) REVERT: E 359 MET cc_start: 0.9009 (mpp) cc_final: 0.8663 (mtt) REVERT: F 168 MET cc_start: 0.1756 (ptt) cc_final: 0.1430 (ttp) REVERT: F 226 GLN cc_start: -0.1466 (OUTLIER) cc_final: -0.2064 (mt0) outliers start: 81 outliers final: 46 residues processed: 211 average time/residue: 0.3369 time to fit residues: 118.7484 Evaluate side-chains 170 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 473 ILE 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 58 VAL Chi-restraints excluded: chain B residue 63 ILE 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 250 ILE Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 380 GLN Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 209 PHE 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 96 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 396 GLU 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 29 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 223 optimal weight: 50.0000 chunk 31 optimal weight: 0.9980 chunk 281 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 140 optimal weight: 30.0000 chunk 139 optimal weight: 0.0470 chunk 137 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.9680 ------------------------------------------------------------------------------- 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** A 491 HIS ** B 146 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 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.103219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.077929 restraints weight = 191432.332| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 7.36 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.9915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 27241 Z= 0.149 Angle : 0.723 15.148 37098 Z= 0.350 Chirality : 0.041 0.282 4610 Planarity : 0.004 0.069 4903 Dihedral : 6.964 151.474 4255 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.22 % Favored : 90.54 % Rotamer: Outliers : 3.61 % Allowed : 23.86 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.16), residues: 2853 helix: 0.17 (0.15), residues: 1271 sheet: -1.17 (0.30), residues: 273 loop : -2.88 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 283 HIS 0.009 0.001 HIS A 116 PHE 0.016 0.001 PHE B 433 TYR 0.018 0.001 TYR F 387 ARG 0.008 0.001 ARG B 372 Details of bonding type rmsd link_TRANS : bond 0.00186 ( 3) link_TRANS : angle 0.67937 ( 9) hydrogen bonds : bond 0.03778 ( 1638) hydrogen bonds : angle 4.69025 ( 4764) covalent geometry : bond 0.00316 (27230) covalent geometry : angle 0.72297 (37089) Misc. bond : bond 0.00082 ( 8) *********************** 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 188 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 112 time to evaluate : 2.695 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: 0.2940 (OUTLIER) cc_final: 0.0253 (mt) REVERT: A 159 MET cc_start: 0.4286 (ppp) cc_final: 0.3588 (ppp) REVERT: A 216 ARG cc_start: 0.7566 (tpm170) cc_final: 0.7052 (ttp80) REVERT: A 330 LYS cc_start: 0.8662 (tptp) cc_final: 0.8312 (ptpt) REVERT: A 429 SER cc_start: 0.5911 (m) cc_final: 0.5614 (t) REVERT: A 473 ILE cc_start: 0.5500 (OUTLIER) cc_final: 0.4086 (mt) REVERT: A 507 LEU cc_start: 0.8627 (mt) cc_final: 0.8016 (tt) REVERT: A 526 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6266 (pm20) REVERT: A 529 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8190 (pp20) REVERT: B 382 MET cc_start: 0.1559 (tpt) cc_final: -0.1220 (tmm) REVERT: C 342 GLU cc_start: 0.9449 (OUTLIER) cc_final: 0.8993 (pm20) REVERT: E 61 MET cc_start: 0.8358 (tpp) cc_final: 0.8035 (mpp) REVERT: F 88 MET cc_start: 0.8733 (tpt) cc_final: 0.8429 (tpp) outliers start: 76 outliers final: 46 residues processed: 183 average time/residue: 0.3519 time to fit residues: 107.3535 Evaluate side-chains 156 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 203 GLU 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 409 CYS Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 473 ILE 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 58 VAL Chi-restraints excluded: chain B residue 63 ILE 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 374 ARG Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 380 GLN Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 138 ILE 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 450 PHE Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 393 ILE 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 212 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 chunk 98 optimal weight: 0.0980 chunk 219 optimal weight: 9.9990 chunk 84 optimal weight: 0.0270 chunk 148 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 280 optimal weight: 30.0000 chunk 173 optimal weight: 2.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- 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** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.104307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.078939 restraints weight = 191100.933| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 7.81 r_work: 0.3701 rms_B_bonded: 7.78 restraints_weight: 2.0000 r_work: 0.3791 rms_B_bonded: 5.68 restraints_weight: 4.0000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 1.0220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27241 Z= 0.131 Angle : 0.703 14.737 37098 Z= 0.337 Chirality : 0.040 0.265 4610 Planarity : 0.004 0.056 4903 Dihedral : 6.689 133.468 4255 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.25 % Favored : 90.54 % Rotamer: Outliers : 3.18 % Allowed : 24.38 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2853 helix: 0.28 (0.15), residues: 1279 sheet: -0.82 (0.31), residues: 284 loop : -2.78 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 283 HIS 0.013 0.001 HIS A 403 PHE 0.044 0.001 PHE D 452 TYR 0.019 0.001 TYR F 172 ARG 0.007 0.000 ARG A 144 Details of bonding type rmsd link_TRANS : bond 0.00171 ( 3) link_TRANS : angle 0.63857 ( 9) hydrogen bonds : bond 0.03615 ( 1638) hydrogen bonds : angle 4.53418 ( 4764) covalent geometry : bond 0.00264 (27230) covalent geometry : angle 0.70298 (37089) Misc. bond : bond 0.00067 ( 8) *********************** 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 188 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 121 time to evaluate : 3.787 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: A 159 MET cc_start: 0.4727 (ppp) cc_final: 0.3867 (ppp) REVERT: A 174 LYS cc_start: 0.6829 (pptt) cc_final: 0.6298 (pptt) REVERT: A 216 ARG cc_start: 0.7396 (tpm170) cc_final: 0.6773 (ttp80) REVERT: A 330 LYS cc_start: 0.8527 (tptp) cc_final: 0.8180 (ptpt) REVERT: A 404 MET cc_start: 0.5832 (OUTLIER) cc_final: 0.5542 (mmt) REVERT: A 429 SER cc_start: 0.6174 (m) cc_final: 0.5557 (t) REVERT: A 457 MET cc_start: 0.8404 (pmm) cc_final: 0.6699 (tpt) REVERT: A 473 ILE cc_start: 0.5231 (OUTLIER) cc_final: 0.4635 (mt) REVERT: A 507 LEU cc_start: 0.8593 (mt) cc_final: 0.8031 (tt) REVERT: A 529 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8211 (mm-30) REVERT: B 382 MET cc_start: 0.1601 (tpt) cc_final: -0.1145 (tmm) REVERT: C 342 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.8891 (pm20) REVERT: E 61 MET cc_start: 0.8358 (tpp) cc_final: 0.8072 (mpp) REVERT: F 88 MET cc_start: 0.8686 (tpt) cc_final: 0.8417 (tpp) REVERT: F 326 MET cc_start: 0.8573 (mpp) cc_final: 0.7735 (mtm) outliers start: 67 outliers final: 45 residues processed: 179 average time/residue: 0.4181 time to fit residues: 126.4555 Evaluate side-chains 156 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 108 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 212 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 336 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 63 ILE 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 292 ILE Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain C residue 380 GLN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 138 ILE 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 450 PHE Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 393 ILE 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 270 optimal weight: 50.0000 chunk 23 optimal weight: 9.9990 chunk 175 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 111 optimal weight: 0.0060 chunk 6 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 overall best weight: 2.4200 ------------------------------------------------------------------------------- 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 302 HIS C 236 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 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 = 0.4398 r_free = 0.4398 target = 0.101642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.079796 restraints weight = 190724.856| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 8.60 r_work: 0.3583 rms_B_bonded: 8.06 restraints_weight: 2.0000 r_work: 0.3683 rms_B_bonded: 5.30 restraints_weight: 4.0000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 1.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 27241 Z= 0.160 Angle : 0.741 14.425 37098 Z= 0.359 Chirality : 0.042 0.264 4610 Planarity : 0.004 0.057 4903 Dihedral : 6.718 131.085 4255 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.85 % Favored : 89.98 % Rotamer: Outliers : 3.14 % Allowed : 24.62 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2853 helix: 0.32 (0.15), residues: 1270 sheet: -0.71 (0.32), residues: 282 loop : -2.76 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 283 HIS 0.013 0.001 HIS A 403 PHE 0.017 0.002 PHE D 452 TYR 0.022 0.002 TYR F 387 ARG 0.007 0.001 ARG C 357 Details of bonding type rmsd link_TRANS : bond 0.00204 ( 3) link_TRANS : angle 0.68354 ( 9) hydrogen bonds : bond 0.03682 ( 1638) hydrogen bonds : angle 4.57445 ( 4764) covalent geometry : bond 0.00347 (27230) covalent geometry : angle 0.74134 (37089) Misc. bond : bond 0.00090 ( 8) *********************** 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 181 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 115 time to evaluate : 4.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.3215 (OUTLIER) cc_final: 0.1174 (tm-30) REVERT: A 159 MET cc_start: 0.3904 (ppp) cc_final: 0.2618 (ppp) REVERT: A 216 ARG cc_start: 0.7891 (tpm170) cc_final: 0.7187 (ttp-170) REVERT: A 330 LYS cc_start: 0.8651 (tptp) cc_final: 0.8253 (ptpt) REVERT: A 404 MET cc_start: 0.5668 (OUTLIER) cc_final: 0.5465 (mpp) REVERT: A 429 SER cc_start: 0.6762 (m) cc_final: 0.6030 (t) REVERT: A 469 MET cc_start: 0.8647 (tmm) cc_final: 0.8337 (tmm) REVERT: A 507 LEU cc_start: 0.8891 (mt) cc_final: 0.8365 (tt) REVERT: A 526 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: A 529 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8578 (pt0) REVERT: B 382 MET cc_start: 0.2795 (tpt) cc_final: -0.0500 (tmm) REVERT: B 435 ASP cc_start: 0.6904 (m-30) cc_final: 0.6238 (p0) REVERT: C 223 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6636 (mp) REVERT: C 359 MET cc_start: 0.5792 (OUTLIER) cc_final: 0.5092 (mpp) REVERT: D 204 LYS cc_start: 0.4984 (tptt) cc_final: 0.4578 (tptt) REVERT: D 218 MET cc_start: 0.1186 (tmm) cc_final: 0.0839 (tpt) REVERT: E 61 MET cc_start: 0.8695 (tpp) cc_final: 0.8303 (mpp) REVERT: F 74 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.9002 (mp) REVERT: F 88 MET cc_start: 0.8943 (tpt) cc_final: 0.8701 (tpp) REVERT: F 326 MET cc_start: 0.8950 (mpp) cc_final: 0.8195 (mtm) REVERT: F 382 MET cc_start: 0.8497 (pmm) cc_final: 0.8237 (pmm) outliers start: 66 outliers final: 39 residues processed: 173 average time/residue: 0.5051 time to fit residues: 150.7917 Evaluate side-chains 153 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 108 time to evaluate : 5.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 212 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 336 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 435 VAL 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 63 ILE 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 292 ILE Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain C residue 402 THR 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 450 PHE Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 LEU 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 242 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 92 optimal weight: 0.0870 chunk 256 optimal weight: 10.0000 chunk 279 optimal weight: 50.0000 chunk 210 optimal weight: 0.7980 chunk 203 optimal weight: 0.3980 chunk 282 optimal weight: 50.0000 chunk 280 optimal weight: 8.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- 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 236 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.102733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.081115 restraints weight = 190931.459| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 7.35 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 1.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27241 Z= 0.130 Angle : 0.717 15.460 37098 Z= 0.342 Chirality : 0.041 0.292 4610 Planarity : 0.004 0.112 4903 Dihedral : 6.546 117.301 4255 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.15 % Favored : 90.68 % Rotamer: Outliers : 2.52 % Allowed : 25.38 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2853 helix: 0.39 (0.15), residues: 1263 sheet: -0.53 (0.33), residues: 274 loop : -2.67 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 283 HIS 0.010 0.001 HIS A 403 PHE 0.071 0.002 PHE F 309 TYR 0.024 0.001 TYR D 446 ARG 0.009 0.000 ARG C 357 Details of bonding type rmsd link_TRANS : bond 0.00176 ( 3) link_TRANS : angle 0.65030 ( 9) hydrogen bonds : bond 0.03505 ( 1638) hydrogen bonds : angle 4.45032 ( 4764) covalent geometry : bond 0.00269 (27230) covalent geometry : angle 0.71724 (37089) Misc. bond : bond 0.00072 ( 8) *********************** 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 172 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 119 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.4872 (ppp) cc_final: 0.3755 (ppp) REVERT: A 211 MET cc_start: 0.5311 (mmt) cc_final: 0.5071 (mpp) REVERT: A 216 ARG cc_start: 0.7782 (tpm170) cc_final: 0.7141 (ttp-170) REVERT: A 330 LYS cc_start: 0.8653 (tptp) cc_final: 0.8262 (ptpt) REVERT: A 429 SER cc_start: 0.5943 (m) cc_final: 0.5426 (t) REVERT: A 507 LEU cc_start: 0.8808 (mt) cc_final: 0.8372 (tt) REVERT: B 88 MET cc_start: 0.9008 (tpt) cc_final: 0.8532 (tpt) REVERT: B 382 MET cc_start: 0.1808 (tpt) cc_final: -0.1321 (tmm) REVERT: B 435 ASP cc_start: 0.6781 (m-30) cc_final: 0.6084 (p0) REVERT: C 61 MET cc_start: 0.3067 (tpp) cc_final: -0.0217 (mmm) REVERT: C 223 LEU cc_start: 0.5717 (OUTLIER) cc_final: 0.5271 (mp) REVERT: C 357 ARG cc_start: 0.5975 (ttm-80) cc_final: 0.5496 (mmm-85) REVERT: D 218 MET cc_start: 0.0050 (tmm) cc_final: -0.0216 (tpt) REVERT: D 450 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7485 (p90) REVERT: E 61 MET cc_start: 0.8354 (tpp) cc_final: 0.8048 (mpp) REVERT: F 326 MET cc_start: 0.8303 (mpp) cc_final: 0.7654 (mtm) outliers start: 53 outliers final: 38 residues processed: 163 average time/residue: 0.3488 time to fit residues: 94.2139 Evaluate side-chains 151 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 THR 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 435 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 63 ILE 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 374 ARG Chi-restraints excluded: chain B residue 405 LEU 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 77 THR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 359 MET 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 450 PHE Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 316 LEU 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 117 optimal weight: 8.9990 chunk 283 optimal weight: 40.0000 chunk 122 optimal weight: 0.9980 chunk 103 optimal weight: 40.0000 chunk 162 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 1 optimal weight: 0.1980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.102123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.080720 restraints weight = 189460.945| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 8.25 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 1.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27241 Z= 0.133 Angle : 0.718 13.984 37098 Z= 0.343 Chirality : 0.041 0.294 4610 Planarity : 0.004 0.097 4903 Dihedral : 6.479 111.161 4255 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.39 % Favored : 90.43 % Rotamer: Outliers : 2.33 % Allowed : 25.24 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 2853 helix: 0.43 (0.15), residues: 1272 sheet: -0.58 (0.32), residues: 282 loop : -2.63 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 283 HIS 0.024 0.001 HIS A 403 PHE 0.053 0.002 PHE F 309 TYR 0.024 0.001 TYR D 446 ARG 0.013 0.000 ARG E 317 Details of bonding type rmsd link_TRANS : bond 0.00189 ( 3) link_TRANS : angle 0.66031 ( 9) hydrogen bonds : bond 0.03449 ( 1638) hydrogen bonds : angle 4.37490 ( 4764) covalent geometry : bond 0.00281 (27230) covalent geometry : angle 0.71786 (37089) Misc. bond : bond 0.00065 ( 8) ********************** 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 163 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 114 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.5129 (ppp) cc_final: 0.4059 (ppp) REVERT: A 216 ARG cc_start: 0.7650 (tpm170) cc_final: 0.6976 (ttp-170) REVERT: A 220 LEU cc_start: 0.5796 (mt) cc_final: 0.4991 (tt) REVERT: A 330 LYS cc_start: 0.8654 (tptp) cc_final: 0.8224 (ptpt) REVERT: A 429 SER cc_start: 0.5977 (m) cc_final: 0.5574 (t) REVERT: A 457 MET cc_start: 0.7763 (pmm) cc_final: 0.6687 (ttt) REVERT: A 507 LEU cc_start: 0.8885 (mt) cc_final: 0.8459 (tt) REVERT: B 88 MET cc_start: 0.9025 (tpt) cc_final: 0.8548 (tpp) REVERT: B 113 MET cc_start: 0.8279 (mmp) cc_final: 0.7921 (mmt) REVERT: B 382 MET cc_start: 0.2282 (tpt) cc_final: -0.0810 (tmm) REVERT: B 435 ASP cc_start: 0.6913 (m-30) cc_final: 0.6095 (p0) REVERT: C 61 MET cc_start: 0.2767 (tpp) cc_final: -0.0532 (mmm) REVERT: C 223 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5659 (mp) REVERT: C 357 ARG cc_start: 0.5598 (ttm-80) cc_final: 0.4915 (mtp85) REVERT: D 204 LYS cc_start: 0.3929 (tptt) cc_final: 0.3690 (tptt) REVERT: D 218 MET cc_start: 0.0149 (tmm) cc_final: -0.0102 (tpt) REVERT: D 443 MET cc_start: 0.6323 (ttm) cc_final: 0.5601 (mmp) REVERT: D 450 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7410 (p90) REVERT: E 61 MET cc_start: 0.8369 (tpp) cc_final: 0.8070 (mpp) REVERT: F 46 MET cc_start: 0.7654 (mpp) cc_final: 0.7439 (mpp) REVERT: F 326 MET cc_start: 0.8630 (mpp) cc_final: 0.8029 (mtm) outliers start: 49 outliers final: 38 residues processed: 157 average time/residue: 0.3530 time to fit residues: 93.4161 Evaluate side-chains 151 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 392 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 63 ILE 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 374 ARG Chi-restraints excluded: chain B residue 405 LEU 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 77 THR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 315 LEU 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 450 PHE Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 316 LEU 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 132 optimal weight: 2.9990 chunk 204 optimal weight: 0.0770 chunk 239 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 283 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 264 optimal weight: 7.9990 chunk 272 optimal weight: 50.0000 chunk 117 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 overall best weight: 1.7742 ------------------------------------------------------------------------------- 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 369 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.101362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.078969 restraints weight = 190038.775| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 7.72 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 1.2105 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= 0.139 Angle : 0.716 13.819 37098 Z= 0.344 Chirality : 0.041 0.265 4610 Planarity : 0.004 0.083 4903 Dihedral : 6.396 111.105 4255 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.25 % Favored : 90.57 % Rotamer: Outliers : 2.09 % Allowed : 25.62 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.16), residues: 2853 helix: 0.45 (0.15), residues: 1272 sheet: -0.61 (0.33), residues: 272 loop : -2.64 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 283 HIS 0.023 0.001 HIS A 403 PHE 0.033 0.002 PHE F 100 TYR 0.022 0.001 TYR D 446 ARG 0.013 0.001 ARG E 317 Details of bonding type rmsd link_TRANS : bond 0.00189 ( 3) link_TRANS : angle 0.67138 ( 9) hydrogen bonds : bond 0.03378 ( 1638) hydrogen bonds : angle 4.34004 ( 4764) covalent geometry : bond 0.00293 (27230) covalent geometry : angle 0.71596 (37089) Misc. bond : bond 0.00066 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23212.58 seconds wall clock time: 408 minutes 58.87 seconds (24538.87 seconds total)