Starting phenix.real_space_refine on Mon Sep 30 00:42:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/09_2024/6bbm_7076.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/09_2024/6bbm_7076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/09_2024/6bbm_7076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/09_2024/6bbm_7076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/09_2024/6bbm_7076.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/09_2024/6bbm_7076.cif" } resolution = 4.1 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= 0.000 sd= 0.006 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 78 5.16 5 C 14763 2.51 5 N 4344 2.21 5 O 4761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23956 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 1 Chain: "B" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3482 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 18, 'TRANS': 428} Chain breaks: 1 Chain: "C" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3526 Classifications: {'peptide': 453} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 18, 'TRANS': 434} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3550 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 19, 'TRANS': 435} Chain: "E" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3539 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 19, 'TRANS': 434} Chain breaks: 2 Chain: "F" Number of atoms: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3490 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 18, 'TRANS': 429} Chain breaks: 1 Chain: "V" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 621 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 121} Link IDs: {'TRANS': 124} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "W" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 621 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 121} Link IDs: {'TRANS': 124} Chain breaks: 2 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "X" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 601 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 117} Link IDs: {'TRANS': 120} Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 121} Unresolved non-hydrogen planarities: 121 Chain: "Y" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 616 Classifications: {'peptide': 124} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 120} Link IDs: {'TRANS': 123} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 124} Unresolved non-hydrogen planarities: 124 Chain: "Z" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 611 Classifications: {'peptide': 123} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 119} Link IDs: {'TRANS': 122} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 123} Unresolved non-hydrogen planarities: 123 Chain: "A" 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: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" 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: 17.44, per 1000 atoms: 0.73 Number of scatterers: 23956 At special positions: 0 Unit cell: (157.29, 131.61, 145.52, 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 78 16.00 P 10 15.00 O 4761 8.00 N 4344 7.00 C 14763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.83 Conformation dependent library (CDL) restraints added in 2.9 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6178 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 14 sheets defined 55.1% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 31 through 41 removed outlier: 3.965A pdb=" N VAL A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.820A pdb=" N GLU A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.786A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 76 " --> pdb=" O MET A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.919A pdb=" N ALA A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 105' Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.578A pdb=" N ASP A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.785A pdb=" N ILE A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.909A pdb=" N LYS A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 248 Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.562A pdb=" N MET A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA A 274 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 319 through 331 removed outlier: 3.735A pdb=" N ARG A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.517A pdb=" N LEU A 347 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 348 " --> pdb=" O LEU A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 348' Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 364 through 373 removed outlier: 4.496A pdb=" N ALA A 370 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.540A pdb=" N ASP A 401 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 402 " --> pdb=" O ASN A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 402' Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.855A pdb=" N TYR A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 Processing helix chain 'B' and resid 37 through 44 removed outlier: 3.531A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 43 " --> pdb=" O GLY B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.759A pdb=" N ALA B 52 " --> pdb=" O TRP B 48 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU B 53 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 72 removed outlier: 3.651A pdb=" N HIS B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 103 through 111 Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.981A pdb=" N ASP B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 removed outlier: 4.091A pdb=" N ILE B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 139 " --> pdb=" O MET B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 166 removed outlier: 4.102A pdb=" N ASP B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 191 removed outlier: 3.844A pdb=" N ASP B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 236 through 249 removed outlier: 3.603A pdb=" N PHE B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 275 removed outlier: 4.077A pdb=" N SER B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.976A pdb=" N LYS B 283 " --> pdb=" O ASP B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 removed outlier: 3.594A pdb=" N ILE B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.541A pdb=" N LEU B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 334 removed outlier: 3.853A pdb=" N ARG B 328 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS B 334 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 348 Processing helix chain 'B' and resid 357 through 375 removed outlier: 3.510A pdb=" N ILE B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE B 364 " --> pdb=" O GLU B 360 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 392 removed outlier: 3.550A pdb=" N GLN B 391 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 removed outlier: 3.799A pdb=" N ALA B 412 " --> pdb=" O GLU B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 removed outlier: 3.567A pdb=" N LEU C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY C 39 " --> pdb=" O GLN C 35 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 40 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.650A pdb=" N ALA C 52 " --> pdb=" O TRP C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 78 removed outlier: 3.634A pdb=" N GLN C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 94 removed outlier: 3.628A pdb=" N GLU C 89 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.665A pdb=" N LEU C 106 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 118 through 132 removed outlier: 3.743A pdb=" N VAL C 126 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 130 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 136 removed outlier: 3.807A pdb=" N ILE C 136 " --> pdb=" O ARG C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 133 through 136' Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.717A pdb=" N LEU C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 163 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 191 removed outlier: 4.383A pdb=" N ALA C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 236 through 246 removed outlier: 3.973A pdb=" N PHE C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 277 removed outlier: 3.561A pdb=" N MET C 269 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 274 " --> pdb=" O MET C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 304 removed outlier: 4.092A pdb=" N ARG C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 304 " --> pdb=" O THR C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 333 removed outlier: 4.117A pdb=" N ARG C 324 " --> pdb=" O PRO C 320 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG C 326 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ARG C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 356 through 361 removed outlier: 4.291A pdb=" N ILE C 361 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.968A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 392 removed outlier: 3.759A pdb=" N LEU C 389 " --> pdb=" O ASN C 386 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN C 391 " --> pdb=" O SER C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 402 Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'D' and resid 31 through 43 removed outlier: 4.018A pdb=" N SER D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY D 40 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.734A pdb=" N VAL D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 52 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.595A pdb=" N ARG D 66 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 68 " --> pdb=" O PRO D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 79 removed outlier: 3.735A pdb=" N GLN D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 removed outlier: 3.558A pdb=" N SER D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 121 through 128 removed outlier: 3.997A pdb=" N ILE D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL D 126 " --> pdb=" O TYR D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 139 removed outlier: 3.614A pdb=" N SER D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 165 removed outlier: 3.542A pdb=" N ALA D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 192 removed outlier: 4.515A pdb=" N ALA D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 217 removed outlier: 3.604A pdb=" N LYS D 216 " --> pdb=" O ASP D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.577A pdb=" N ALA D 241 " --> pdb=" O LYS D 237 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 removed outlier: 3.738A pdb=" N MET D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ALA D 274 " --> pdb=" O MET D 270 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 286 removed outlier: 3.928A pdb=" N THR D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 307 removed outlier: 4.238A pdb=" N ARG D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.967A pdb=" N ALA D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 392 Processing helix chain 'D' and resid 398 through 402 removed outlier: 3.560A pdb=" N LEU D 402 " --> pdb=" O ASN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 removed outlier: 3.801A pdb=" N ALA D 412 " --> pdb=" O ILE D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 425 removed outlier: 3.783A pdb=" N TYR D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 458 Processing helix chain 'E' and resid 30 through 43 removed outlier: 3.506A pdb=" N GLU E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU E 38 " --> pdb=" O GLU E 34 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY E 39 " --> pdb=" O GLN E 35 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU E 43 " --> pdb=" O GLY E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 3.568A pdb=" N VAL E 51 " --> pdb=" O ARG E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 77 removed outlier: 3.741A pdb=" N ARG E 66 " --> pdb=" O THR E 62 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU E 71 " --> pdb=" O HIS E 67 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E 73 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 94 removed outlier: 4.200A pdb=" N GLU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 110 removed outlier: 4.172A pdb=" N LEU E 109 " --> pdb=" O TYR E 105 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 105 through 110' Processing helix chain 'E' and resid 118 through 121 removed outlier: 3.720A pdb=" N ALA E 121 " --> pdb=" O ASN E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 118 through 121' Processing helix chain 'E' and resid 122 through 144 removed outlier: 3.537A pdb=" N VAL E 126 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL E 131 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 154 No H-bonds generated for 'chain 'E' and resid 153 through 154' Processing helix chain 'E' and resid 155 through 155 No H-bonds generated for 'chain 'E' and resid 155 through 155' Processing helix chain 'E' and resid 156 through 170 removed outlier: 3.541A pdb=" N LEU E 160 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG E 164 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS E 167 " --> pdb=" O SER E 163 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E 169 " --> pdb=" O VAL E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 191 removed outlier: 4.112A pdb=" N ASP E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 218 removed outlier: 4.128A pdb=" N LYS E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 247 removed outlier: 3.623A pdb=" N PHE E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA E 241 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'E' and resid 281 through 286 removed outlier: 3.688A pdb=" N THR E 286 " --> pdb=" O THR E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 305 removed outlier: 4.431A pdb=" N ALA E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 334 removed outlier: 3.663A pdb=" N ARG E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 367 removed outlier: 3.692A pdb=" N ARG E 366 " --> pdb=" O GLU E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 376 removed outlier: 4.127A pdb=" N ALA E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS E 373 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU E 374 " --> pdb=" O ALA E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 391 removed outlier: 4.122A pdb=" N LEU E 389 " --> pdb=" O ASN E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 402 removed outlier: 3.613A pdb=" N LEU E 402 " --> pdb=" O ASN E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 removed outlier: 4.512A pdb=" N ASP E 411 " --> pdb=" O SER E 407 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 412 " --> pdb=" O ILE E 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 407 through 412' Processing helix chain 'E' and resid 420 through 424 removed outlier: 3.930A pdb=" N VAL E 423 " --> pdb=" O ARG E 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 43 removed outlier: 3.764A pdb=" N SER F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU F 38 " --> pdb=" O GLU F 34 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 43 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 47 No H-bonds generated for 'chain 'F' and resid 45 through 47' Processing helix chain 'F' and resid 48 through 53 removed outlier: 3.625A pdb=" N GLU F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 78 removed outlier: 3.648A pdb=" N HIS F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE F 68 " --> pdb=" O PRO F 64 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE F 69 " --> pdb=" O HIS F 65 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA F 73 " --> pdb=" O PHE F 69 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN F 76 " --> pdb=" O MET F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 95 removed outlier: 3.595A pdb=" N ALA F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 112 removed outlier: 4.010A pdb=" N GLU F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU F 109 " --> pdb=" O TYR F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 129 removed outlier: 3.502A pdb=" N ILE F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL F 126 " --> pdb=" O TYR F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 147 removed outlier: 3.657A pdb=" N ILE F 136 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER F 137 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU F 141 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE F 147 " --> pdb=" O ALA F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 170 removed outlier: 4.220A pdb=" N ARG F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA F 169 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 194 Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 238 through 250 removed outlier: 3.721A pdb=" N VAL F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 273 removed outlier: 4.014A pdb=" N MET F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG F 271 " --> pdb=" O GLN F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 293 through 305 Processing helix chain 'F' and resid 320 through 325 removed outlier: 3.792A pdb=" N ARG F 324 " --> pdb=" O PRO F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 334 removed outlier: 3.938A pdb=" N ILE F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA F 331 " --> pdb=" O ALA F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 356 through 365 removed outlier: 3.808A pdb=" N ALA F 362 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU F 363 " --> pdb=" O LEU F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 386 through 392 removed outlier: 3.622A pdb=" N GLU F 390 " --> pdb=" O ARG F 387 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN F 391 " --> pdb=" O SER F 388 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG F 392 " --> pdb=" O LEU F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 402 removed outlier: 3.534A pdb=" N LEU F 402 " --> pdb=" O ASN F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 Processing helix chain 'V' and resid 117 through 129 removed outlier: 3.664A pdb=" N UNK V 122 " --> pdb=" O UNK V 118 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N UNK V 123 " --> pdb=" O UNK V 119 " (cutoff:3.500A) Processing helix chain 'V' and resid 140 through 148 Processing helix chain 'V' and resid 154 through 163 removed outlier: 3.987A pdb=" N UNK V 161 " --> pdb=" O UNK V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 176 through 186 Processing helix chain 'V' and resid 221 through 228 removed outlier: 3.512A pdb=" N UNK V 227 " --> pdb=" O UNK V 223 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N UNK V 228 " --> pdb=" O UNK V 224 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 128 Processing helix chain 'W' and resid 141 through 146 Processing helix chain 'W' and resid 147 through 150 Processing helix chain 'W' and resid 153 through 163 removed outlier: 3.580A pdb=" N UNK W 157 " --> pdb=" O UNK W 153 " (cutoff:3.500A) Processing helix chain 'W' and resid 176 through 178 No H-bonds generated for 'chain 'W' and resid 176 through 178' Processing helix chain 'W' and resid 179 through 185 Processing helix chain 'W' and resid 200 through 205 Processing helix chain 'W' and resid 221 through 232 removed outlier: 3.606A pdb=" N UNK W 225 " --> pdb=" O UNK W 221 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N UNK W 226 " --> pdb=" O UNK W 222 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N UNK W 229 " --> pdb=" O UNK W 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 134 removed outlier: 3.551A pdb=" N UNK X 127 " --> pdb=" O UNK X 123 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N UNK X 129 " --> pdb=" O UNK X 125 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N UNK X 132 " --> pdb=" O UNK X 128 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 144 removed outlier: 3.574A pdb=" N UNK X 144 " --> pdb=" O UNK X 141 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 154 removed outlier: 3.754A pdb=" N UNK X 151 " --> pdb=" O UNK X 147 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N UNK X 154 " --> pdb=" O UNK X 150 " (cutoff:3.500A) Processing helix chain 'X' and resid 157 through 165 removed outlier: 3.701A pdb=" N UNK X 162 " --> pdb=" O UNK X 158 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N UNK X 164 " --> pdb=" O UNK X 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 177 through 187 removed outlier: 3.745A pdb=" N UNK X 180 " --> pdb=" O UNK X 177 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N UNK X 181 " --> pdb=" O UNK X 178 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N UNK X 182 " --> pdb=" O UNK X 179 " (cutoff:3.500A) Processing helix chain 'X' and resid 226 through 230 Processing helix chain 'Y' and resid 120 through 129 Processing helix chain 'Y' and resid 143 through 148 removed outlier: 3.885A pdb=" N UNK Y 148 " --> pdb=" O UNK Y 144 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 158 Processing helix chain 'Y' and resid 180 through 189 removed outlier: 4.381A pdb=" N UNK Y 186 " --> pdb=" O UNK Y 182 " (cutoff:3.500A) Processing helix chain 'Y' and resid 200 through 205 removed outlier: 4.189A pdb=" N UNK Y 204 " --> pdb=" O UNK Y 200 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N UNK Y 205 " --> pdb=" O UNK Y 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 200 through 205' Processing helix chain 'Y' and resid 221 through 232 Processing helix chain 'Z' and resid 119 through 131 removed outlier: 4.095A pdb=" N UNK Z 123 " --> pdb=" O UNK Z 119 " (cutoff:3.500A) Processing helix chain 'Z' and resid 140 through 145 Processing helix chain 'Z' and resid 146 through 148 No H-bonds generated for 'chain 'Z' and resid 146 through 148' Processing helix chain 'Z' and resid 153 through 157 Processing helix chain 'Z' and resid 166 through 171 removed outlier: 3.805A pdb=" N UNK Z 171 " --> pdb=" O UNK Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 180 through 188 removed outlier: 3.623A pdb=" N UNK Z 185 " --> pdb=" O UNK Z 181 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N UNK Z 186 " --> pdb=" O UNK Z 182 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N UNK Z 188 " --> pdb=" O UNK Z 184 " (cutoff:3.500A) Processing helix chain 'Z' and resid 202 through 207 removed outlier: 3.644A pdb=" N UNK Z 206 " --> pdb=" O UNK Z 202 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N UNK Z 207 " --> pdb=" O UNK Z 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 202 through 207' Processing helix chain 'Z' and resid 221 through 231 removed outlier: 3.621A pdb=" N UNK Z 225 " --> pdb=" O UNK Z 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 313 removed outlier: 6.369A pdb=" N VAL A 256 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASP A 313 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 258 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE A 340 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU A 382 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 342 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE A 228 " --> pdb=" O MET A 416 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE A 418 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 415 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ARG A 450 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR A 463 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR A 452 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 258 through 260 removed outlier: 3.521A pdb=" N LEU B 414 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 230 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 415 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 311 through 313 removed outlier: 6.206A pdb=" N ILE C 258 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 228 " --> pdb=" O MET C 416 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE C 418 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA C 230 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ARG C 420 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE C 415 " --> pdb=" O GLY C 439 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 419 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE C 438 " --> pdb=" O GLY C 447 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY C 447 " --> pdb=" O ILE C 438 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 311 through 313 removed outlier: 6.206A pdb=" N ILE C 258 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 228 " --> pdb=" O MET C 416 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE C 418 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA C 230 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ARG C 420 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE C 415 " --> pdb=" O GLY C 439 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 419 " --> pdb=" O GLU C 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 381 through 383 removed outlier: 6.471A pdb=" N ILE D 415 " --> pdb=" O GLY D 439 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY D 447 " --> pdb=" O ILE D 438 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 258 through 260 removed outlier: 7.069A pdb=" N PHE D 259 " --> pdb=" O ASP D 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 451 through 454 Processing sheet with id=AA8, first strand: chain 'E' and resid 179 through 180 Processing sheet with id=AA9, first strand: chain 'E' and resid 227 through 231 removed outlier: 3.740A pdb=" N ILE E 438 " --> pdb=" O GLY E 447 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY E 447 " --> pdb=" O ILE E 438 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 257 through 259 Processing sheet with id=AB2, first strand: chain 'E' and resid 452 through 454 removed outlier: 3.737A pdb=" N ARG E 459 " --> pdb=" O ASN E 454 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 228 through 229 removed outlier: 6.566A pdb=" N ILE F 228 " --> pdb=" O MET F 416 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS F 440 " --> pdb=" O ILE F 415 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 341 through 342 Processing sheet with id=AB5, first strand: chain 'F' and resid 433 through 436 689 hydrogen bonds defined for protein. 1893 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: 8.24 Time building geometry restraints manager: 7.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7871 1.33 - 1.45: 3135 1.45 - 1.57: 13075 1.57 - 1.69: 15 1.69 - 1.81: 156 Bond restraints: 24252 Sorted by residual: bond pdb=" C VAL F 379 " pdb=" N VAL F 380 " ideal model delta sigma weight residual 1.335 1.290 0.045 1.16e-02 7.43e+03 1.49e+01 bond pdb=" N GLU E 170 " pdb=" CA GLU E 170 " ideal model delta sigma weight residual 1.463 1.505 -0.042 1.24e-02 6.50e+03 1.14e+01 bond pdb=" C LEU A 318 " pdb=" N THR A 319 " ideal model delta sigma weight residual 1.330 1.285 0.046 1.37e-02 5.33e+03 1.11e+01 bond pdb=" N GLY A 465 " pdb=" CA GLY A 465 " ideal model delta sigma weight residual 1.443 1.485 -0.043 1.37e-02 5.33e+03 9.75e+00 bond pdb=" N GLU D 170 " pdb=" CA GLU D 170 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.25e-02 6.40e+03 7.61e+00 ... (remaining 24247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 32009 3.02 - 6.04: 808 6.04 - 9.05: 108 9.05 - 12.07: 14 12.07 - 15.09: 1 Bond angle restraints: 32940 Sorted by residual: angle pdb=" N VAL C 138 " pdb=" CA VAL C 138 " pdb=" C VAL C 138 " ideal model delta sigma weight residual 112.12 106.89 5.23 8.40e-01 1.42e+00 3.88e+01 angle pdb=" C UNK X 169 " pdb=" N UNK X 170 " pdb=" CA UNK X 170 " ideal model delta sigma weight residual 121.70 131.91 -10.21 1.80e+00 3.09e-01 3.21e+01 angle pdb=" C ARG C 152 " pdb=" N THR C 153 " pdb=" CA THR C 153 " ideal model delta sigma weight residual 122.41 134.13 -11.72 2.09e+00 2.29e-01 3.14e+01 angle pdb=" N VAL E 165 " pdb=" CA VAL E 165 " pdb=" C VAL E 165 " ideal model delta sigma weight residual 113.22 106.78 6.44 1.23e+00 6.61e-01 2.74e+01 angle pdb=" C ARG C 54 " pdb=" N VAL C 55 " pdb=" CA VAL C 55 " ideal model delta sigma weight residual 121.97 131.34 -9.37 1.80e+00 3.09e-01 2.71e+01 ... (remaining 32935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 14532 35.04 - 70.08: 324 70.08 - 105.12: 32 105.12 - 140.17: 5 140.17 - 175.21: 4 Dihedral angle restraints: 14897 sinusoidal: 5398 harmonic: 9499 Sorted by residual: dihedral pdb=" CA ALA B 169 " pdb=" C ALA B 169 " pdb=" N GLU B 170 " pdb=" CA GLU B 170 " ideal model delta harmonic sigma weight residual 180.00 93.00 87.00 0 5.00e+00 4.00e-02 3.03e+02 dihedral pdb=" CA LYS F 180 " pdb=" C LYS F 180 " pdb=" N ASN F 181 " pdb=" CA ASN F 181 " ideal model delta harmonic sigma weight residual 180.00 116.20 63.80 0 5.00e+00 4.00e-02 1.63e+02 dihedral pdb=" CA PRO D 27 " pdb=" C PRO D 27 " pdb=" N PRO D 28 " pdb=" CA PRO D 28 " ideal model delta harmonic sigma weight residual 180.00 123.12 56.88 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 14894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2450 0.054 - 0.107: 1109 0.107 - 0.161: 239 0.161 - 0.214: 42 0.214 - 0.268: 8 Chirality restraints: 3848 Sorted by residual: chirality pdb=" CB ILE D 227 " pdb=" CA ILE D 227 " pdb=" CG1 ILE D 227 " pdb=" CG2 ILE D 227 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE B 193 " pdb=" CA ILE B 193 " pdb=" CG1 ILE B 193 " pdb=" CG2 ILE B 193 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE B 227 " pdb=" CA ILE B 227 " pdb=" CG1 ILE B 227 " pdb=" CG2 ILE B 227 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 3845 not shown) Planarity restraints: 4404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 169 " 0.034 2.00e-02 2.50e+03 6.81e-02 4.63e+01 pdb=" C ALA D 169 " -0.118 2.00e-02 2.50e+03 pdb=" O ALA D 169 " 0.046 2.00e-02 2.50e+03 pdb=" N GLU D 170 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 169 " 0.033 2.00e-02 2.50e+03 6.52e-02 4.26e+01 pdb=" C ALA C 169 " -0.113 2.00e-02 2.50e+03 pdb=" O ALA C 169 " 0.044 2.00e-02 2.50e+03 pdb=" N GLU C 170 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 464 " 0.031 2.00e-02 2.50e+03 6.14e-02 3.77e+01 pdb=" C ALA E 464 " -0.106 2.00e-02 2.50e+03 pdb=" O ALA E 464 " 0.041 2.00e-02 2.50e+03 pdb=" N GLY E 465 " 0.035 2.00e-02 2.50e+03 ... (remaining 4401 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5083 2.76 - 3.30: 22686 3.30 - 3.83: 38848 3.83 - 4.37: 45192 4.37 - 4.90: 73213 Nonbonded interactions: 185022 Sorted by model distance: nonbonded pdb=" O ARG C 74 " pdb=" OG SER C 78 " model vdw 2.231 3.040 nonbonded pdb=" O LEU B 109 " pdb=" OG1 THR B 113 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASN D 140 " pdb=" OG SER F 115 " model vdw 2.238 3.040 nonbonded pdb=" OG SER D 224 " pdb=" O ALA D 372 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR A 344 " pdb=" OD1 ASP F 411 " model vdw 2.252 3.040 ... (remaining 185017 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 27 through 464) selection = (chain 'B' and (resid 27 through 166 or resid 204 through 464)) selection = (chain 'C' and (resid 27 through 166 or resid 204 through 464)) selection = (chain 'D' and (resid 27 through 166 or resid 204 through 464)) selection = (chain 'E' and (resid 27 through 166 or resid 204 through 464)) selection = (chain 'F' and (resid 27 through 166 or resid 204 through 464)) } ncs_group { reference = (chain 'V' and ((resid 113 through 121 and (name N or name CA or name C or name \ O )) or resid 122 through 232)) selection = (chain 'W' and ((resid 114 through 122 and (name N or name CA or name C or name \ O )) or resid 123 through 233)) selection = (chain 'X' and ((resid 113 through 121 and (name N or name CA or name C or name \ O )) or resid 122 through 232)) selection = (chain 'Y' and ((resid 113 through 121 and (name N or name CA or name C or name \ O )) or resid 122 through 232)) selection = (chain 'Z' and ((resid 113 through 121 and (name N or name CA or name C or name \ O )) or resid 122 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.050 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: 0.000 Extract box with map and model: 2.740 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 56.230 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 : 0.008 0.064 24252 Z= 0.520 Angle : 1.201 15.089 32940 Z= 0.654 Chirality : 0.061 0.268 3848 Planarity : 0.008 0.123 4404 Dihedral : 16.696 175.208 8719 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.75 % Favored : 86.06 % Rotamer: Outliers : 0.58 % Allowed : 11.95 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.83 % 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: -5.97 (0.12), residues: 2640 helix: -4.57 (0.07), residues: 1104 sheet: -3.68 (0.26), residues: 257 loop : -3.39 (0.15), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 457 HIS 0.009 0.002 HIS A 29 PHE 0.031 0.003 PHE D 259 TYR 0.029 0.002 TYR D 344 ARG 0.012 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 367 time to evaluate : 2.745 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 267 GLN cc_start: 0.8398 (mm110) cc_final: 0.7896 (mm-40) REVERT: A 270 MET cc_start: 0.6864 (mtp) cc_final: 0.6284 (ttm) REVERT: B 222 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8178 (mp10) REVERT: B 291 ASP cc_start: 0.6987 (t70) cc_final: 0.5871 (t0) REVERT: B 294 TRP cc_start: 0.5092 (m100) cc_final: 0.3699 (t-100) REVERT: B 366 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7438 (mtm110) REVERT: C 180 LYS cc_start: 0.8305 (mttt) cc_final: 0.7981 (mmtt) REVERT: C 197 PHE cc_start: 0.6280 (m-80) cc_final: 0.5772 (p90) REVERT: C 243 ASN cc_start: 0.7070 (t0) cc_final: 0.6455 (t0) REVERT: C 357 ARG cc_start: 0.8453 (mmm160) cc_final: 0.8244 (tpp80) REVERT: C 449 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.8011 (t) REVERT: D 112 ASN cc_start: 0.8399 (m-40) cc_final: 0.7543 (t0) REVERT: E 237 LYS cc_start: 0.7225 (ttpt) cc_final: 0.6910 (ttpp) REVERT: E 244 LEU cc_start: 0.9272 (tt) cc_final: 0.9067 (tt) REVERT: E 310 ILE cc_start: 0.8818 (mt) cc_final: 0.8539 (tt) REVERT: E 341 MET cc_start: 0.7760 (ttp) cc_final: 0.7479 (ttp) REVERT: E 349 ARG cc_start: 0.8467 (mtm110) cc_final: 0.8020 (ptp-110) REVERT: E 401 ASP cc_start: 0.7929 (m-30) cc_final: 0.7458 (t0) REVERT: E 411 ASP cc_start: 0.8048 (m-30) cc_final: 0.7199 (m-30) REVERT: E 443 ASN cc_start: 0.7402 (p0) cc_final: 0.7139 (p0) REVERT: F 366 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7940 (mtm-85) outliers start: 13 outliers final: 5 residues processed: 380 average time/residue: 0.4400 time to fit residues: 242.7170 Evaluate side-chains 242 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 236 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 30.0000 chunk 244 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 253 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 293 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 281 GLN ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN A 456 GLN B 198 GLN B 243 ASN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS C 45 ASN C 112 ASN C 174 ASN C 399 ASN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN D 76 GLN D 140 ASN D 243 ASN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS E 427 ASN F 45 ASN F 208 ASN F 267 GLN F 391 GLN F 399 ASN F 425 HIS ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24252 Z= 0.236 Angle : 0.798 11.815 32940 Z= 0.394 Chirality : 0.046 0.206 3848 Planarity : 0.006 0.109 4404 Dihedral : 10.960 172.681 3585 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.53 % Favored : 89.32 % Rotamer: Outliers : 0.04 % Allowed : 6.13 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.39 % 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: -5.15 (0.13), residues: 2640 helix: -3.61 (0.10), residues: 1177 sheet: -3.36 (0.26), residues: 271 loop : -3.10 (0.16), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 294 HIS 0.008 0.001 HIS E 425 PHE 0.018 0.002 PHE D 259 TYR 0.026 0.002 TYR D 344 ARG 0.014 0.001 ARG C 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 340 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.8249 (mt) cc_final: 0.8014 (mm) REVERT: B 222 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8231 (mp10) REVERT: C 69 PHE cc_start: 0.7325 (t80) cc_final: 0.6807 (t80) REVERT: C 197 PHE cc_start: 0.6391 (m-80) cc_final: 0.6020 (p90) REVERT: C 237 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8319 (ttmm) REVERT: C 316 SER cc_start: 0.8568 (m) cc_final: 0.7924 (t) REVERT: D 112 ASN cc_start: 0.8310 (m-40) cc_final: 0.7478 (t0) REVERT: D 344 TYR cc_start: 0.7134 (t80) cc_final: 0.6423 (t80) REVERT: D 366 ARG cc_start: 0.7938 (mpp80) cc_final: 0.7143 (mtt90) REVERT: E 150 GLN cc_start: 0.6570 (mp10) cc_final: 0.6280 (mp10) REVERT: E 237 LYS cc_start: 0.7900 (ttpt) cc_final: 0.7664 (ttpt) REVERT: E 349 ARG cc_start: 0.8415 (mtm110) cc_final: 0.7615 (ptm160) REVERT: E 443 ASN cc_start: 0.7056 (p0) cc_final: 0.6772 (p0) REVERT: F 366 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7945 (ttp-110) outliers start: 1 outliers final: 0 residues processed: 340 average time/residue: 0.4106 time to fit residues: 207.8436 Evaluate side-chains 232 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 163 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 199 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 293 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 261 optimal weight: 0.0270 chunk 291 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 235 optimal weight: 4.9990 overall best weight: 2.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 GLN ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN C 441 GLN D 45 ASN D 76 GLN D 140 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 ASN F 76 GLN F 399 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24252 Z= 0.210 Angle : 0.732 11.701 32940 Z= 0.360 Chirality : 0.045 0.195 3848 Planarity : 0.005 0.104 4404 Dihedral : 10.385 178.871 3585 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.06 % Favored : 88.86 % Rotamer: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.28 % 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: -4.52 (0.14), residues: 2640 helix: -2.95 (0.12), residues: 1175 sheet: -3.02 (0.27), residues: 268 loop : -2.94 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 294 HIS 0.005 0.001 HIS B 29 PHE 0.015 0.001 PHE D 259 TYR 0.022 0.001 TYR D 344 ARG 0.007 0.001 ARG F 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 307 time to evaluate : 2.715 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 270 MET cc_start: 0.7988 (mmm) cc_final: 0.7709 (tpp) REVERT: B 34 GLU cc_start: 0.7911 (tt0) cc_final: 0.7683 (tt0) REVERT: B 222 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8153 (mp10) REVERT: B 291 ASP cc_start: 0.7327 (t0) cc_final: 0.5907 (t0) REVERT: B 294 TRP cc_start: 0.5017 (m100) cc_final: 0.3918 (t-100) REVERT: C 197 PHE cc_start: 0.6387 (m-80) cc_final: 0.6040 (p90) REVERT: C 237 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8100 (ttmm) REVERT: C 316 SER cc_start: 0.8522 (m) cc_final: 0.7955 (t) REVERT: D 42 MET cc_start: 0.6879 (mtm) cc_final: 0.6542 (mtm) REVERT: D 112 ASN cc_start: 0.8310 (m-40) cc_final: 0.7660 (t0) REVERT: E 150 GLN cc_start: 0.6518 (mp10) cc_final: 0.6298 (mp10) REVERT: E 222 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7140 (mp10) REVERT: E 349 ARG cc_start: 0.8299 (mtm110) cc_final: 0.7882 (ptp-110) REVERT: F 266 GLU cc_start: 0.8260 (tt0) cc_final: 0.7570 (mp0) REVERT: F 270 MET cc_start: 0.8370 (mtp) cc_final: 0.8133 (mtm) REVERT: F 401 ASP cc_start: 0.6420 (m-30) cc_final: 0.6023 (t0) outliers start: 2 outliers final: 0 residues processed: 308 average time/residue: 0.3651 time to fit residues: 175.2649 Evaluate side-chains 219 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 152 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 294 optimal weight: 20.0000 chunk 312 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN B 399 ASN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN C 399 ASN C 425 HIS ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN F 399 ASN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24252 Z= 0.249 Angle : 0.744 11.112 32940 Z= 0.364 Chirality : 0.045 0.218 3848 Planarity : 0.005 0.098 4404 Dihedral : 10.193 179.555 3585 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.40 % Favored : 88.48 % Rotamer: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.28 % 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: -4.08 (0.15), residues: 2640 helix: -2.51 (0.13), residues: 1167 sheet: -2.84 (0.27), residues: 274 loop : -2.78 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 48 HIS 0.004 0.001 HIS B 29 PHE 0.014 0.002 PHE C 460 TYR 0.020 0.002 TYR D 344 ARG 0.006 0.001 ARG E 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 285 time to evaluate : 2.734 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: B 222 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8174 (mp10) REVERT: B 291 ASP cc_start: 0.7442 (t70) cc_final: 0.5932 (t0) REVERT: B 294 TRP cc_start: 0.5538 (m100) cc_final: 0.3832 (t-100) REVERT: C 69 PHE cc_start: 0.7285 (t80) cc_final: 0.6963 (t80) REVERT: C 180 LYS cc_start: 0.8316 (mtmt) cc_final: 0.7933 (mmtt) REVERT: C 197 PHE cc_start: 0.6422 (m-80) cc_final: 0.6128 (p90) REVERT: C 237 LYS cc_start: 0.8503 (ttmt) cc_final: 0.8140 (ttmm) REVERT: C 316 SER cc_start: 0.8520 (m) cc_final: 0.7915 (t) REVERT: D 42 MET cc_start: 0.6799 (mtm) cc_final: 0.6498 (mtm) REVERT: D 112 ASN cc_start: 0.8351 (m-40) cc_final: 0.7382 (t0) REVERT: D 192 ARG cc_start: 0.6817 (tpm170) cc_final: 0.6442 (tmt170) REVERT: E 222 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7119 (mp10) REVERT: E 349 ARG cc_start: 0.8289 (mtm110) cc_final: 0.7844 (ptp-110) outliers start: 2 outliers final: 0 residues processed: 286 average time/residue: 0.3721 time to fit residues: 165.7978 Evaluate side-chains 216 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 260 optimal weight: 0.0270 chunk 177 optimal weight: 4.9990 chunk 4 optimal weight: 40.0000 chunk 232 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 chunk 266 optimal weight: 30.0000 chunk 215 optimal weight: 0.0970 chunk 0 optimal weight: 40.0000 chunk 159 optimal weight: 7.9990 chunk 280 optimal weight: 20.0000 chunk 78 optimal weight: 0.5980 overall best weight: 1.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN C 399 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 GLN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN E 456 GLN F 399 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24252 Z= 0.192 Angle : 0.698 10.770 32940 Z= 0.340 Chirality : 0.044 0.300 3848 Planarity : 0.005 0.094 4404 Dihedral : 9.866 176.442 3585 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.57 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.28 % 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: -3.80 (0.15), residues: 2640 helix: -2.23 (0.14), residues: 1174 sheet: -2.60 (0.29), residues: 271 loop : -2.72 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 457 HIS 0.004 0.001 HIS B 29 PHE 0.024 0.001 PHE D 259 TYR 0.019 0.001 TYR A 105 ARG 0.007 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8117 (tpp) cc_final: 0.7881 (tpp) REVERT: B 222 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8186 (mp10) REVERT: B 291 ASP cc_start: 0.7451 (t70) cc_final: 0.6076 (t0) REVERT: B 294 TRP cc_start: 0.5155 (m100) cc_final: 0.3966 (t-100) REVERT: C 180 LYS cc_start: 0.8278 (mtmt) cc_final: 0.7919 (mmtt) REVERT: C 197 PHE cc_start: 0.6417 (m-80) cc_final: 0.6149 (p90) REVERT: C 237 LYS cc_start: 0.8498 (ttmt) cc_final: 0.8180 (ttmm) REVERT: C 316 SER cc_start: 0.8426 (m) cc_final: 0.7929 (t) REVERT: C 359 LEU cc_start: 0.9225 (mm) cc_final: 0.8898 (tp) REVERT: D 42 MET cc_start: 0.6683 (mtm) cc_final: 0.6402 (mtm) REVERT: D 112 ASN cc_start: 0.8378 (m-40) cc_final: 0.7538 (t0) REVERT: D 192 ARG cc_start: 0.6832 (tpm170) cc_final: 0.6562 (tmt170) REVERT: E 222 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7111 (mp10) REVERT: E 349 ARG cc_start: 0.8204 (mtm110) cc_final: 0.7751 (ptp-110) REVERT: F 48 TRP cc_start: 0.8077 (t-100) cc_final: 0.7834 (t60) REVERT: F 68 ILE cc_start: 0.9318 (mt) cc_final: 0.8981 (mt) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.3519 time to fit residues: 164.8437 Evaluate side-chains 217 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 105 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 312 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 GLN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN C 243 ASN C 399 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 GLN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24252 Z= 0.256 Angle : 0.732 10.370 32940 Z= 0.357 Chirality : 0.045 0.224 3848 Planarity : 0.005 0.089 4404 Dihedral : 9.877 175.300 3585 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.86 % Favored : 88.11 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.28 % 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: -3.65 (0.15), residues: 2640 helix: -2.08 (0.14), residues: 1168 sheet: -2.67 (0.29), residues: 267 loop : -2.64 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 48 HIS 0.005 0.001 HIS B 29 PHE 0.013 0.002 PHE C 460 TYR 0.019 0.001 TYR A 105 ARG 0.007 0.001 ARG F 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 2.471 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: A 267 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7579 (mm-40) REVERT: A 270 MET cc_start: 0.8265 (tpp) cc_final: 0.7785 (tpp) REVERT: B 222 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8186 (mp10) REVERT: B 291 ASP cc_start: 0.7519 (t70) cc_final: 0.6183 (t0) REVERT: B 294 TRP cc_start: 0.5561 (m100) cc_final: 0.3992 (t-100) REVERT: C 70 THR cc_start: 0.8330 (m) cc_final: 0.8099 (t) REVERT: C 180 LYS cc_start: 0.8301 (mtmt) cc_final: 0.7896 (mmtt) REVERT: C 237 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8233 (ttmm) REVERT: C 316 SER cc_start: 0.8407 (m) cc_final: 0.7946 (t) REVERT: C 359 LEU cc_start: 0.9215 (mm) cc_final: 0.8947 (tp) REVERT: D 42 MET cc_start: 0.6817 (mtm) cc_final: 0.6585 (mtm) REVERT: D 112 ASN cc_start: 0.8483 (m-40) cc_final: 0.7361 (t0) REVERT: D 341 MET cc_start: 0.8591 (tmm) cc_final: 0.8379 (tmm) REVERT: D 357 ARG cc_start: 0.7952 (mmm160) cc_final: 0.7228 (mmp80) REVERT: E 192 ARG cc_start: 0.7588 (tpm170) cc_final: 0.7272 (tpp-160) REVERT: E 222 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7127 (mp10) REVERT: E 349 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7584 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.3502 time to fit residues: 158.1980 Evaluate side-chains 211 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 178 optimal weight: 0.9990 chunk 228 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 263 optimal weight: 30.0000 chunk 174 optimal weight: 2.9990 chunk 311 optimal weight: 30.0000 chunk 194 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN B 243 ASN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN C 399 ASN C 467 GLN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 GLN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24252 Z= 0.257 Angle : 0.740 11.597 32940 Z= 0.360 Chirality : 0.046 0.293 3848 Planarity : 0.005 0.085 4404 Dihedral : 9.841 171.916 3585 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.36 % Favored : 88.60 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.28 % 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 (0.15), residues: 2640 helix: -1.91 (0.14), residues: 1163 sheet: -2.57 (0.29), residues: 267 loop : -2.66 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 457 HIS 0.005 0.001 HIS B 29 PHE 0.015 0.002 PHE C 460 TYR 0.029 0.002 TYR D 344 ARG 0.005 0.001 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 2.657 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 267 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7371 (mm-40) REVERT: A 270 MET cc_start: 0.8338 (tpp) cc_final: 0.7799 (tpp) REVERT: B 222 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8193 (mp10) REVERT: B 229 VAL cc_start: 0.8223 (t) cc_final: 0.8016 (t) REVERT: B 291 ASP cc_start: 0.7456 (t70) cc_final: 0.6198 (t0) REVERT: B 294 TRP cc_start: 0.5696 (m100) cc_final: 0.4040 (t-100) REVERT: C 180 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7785 (mmtt) REVERT: C 235 MET cc_start: 0.7498 (tpt) cc_final: 0.7208 (tpt) REVERT: C 237 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8253 (ttmm) REVERT: C 316 SER cc_start: 0.8381 (m) cc_final: 0.7939 (t) REVERT: D 357 ARG cc_start: 0.7967 (mmm160) cc_final: 0.7254 (mmp80) REVERT: E 222 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7186 (mp10) REVERT: E 349 ARG cc_start: 0.7947 (mtm110) cc_final: 0.7407 (ptp-110) REVERT: F 401 ASP cc_start: 0.6576 (m-30) cc_final: 0.6229 (t70) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.3435 time to fit residues: 150.9472 Evaluate side-chains 211 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 192 optimal weight: 0.5980 chunk 124 optimal weight: 0.1980 chunk 185 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 243 ASN A 334 HIS ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN C 281 GLN C 399 ASN C 467 GLN D 201 HIS D 243 ASN D 247 ASN D 309 ASN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24252 Z= 0.158 Angle : 0.690 12.784 32940 Z= 0.329 Chirality : 0.043 0.258 3848 Planarity : 0.004 0.078 4404 Dihedral : 9.380 166.905 3585 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.20 % 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: -3.15 (0.16), residues: 2640 helix: -1.59 (0.15), residues: 1144 sheet: -2.42 (0.29), residues: 279 loop : -2.44 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 457 HIS 0.005 0.001 HIS B 29 PHE 0.010 0.001 PHE E 417 TYR 0.021 0.001 TYR A 105 ARG 0.011 0.000 ARG D 329 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.507 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: A 267 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7095 (mm-40) REVERT: A 270 MET cc_start: 0.8296 (tpp) cc_final: 0.7974 (tpp) REVERT: B 92 GLU cc_start: 0.7048 (tp30) cc_final: 0.6515 (pp20) REVERT: B 222 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8170 (mp10) REVERT: B 235 MET cc_start: 0.6087 (mmt) cc_final: 0.5814 (mmt) REVERT: B 242 MET cc_start: 0.8183 (mmp) cc_final: 0.7691 (mtp) REVERT: B 291 ASP cc_start: 0.7396 (t70) cc_final: 0.6341 (t0) REVERT: B 294 TRP cc_start: 0.5291 (m100) cc_final: 0.4170 (t-100) REVERT: C 180 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7902 (mmtt) REVERT: C 237 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8180 (ttmm) REVERT: C 263 MET cc_start: 0.7667 (ttm) cc_final: 0.7455 (ttm) REVERT: C 316 SER cc_start: 0.8343 (m) cc_final: 0.7829 (t) REVERT: C 347 LEU cc_start: 0.8228 (mm) cc_final: 0.8013 (tp) REVERT: C 359 LEU cc_start: 0.9211 (mm) cc_final: 0.8762 (tp) REVERT: D 42 MET cc_start: 0.6538 (mtm) cc_final: 0.6283 (mtm) REVERT: D 341 MET cc_start: 0.8411 (tmm) cc_final: 0.8037 (tmm) REVERT: D 357 ARG cc_start: 0.7803 (mmm160) cc_final: 0.7373 (mmp80) REVERT: E 222 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7121 (mp10) REVERT: E 349 ARG cc_start: 0.8087 (mtm110) cc_final: 0.7716 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.3507 time to fit residues: 169.3999 Evaluate side-chains 220 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 283 optimal weight: 40.0000 chunk 298 optimal weight: 20.0000 chunk 272 optimal weight: 30.0000 chunk 290 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 227 optimal weight: 0.0970 chunk 89 optimal weight: 3.9990 chunk 262 optimal weight: 0.7980 chunk 274 optimal weight: 30.0000 chunk 289 optimal weight: 9.9990 overall best weight: 3.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 334 HIS ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN B 243 ASN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 ASN C 399 ASN C 467 GLN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 24252 Z= 0.278 Angle : 0.749 13.444 32940 Z= 0.365 Chirality : 0.046 0.233 3848 Planarity : 0.005 0.076 4404 Dihedral : 9.495 163.033 3585 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.12 % Favored : 87.84 % Rotamer: Outliers : 0.04 % Allowed : 0.98 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.28 (0.16), residues: 2640 helix: -1.64 (0.15), residues: 1164 sheet: -2.41 (0.29), residues: 271 loop : -2.61 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 457 HIS 0.010 0.001 HIS B 67 PHE 0.018 0.002 PHE C 460 TYR 0.029 0.002 TYR D 344 ARG 0.017 0.001 ARG D 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 2.727 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: A 267 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7566 (mm-40) REVERT: A 270 MET cc_start: 0.8411 (tpp) cc_final: 0.7946 (tpp) REVERT: A 387 ARG cc_start: 0.8121 (ptm160) cc_final: 0.7684 (ptm160) REVERT: B 222 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8210 (mp10) REVERT: B 291 ASP cc_start: 0.7610 (t70) cc_final: 0.6332 (t0) REVERT: B 294 TRP cc_start: 0.5741 (m100) cc_final: 0.4089 (t-100) REVERT: B 348 MET cc_start: 0.7260 (mtp) cc_final: 0.7044 (mtp) REVERT: B 376 ASN cc_start: 0.8265 (m-40) cc_final: 0.8023 (m-40) REVERT: C 69 PHE cc_start: 0.7339 (t80) cc_final: 0.6562 (t80) REVERT: C 180 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7948 (mmtt) REVERT: C 237 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8247 (ttmm) REVERT: C 316 SER cc_start: 0.8318 (m) cc_final: 0.7896 (t) REVERT: C 359 LEU cc_start: 0.9123 (mm) cc_final: 0.8501 (tt) REVERT: D 42 MET cc_start: 0.6827 (mtm) cc_final: 0.6587 (mtm) REVERT: D 357 ARG cc_start: 0.8168 (mmm160) cc_final: 0.7701 (mmp80) REVERT: E 222 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7175 (mp10) REVERT: E 349 ARG cc_start: 0.8128 (mtm110) cc_final: 0.7732 (ptp-110) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.3491 time to fit residues: 150.7934 Evaluate side-chains 214 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 190 optimal weight: 0.9990 chunk 306 optimal weight: 20.0000 chunk 187 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 321 optimal weight: 20.0000 chunk 296 optimal weight: 20.0000 chunk 256 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 334 HIS ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN C 467 GLN D 243 ASN D 410 GLN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 ASN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24252 Z= 0.213 Angle : 0.726 13.132 32940 Z= 0.350 Chirality : 0.045 0.246 3848 Planarity : 0.005 0.071 4404 Dihedral : 9.339 162.596 3585 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.95 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.10 (0.16), residues: 2640 helix: -1.49 (0.15), residues: 1150 sheet: -2.48 (0.29), residues: 268 loop : -2.47 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 457 HIS 0.004 0.001 HIS B 67 PHE 0.029 0.002 PHE A 69 TYR 0.028 0.002 TYR D 344 ARG 0.010 0.000 ARG D 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7618 (mm-40) REVERT: A 270 MET cc_start: 0.8396 (tpp) cc_final: 0.7993 (tpp) REVERT: B 202 ASP cc_start: 0.6601 (m-30) cc_final: 0.5319 (t70) REVERT: B 222 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8233 (mp10) REVERT: B 235 MET cc_start: 0.6256 (mmt) cc_final: 0.5883 (mmt) REVERT: B 242 MET cc_start: 0.8199 (mmp) cc_final: 0.7703 (mtp) REVERT: B 291 ASP cc_start: 0.7627 (t70) cc_final: 0.6466 (t0) REVERT: B 294 TRP cc_start: 0.5492 (m100) cc_final: 0.4156 (t-100) REVERT: B 376 ASN cc_start: 0.8247 (m-40) cc_final: 0.8033 (m-40) REVERT: C 42 MET cc_start: 0.4404 (ptt) cc_final: 0.3803 (ptt) REVERT: C 69 PHE cc_start: 0.7330 (t80) cc_final: 0.6646 (t80) REVERT: C 180 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7922 (mmtt) REVERT: C 237 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8201 (ttmm) REVERT: C 316 SER cc_start: 0.8316 (m) cc_final: 0.7871 (t) REVERT: C 359 LEU cc_start: 0.9110 (mm) cc_final: 0.8569 (tt) REVERT: D 42 MET cc_start: 0.6703 (mtm) cc_final: 0.6501 (mtm) REVERT: D 341 MET cc_start: 0.8400 (tmm) cc_final: 0.8006 (ttp) REVERT: D 357 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7642 (mmp80) REVERT: D 410 GLN cc_start: 0.6190 (tt0) cc_final: 0.5946 (tt0) REVERT: E 222 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7163 (mp10) REVERT: E 349 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7458 (ptp-110) REVERT: E 416 MET cc_start: 0.8405 (mmm) cc_final: 0.8036 (tpp) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.3284 time to fit residues: 140.4308 Evaluate side-chains 207 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 203 optimal weight: 9.9990 chunk 272 optimal weight: 30.0000 chunk 78 optimal weight: 0.0010 chunk 236 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 256 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 263 optimal weight: 30.0000 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 3.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 334 HIS ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN B 243 ASN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.116755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.099564 restraints weight = 65475.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.099497 restraints weight = 56694.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.100515 restraints weight = 55012.771| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24252 Z= 0.269 Angle : 0.751 12.759 32940 Z= 0.364 Chirality : 0.046 0.308 3848 Planarity : 0.005 0.072 4404 Dihedral : 9.420 160.706 3585 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.24 (0.16), residues: 2640 helix: -1.57 (0.15), residues: 1176 sheet: -2.56 (0.29), residues: 268 loop : -2.59 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 457 HIS 0.004 0.001 HIS D 334 PHE 0.021 0.002 PHE D 166 TYR 0.025 0.002 TYR F 344 ARG 0.011 0.001 ARG E 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4188.16 seconds wall clock time: 76 minutes 5.32 seconds (4565.32 seconds total)