Starting phenix.real_space_refine on Mon Nov 18 02:35:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wda_37459/11_2024/8wda_37459.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wda_37459/11_2024/8wda_37459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wda_37459/11_2024/8wda_37459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wda_37459/11_2024/8wda_37459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wda_37459/11_2024/8wda_37459.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wda_37459/11_2024/8wda_37459.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3598 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 7897 2.51 5 N 2205 2.21 5 O 2231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12359 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3962 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 41, 'TRANS': 475} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2233 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Chain: "C" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2123 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 23 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "D" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3975 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 27, 'TRANS': 496} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'9XX': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 8.15, per 1000 atoms: 0.66 Number of scatterers: 12359 At special positions: 0 Unit cell: (86.92, 94.3, 164.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 2231 8.00 N 2205 7.00 C 7897 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.7 seconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 11 sheets defined 48.0% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.704A pdb=" N THR A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 4.865A pdb=" N ILE A 59 " --> pdb=" O ASN A 55 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 removed outlier: 3.787A pdb=" N PHE A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 178 through 182 removed outlier: 4.203A pdb=" N GLY A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 195 through 200 removed outlier: 3.608A pdb=" N PHE A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 200' Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.809A pdb=" N LEU A 276 " --> pdb=" O PRO A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 319 through 322 removed outlier: 3.598A pdb=" N ALA A 322 " --> pdb=" O LEU A 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 322' Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.592A pdb=" N GLN A 330 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 removed outlier: 3.731A pdb=" N ARG A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 421 through 431 removed outlier: 6.240A pdb=" N THR A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 490 through 504 removed outlier: 3.719A pdb=" N ARG A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 29 removed outlier: 4.166A pdb=" N ALA B 6 " --> pdb=" O GLY B 2 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG B 7 " --> pdb=" O TRP B 3 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 10 " --> pdb=" O ALA B 6 " (cutoff:3.500A) Proline residue: B 14 - end of helix removed outlier: 3.967A pdb=" N LEU B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.709A pdb=" N ARG B 53 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 75 removed outlier: 3.533A pdb=" N GLN B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 104 Proline residue: B 96 - end of helix removed outlier: 3.813A pdb=" N ILE B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.949A pdb=" N ILE B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 140 removed outlier: 3.581A pdb=" N ILE B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.694A pdb=" N GLY B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 202 removed outlier: 3.599A pdb=" N ALA B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.886A pdb=" N ARG B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 230 through 240 Processing helix chain 'B' and resid 240 through 255 removed outlier: 3.664A pdb=" N GLY B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 254 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 273 through 302 removed outlier: 3.756A pdb=" N VAL B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.605A pdb=" N ARG B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 307' Processing helix chain 'C' and resid 7 through 16 removed outlier: 3.863A pdb=" N ALA C 11 " --> pdb=" O PHE C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 37 removed outlier: 3.673A pdb=" N ALA C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 41 Processing helix chain 'C' and resid 72 through 106 removed outlier: 3.591A pdb=" N ARG C 76 " --> pdb=" O ASP C 72 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA C 94 " --> pdb=" O GLY C 90 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 128 through 139 removed outlier: 3.549A pdb=" N ALA C 132 " --> pdb=" O PRO C 128 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 157 removed outlier: 3.693A pdb=" N PHE C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TRP C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.533A pdb=" N GLU C 170 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 186 through 196 Processing helix chain 'C' and resid 201 through 224 removed outlier: 4.031A pdb=" N VAL C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 253 through 279 removed outlier: 3.595A pdb=" N ALA C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 57 removed outlier: 3.770A pdb=" N THR D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 88 removed outlier: 3.629A pdb=" N ARG D 86 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 116 Processing helix chain 'D' and resid 130 through 138 removed outlier: 3.682A pdb=" N LEU D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 149 removed outlier: 3.739A pdb=" N ARG D 149 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 removed outlier: 3.714A pdb=" N GLN D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 200 removed outlier: 3.834A pdb=" N GLN D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY D 198 " --> pdb=" O ASP D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 247 through 255 Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.729A pdb=" N THR D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 339 removed outlier: 3.609A pdb=" N ARG D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 338 " --> pdb=" O ALA D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 393 removed outlier: 3.566A pdb=" N ILE D 392 " --> pdb=" O VAL D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 399 removed outlier: 3.966A pdb=" N HIS D 399 " --> pdb=" O PRO D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 418 removed outlier: 3.530A pdb=" N ARG D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL D 411 " --> pdb=" O ARG D 407 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP D 416 " --> pdb=" O ARG D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 removed outlier: 3.508A pdb=" N GLU D 431 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU D 432 " --> pdb=" O PRO D 429 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER D 433 " --> pdb=" O ARG D 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 428 through 433' Processing helix chain 'D' and resid 437 through 446 removed outlier: 3.668A pdb=" N ALA D 441 " --> pdb=" O ARG D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 475 removed outlier: 3.648A pdb=" N ALA D 468 " --> pdb=" O VAL D 464 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 480 removed outlier: 3.884A pdb=" N ALA D 479 " --> pdb=" O ALA D 475 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 475 through 480' Processing helix chain 'D' and resid 531 through 535 removed outlier: 3.858A pdb=" N ALA D 534 " --> pdb=" O LEU D 531 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D 535 " --> pdb=" O LEU D 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 531 through 535' Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 86 removed outlier: 4.025A pdb=" N SER A 83 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.808A pdb=" N GLN A 296 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASP A 511 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE A 294 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE A 513 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA A 292 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL A 515 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLY A 290 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLY A 517 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR A 288 " --> pdb=" O GLY A 517 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP A 442 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASN A 390 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 11.324A pdb=" N GLY A 441 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A 385 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ALA A 417 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE A 387 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLN A 419 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR A 389 " --> pdb=" O GLN A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 12 through 18 removed outlier: 7.080A pdb=" N GLY D 13 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY D 68 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU D 15 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D 17 " --> pdb=" O ARG D 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 94 through 96 removed outlier: 3.854A pdb=" N GLU D 234 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG D 228 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 72 removed outlier: 3.732A pdb=" N ARG D 75 " --> pdb=" O PHE D 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 282 through 293 removed outlier: 7.098A pdb=" N VAL D 283 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG D 313 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER D 285 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER D 311 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU D 287 " --> pdb=" O GLY D 309 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 307 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR D 291 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ARG D 305 " --> pdb=" O TYR D 291 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLU D 293 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU D 303 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 372 through 374 removed outlier: 7.390A pdb=" N GLN D 372 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASP D 456 " --> pdb=" O GLN D 372 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL D 374 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU D 453 " --> pdb=" O LEU D 486 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE D 488 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS D 455 " --> pdb=" O ILE D 488 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA D 321 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N MET D 505 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL D 323 " --> pdb=" O MET D 505 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL D 502 " --> pdb=" O HIS D 513 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N HIS D 513 " --> pdb=" O VAL D 502 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL D 504 " --> pdb=" O VAL D 511 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1353 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: 2.90 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2013 1.31 - 1.43: 3302 1.43 - 1.56: 7258 1.56 - 1.68: 0 1.68 - 1.81: 47 Bond restraints: 12620 Sorted by residual: bond pdb=" CA ALA D 257 " pdb=" C ALA D 257 " ideal model delta sigma weight residual 1.527 1.474 0.053 1.31e-02 5.83e+03 1.63e+01 bond pdb=" O 9XX A 602 " pdb=" C15 9XX A 602 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C18 9XX A 602 " pdb=" O1 9XX A 602 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" N ALA D 257 " pdb=" CA ALA D 257 " ideal model delta sigma weight residual 1.458 1.416 0.042 1.48e-02 4.57e+03 8.02e+00 bond pdb=" CA PRO D 258 " pdb=" CB PRO D 258 " ideal model delta sigma weight residual 1.534 1.499 0.035 1.40e-02 5.10e+03 6.10e+00 ... (remaining 12615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 16932 2.41 - 4.83: 236 4.83 - 7.24: 38 7.24 - 9.65: 3 9.65 - 12.07: 1 Bond angle restraints: 17210 Sorted by residual: angle pdb=" N VAL A 90 " pdb=" CA VAL A 90 " pdb=" C VAL A 90 " ideal model delta sigma weight residual 113.71 108.42 5.29 9.50e-01 1.11e+00 3.10e+01 angle pdb=" N ALA D 257 " pdb=" CA ALA D 257 " pdb=" C ALA D 257 " ideal model delta sigma weight residual 110.07 104.31 5.76 1.26e+00 6.30e-01 2.09e+01 angle pdb=" N ARG B 7 " pdb=" CA ARG B 7 " pdb=" C ARG B 7 " ideal model delta sigma weight residual 113.41 108.35 5.06 1.22e+00 6.72e-01 1.72e+01 angle pdb=" N VAL A 80 " pdb=" CA VAL A 80 " pdb=" C VAL A 80 " ideal model delta sigma weight residual 111.90 108.80 3.10 8.10e-01 1.52e+00 1.47e+01 angle pdb=" N LEU B 215 " pdb=" CA LEU B 215 " pdb=" C LEU B 215 " ideal model delta sigma weight residual 110.35 115.67 -5.32 1.40e+00 5.10e-01 1.45e+01 ... (remaining 17205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 7355 34.47 - 68.93: 127 68.93 - 103.40: 12 103.40 - 137.87: 3 137.87 - 172.33: 1 Dihedral angle restraints: 7498 sinusoidal: 2875 harmonic: 4623 Sorted by residual: dihedral pdb=" C THR D 261 " pdb=" N THR D 261 " pdb=" CA THR D 261 " pdb=" CB THR D 261 " ideal model delta harmonic sigma weight residual -122.00 -137.85 15.85 0 2.50e+00 1.60e-01 4.02e+01 dihedral pdb=" N THR D 261 " pdb=" C THR D 261 " pdb=" CA THR D 261 " pdb=" CB THR D 261 " ideal model delta harmonic sigma weight residual 123.40 137.67 -14.27 0 2.50e+00 1.60e-01 3.26e+01 dihedral pdb=" C16 9XX A 602 " pdb=" O 9XX A 602 " pdb=" C15 9XX A 602 " pdb=" O6 9XX A 602 " ideal model delta sinusoidal sigma weight residual -2.46 169.87 -172.33 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 7495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1978 0.124 - 0.247: 24 0.247 - 0.371: 1 0.371 - 0.495: 0 0.495 - 0.618: 1 Chirality restraints: 2004 Sorted by residual: chirality pdb=" CA THR D 261 " pdb=" N THR D 261 " pdb=" C THR D 261 " pdb=" CB THR D 261 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.62 2.00e-01 2.50e+01 9.55e+00 chirality pdb=" CA ARG B 7 " pdb=" N ARG B 7 " pdb=" C ARG B 7 " pdb=" CB ARG B 7 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA SER D 259 " pdb=" N SER D 259 " pdb=" C SER D 259 " pdb=" CB SER D 259 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 2001 not shown) Planarity restraints: 2239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 192 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.94e+00 pdb=" C LEU C 192 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU C 192 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG C 193 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 257 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO D 258 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 258 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 258 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 60 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO B 61 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 61 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 61 " -0.036 5.00e-02 4.00e+02 ... (remaining 2236 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2236 2.76 - 3.30: 11537 3.30 - 3.83: 18849 3.83 - 4.37: 22967 4.37 - 4.90: 40319 Nonbonded interactions: 95908 Sorted by model distance: nonbonded pdb=" OH TYR A 70 " pdb=" O LEU A 178 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR A 468 " pdb=" OD2 ASP A 503 " model vdw 2.243 3.040 nonbonded pdb=" NE2 GLN D 160 " pdb=" O PRO D 180 " model vdw 2.250 3.120 nonbonded pdb=" OD1 ASP A 259 " pdb=" OG1 THR B 165 " model vdw 2.262 3.040 nonbonded pdb=" OD2 ASP C 45 " pdb=" OG1 THR C 47 " model vdw 2.313 3.040 ... (remaining 95903 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.040 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 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 : 0.004 0.069 12620 Z= 0.277 Angle : 0.724 12.065 17210 Z= 0.410 Chirality : 0.048 0.618 2004 Planarity : 0.005 0.070 2239 Dihedral : 14.237 172.335 4538 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.87 % Favored : 91.00 % Rotamer: Outliers : 0.55 % Allowed : 4.49 % Favored : 94.96 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.18), residues: 1612 helix: -2.61 (0.16), residues: 742 sheet: -2.40 (0.40), residues: 153 loop : -3.34 (0.20), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 12 HIS 0.004 0.001 HIS C 71 PHE 0.013 0.001 PHE A 165 TYR 0.022 0.001 TYR D 354 ARG 0.002 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 1.387 Fit side-chains REVERT: B 28 PHE cc_start: 0.7962 (t80) cc_final: 0.7579 (t80) REVERT: B 68 ARG cc_start: 0.7615 (mmt180) cc_final: 0.7225 (ttm-80) REVERT: C 112 TRP cc_start: 0.7411 (t60) cc_final: 0.6876 (t-100) REVERT: D 404 ARG cc_start: 0.7321 (mmt180) cc_final: 0.7024 (mtm-85) outliers start: 7 outliers final: 2 residues processed: 132 average time/residue: 0.3447 time to fit residues: 60.6962 Evaluate side-chains 94 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain C residue 286 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 81 optimal weight: 0.0060 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 497 GLN B 65 GLN B 152 GLN B 201 ASN ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN C 198 ASN D 103 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12620 Z= 0.171 Angle : 0.596 10.881 17210 Z= 0.305 Chirality : 0.044 0.166 2004 Planarity : 0.005 0.068 2239 Dihedral : 8.579 139.383 1835 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 1.02 % Allowed : 8.82 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.20), residues: 1612 helix: -1.51 (0.19), residues: 722 sheet: -1.84 (0.41), residues: 156 loop : -2.71 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 518 HIS 0.004 0.001 HIS C 71 PHE 0.011 0.001 PHE C 7 TYR 0.014 0.001 TYR D 354 ARG 0.013 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.378 Fit side-chains REVERT: B 12 MET cc_start: 0.7874 (ttp) cc_final: 0.7665 (ttp) REVERT: B 28 PHE cc_start: 0.7815 (t80) cc_final: 0.7505 (t80) REVERT: B 68 ARG cc_start: 0.7573 (mmt180) cc_final: 0.7192 (ttm-80) REVERT: B 215 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8097 (pp) REVERT: C 112 TRP cc_start: 0.7325 (t60) cc_final: 0.6810 (t-100) REVERT: C 175 ASP cc_start: 0.8450 (p0) cc_final: 0.8175 (p0) REVERT: C 283 ARG cc_start: 0.8006 (ttm170) cc_final: 0.7744 (ttm170) REVERT: D 404 ARG cc_start: 0.7160 (mmt180) cc_final: 0.6901 (mtm-85) outliers start: 13 outliers final: 4 residues processed: 123 average time/residue: 0.2838 time to fit residues: 49.3784 Evaluate side-chains 105 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 9.9990 chunk 45 optimal weight: 0.4980 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 0.1980 chunk 129 optimal weight: 4.9990 chunk 144 optimal weight: 0.0870 chunk 49 optimal weight: 0.0060 chunk 116 optimal weight: 3.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12620 Z= 0.132 Angle : 0.555 9.379 17210 Z= 0.282 Chirality : 0.042 0.155 2004 Planarity : 0.004 0.067 2239 Dihedral : 7.824 117.667 1830 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.73 % Allowed : 9.06 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.21), residues: 1612 helix: -0.97 (0.19), residues: 728 sheet: -1.36 (0.44), residues: 147 loop : -2.27 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 518 HIS 0.003 0.000 HIS C 71 PHE 0.009 0.001 PHE B 62 TYR 0.012 0.001 TYR C 176 ARG 0.007 0.000 ARG D 361 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.381 Fit side-chains REVERT: B 28 PHE cc_start: 0.7718 (t80) cc_final: 0.7411 (t80) REVERT: B 68 ARG cc_start: 0.7525 (mmt180) cc_final: 0.7217 (ttm-80) REVERT: B 176 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8979 (tt) REVERT: C 112 TRP cc_start: 0.7204 (t60) cc_final: 0.6801 (t-100) REVERT: C 175 ASP cc_start: 0.8398 (p0) cc_final: 0.8108 (p0) REVERT: C 270 MET cc_start: 0.8410 (tpp) cc_final: 0.8194 (tpp) REVERT: D 404 ARG cc_start: 0.7057 (mmt180) cc_final: 0.6853 (mtm-85) REVERT: D 430 ARG cc_start: 0.8146 (mtp-110) cc_final: 0.7929 (ptm-80) outliers start: 22 outliers final: 6 residues processed: 133 average time/residue: 0.2600 time to fit residues: 49.5642 Evaluate side-chains 112 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 146 optimal weight: 0.2980 chunk 154 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN B 224 HIS D 363 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12620 Z= 0.201 Angle : 0.581 10.448 17210 Z= 0.292 Chirality : 0.043 0.151 2004 Planarity : 0.004 0.066 2239 Dihedral : 7.634 115.839 1830 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 1.42 % Allowed : 10.55 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.21), residues: 1612 helix: -0.70 (0.20), residues: 728 sheet: -1.15 (0.45), residues: 149 loop : -2.11 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 398 HIS 0.004 0.001 HIS C 71 PHE 0.011 0.001 PHE A 165 TYR 0.012 0.001 TYR D 354 ARG 0.004 0.000 ARG D 361 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.453 Fit side-chains REVERT: B 28 PHE cc_start: 0.7653 (t80) cc_final: 0.7386 (t80) REVERT: B 68 ARG cc_start: 0.7544 (mmt180) cc_final: 0.7299 (ttm-80) REVERT: B 95 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8258 (t80) REVERT: B 169 ARG cc_start: 0.8341 (ttp-110) cc_final: 0.7975 (mtm180) REVERT: B 176 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9018 (tt) REVERT: C 112 TRP cc_start: 0.7243 (t60) cc_final: 0.6821 (t-100) REVERT: C 175 ASP cc_start: 0.8385 (p0) cc_final: 0.8145 (p0) REVERT: D 430 ARG cc_start: 0.8184 (mtp-110) cc_final: 0.7947 (ptm-80) outliers start: 18 outliers final: 12 residues processed: 121 average time/residue: 0.2868 time to fit residues: 48.8883 Evaluate side-chains 109 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 0.1980 chunk 115 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12620 Z= 0.242 Angle : 0.592 11.193 17210 Z= 0.299 Chirality : 0.044 0.148 2004 Planarity : 0.004 0.064 2239 Dihedral : 7.577 113.737 1830 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 1.65 % Allowed : 11.73 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.21), residues: 1612 helix: -0.55 (0.20), residues: 728 sheet: -1.03 (0.44), residues: 154 loop : -2.08 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 398 HIS 0.004 0.001 HIS C 71 PHE 0.012 0.001 PHE A 165 TYR 0.015 0.001 TYR D 354 ARG 0.004 0.000 ARG C 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.222 Fit side-chains REVERT: B 28 PHE cc_start: 0.7654 (t80) cc_final: 0.7396 (t80) REVERT: B 95 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8265 (t80) REVERT: B 169 ARG cc_start: 0.8354 (ttp-110) cc_final: 0.7918 (mtm110) REVERT: C 112 TRP cc_start: 0.7255 (t60) cc_final: 0.6817 (t-100) REVERT: C 175 ASP cc_start: 0.8377 (p0) cc_final: 0.8104 (p0) REVERT: D 430 ARG cc_start: 0.8208 (mtp-110) cc_final: 0.7937 (ptm-80) outliers start: 21 outliers final: 13 residues processed: 116 average time/residue: 0.2817 time to fit residues: 46.6580 Evaluate side-chains 106 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.0270 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12620 Z= 0.183 Angle : 0.573 10.565 17210 Z= 0.287 Chirality : 0.043 0.147 2004 Planarity : 0.004 0.064 2239 Dihedral : 7.381 111.463 1830 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 1.50 % Allowed : 12.36 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.21), residues: 1612 helix: -0.32 (0.20), residues: 728 sheet: -0.94 (0.47), residues: 146 loop : -1.96 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 398 HIS 0.004 0.001 HIS C 71 PHE 0.009 0.001 PHE A 165 TYR 0.013 0.001 TYR D 354 ARG 0.006 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.452 Fit side-chains REVERT: B 28 PHE cc_start: 0.7629 (t80) cc_final: 0.7373 (t80) REVERT: B 95 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8247 (t80) REVERT: C 112 TRP cc_start: 0.7221 (t60) cc_final: 0.6825 (t-100) REVERT: D 430 ARG cc_start: 0.8237 (mtp-110) cc_final: 0.7951 (ptm-80) outliers start: 19 outliers final: 14 residues processed: 119 average time/residue: 0.2730 time to fit residues: 46.5752 Evaluate side-chains 108 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 0.0270 chunk 113 optimal weight: 0.0020 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 154 optimal weight: 0.0470 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN B 258 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12620 Z= 0.132 Angle : 0.564 12.166 17210 Z= 0.280 Chirality : 0.042 0.149 2004 Planarity : 0.004 0.064 2239 Dihedral : 7.161 110.835 1830 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.81 % Allowed : 12.68 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.21), residues: 1612 helix: -0.00 (0.20), residues: 727 sheet: -0.87 (0.47), residues: 147 loop : -1.80 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 518 HIS 0.003 0.000 HIS C 71 PHE 0.007 0.001 PHE B 62 TYR 0.013 0.001 TYR C 176 ARG 0.007 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.596 Fit side-chains REVERT: B 28 PHE cc_start: 0.7625 (t80) cc_final: 0.7359 (t80) REVERT: B 95 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8140 (t80) REVERT: C 112 TRP cc_start: 0.7161 (t60) cc_final: 0.6830 (t-100) REVERT: D 430 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7919 (ptm-80) outliers start: 23 outliers final: 15 residues processed: 124 average time/residue: 0.2652 time to fit residues: 48.2071 Evaluate side-chains 118 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 30 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN B 65 GLN B 201 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12620 Z= 0.148 Angle : 0.574 12.080 17210 Z= 0.285 Chirality : 0.042 0.194 2004 Planarity : 0.004 0.064 2239 Dihedral : 7.062 110.285 1830 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.65 % Allowed : 13.78 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.22), residues: 1612 helix: 0.13 (0.20), residues: 727 sheet: -0.79 (0.47), residues: 147 loop : -1.71 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 518 HIS 0.003 0.000 HIS C 71 PHE 0.009 0.001 PHE B 145 TYR 0.011 0.001 TYR C 176 ARG 0.007 0.000 ARG D 361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.301 Fit side-chains REVERT: B 28 PHE cc_start: 0.7607 (t80) cc_final: 0.7336 (t80) REVERT: B 95 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8177 (t80) REVERT: C 112 TRP cc_start: 0.7164 (t60) cc_final: 0.6820 (t-100) REVERT: D 430 ARG cc_start: 0.8182 (mtp-110) cc_final: 0.7927 (ptm-80) outliers start: 21 outliers final: 15 residues processed: 121 average time/residue: 0.2671 time to fit residues: 46.7793 Evaluate side-chains 116 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 0.4980 chunk 134 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 12620 Z= 0.385 Angle : 0.681 13.426 17210 Z= 0.344 Chirality : 0.047 0.162 2004 Planarity : 0.005 0.062 2239 Dihedral : 7.463 107.850 1830 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 1.42 % Allowed : 13.86 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.21), residues: 1612 helix: -0.16 (0.20), residues: 727 sheet: -0.77 (0.46), residues: 149 loop : -1.96 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 398 HIS 0.005 0.001 HIS C 71 PHE 0.016 0.002 PHE A 165 TYR 0.029 0.001 TYR D 354 ARG 0.004 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.347 Fit side-chains REVERT: B 28 PHE cc_start: 0.7702 (t80) cc_final: 0.7442 (t80) REVERT: B 95 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8259 (t80) REVERT: C 112 TRP cc_start: 0.7326 (t60) cc_final: 0.6855 (t-100) outliers start: 18 outliers final: 15 residues processed: 113 average time/residue: 0.2961 time to fit residues: 46.7256 Evaluate side-chains 110 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.0000 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 159 optimal weight: 0.4980 chunk 146 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12620 Z= 0.158 Angle : 0.595 11.891 17210 Z= 0.297 Chirality : 0.043 0.163 2004 Planarity : 0.004 0.063 2239 Dihedral : 7.164 107.745 1830 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.34 % Allowed : 14.25 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.22), residues: 1612 helix: 0.17 (0.20), residues: 726 sheet: -0.86 (0.46), residues: 151 loop : -1.83 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 398 HIS 0.004 0.000 HIS C 71 PHE 0.008 0.001 PHE A 422 TYR 0.012 0.001 TYR C 176 ARG 0.009 0.000 ARG D 361 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.365 Fit side-chains REVERT: B 28 PHE cc_start: 0.7557 (t80) cc_final: 0.7287 (t80) REVERT: B 95 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8240 (t80) REVERT: C 112 TRP cc_start: 0.7178 (t60) cc_final: 0.6812 (t-100) REVERT: D 430 ARG cc_start: 0.8212 (mtp-110) cc_final: 0.7947 (ptm-80) outliers start: 17 outliers final: 14 residues processed: 117 average time/residue: 0.2825 time to fit residues: 46.8696 Evaluate side-chains 111 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.100390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.081187 restraints weight = 20767.735| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.33 r_work: 0.2813 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 12620 Z= 0.235 Angle : 0.834 59.196 17210 Z= 0.456 Chirality : 0.044 0.302 2004 Planarity : 0.004 0.063 2239 Dihedral : 7.171 107.820 1830 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.42 % Allowed : 14.25 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1612 helix: 0.16 (0.20), residues: 726 sheet: -0.85 (0.46), residues: 151 loop : -1.82 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 398 HIS 0.004 0.001 HIS C 71 PHE 0.009 0.001 PHE A 165 TYR 0.012 0.001 TYR C 176 ARG 0.009 0.000 ARG D 430 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2548.14 seconds wall clock time: 46 minutes 56.05 seconds (2816.05 seconds total)