Starting phenix.real_space_refine on Thu Mar 14 15:30:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj1_33868/03_2024/7yj1_33868_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj1_33868/03_2024/7yj1_33868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj1_33868/03_2024/7yj1_33868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj1_33868/03_2024/7yj1_33868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj1_33868/03_2024/7yj1_33868_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj1_33868/03_2024/7yj1_33868_updated.pdb" } resolution = 3.1 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= 0.004 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 1 5.49 5 S 50 5.16 5 C 5889 2.51 5 N 1545 2.21 5 O 1655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B ASP 369": "OD1" <-> "OD2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B ASP 465": "OD1" <-> "OD2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B ASP 533": "OD1" <-> "OD2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "E TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 120": "OD1" <-> "OD2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 408": "OD1" <-> "OD2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A GLU 466": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9140 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3962 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 483} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1165 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "C" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 411 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "A" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3285 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.04, per 1000 atoms: 0.55 Number of scatterers: 9140 At special positions: 0 Unit cell: (92.88, 83.16, 123.12, 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 50 16.00 P 1 15.00 O 1655 8.00 N 1545 7.00 C 5889 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 - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.9 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 7 sheets defined 40.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'B' and resid 68 through 94 removed outlier: 3.592A pdb=" N THR B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 76 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TRP B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 188 through 194 removed outlier: 3.516A pdb=" N ALA B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.527A pdb=" N GLU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 242 No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 288 through 291 No H-bonds generated for 'chain 'B' and resid 288 through 291' Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.690A pdb=" N LYS B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 392 through 398 removed outlier: 3.573A pdb=" N TYR B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 426 removed outlier: 3.622A pdb=" N GLN B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 456 removed outlier: 3.569A pdb=" N ALA B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 489 removed outlier: 3.728A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 535 Processing helix chain 'E' and resid 11 through 18 removed outlier: 3.949A pdb=" N GLN E 15 " --> pdb=" O VAL E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 37 removed outlier: 3.523A pdb=" N LEU E 27 " --> pdb=" O TYR E 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 38 removed outlier: 3.622A pdb=" N ILE D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 65 Processing helix chain 'D' and resid 89 through 92 Processing helix chain 'D' and resid 97 through 115 removed outlier: 3.664A pdb=" N THR D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) Proline residue: D 106 - end of helix removed outlier: 3.512A pdb=" N TYR D 110 " --> pdb=" O PRO D 106 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 133 removed outlier: 3.598A pdb=" N SER D 133 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'C' and resid 10 through 23 removed outlier: 3.537A pdb=" N TRP C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE C 16 " --> pdb=" O GLN C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 54 removed outlier: 3.790A pdb=" N VAL C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 44 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 51 " --> pdb=" O MET C 47 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 61 removed outlier: 3.632A pdb=" N GLU A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 removed outlier: 4.077A pdb=" N SER A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.729A pdb=" N ALA A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 175 through 178 No H-bonds generated for 'chain 'A' and resid 175 through 178' Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 214 through 229 removed outlier: 3.522A pdb=" N GLN A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 267 removed outlier: 4.064A pdb=" N LYS A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 322 through 329 removed outlier: 3.670A pdb=" N ASP A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 329' Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.509A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.616A pdb=" N LYS A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS A 374 " --> pdb=" O CYS A 370 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.555A pdb=" N VAL A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 466 removed outlier: 3.641A pdb=" N LYS A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 151 through 153 Processing sheet with id= B, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.513A pdb=" N LEU B 255 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU B 313 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU B 257 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N GLU B 315 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N ASP B 259 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B 276 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N SER B 258 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG B 278 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 494 through 496 removed outlier: 3.939A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG B 507 " --> pdb=" O VAL B 496 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 92 through 94 Processing sheet with id= E, first strand: chain 'A' and resid 160 through 164 Processing sheet with id= F, first strand: chain 'A' and resid 205 through 209 removed outlier: 3.571A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG A 270 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL A 244 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N PHE A 272 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 383 through 386 removed outlier: 3.509A pdb=" N LYS A 384 " --> pdb=" O GLN A 397 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 386 " --> pdb=" O HIS A 395 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 774 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: 2.18 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2924 1.34 - 1.46: 1484 1.46 - 1.57: 4850 1.57 - 1.69: 1 1.69 - 1.81: 83 Bond restraints: 9342 Sorted by residual: bond pdb=" C2 PLP B 601 " pdb=" C3 PLP B 601 " ideal model delta sigma weight residual 1.390 1.484 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C4 PLP B 601 " pdb=" C5 PLP B 601 " ideal model delta sigma weight residual 1.390 1.483 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C3 PLP B 601 " pdb=" C4 PLP B 601 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" CA ASN A 107 " pdb=" CB ASN A 107 " ideal model delta sigma weight residual 1.525 1.555 -0.030 1.47e-02 4.63e+03 4.12e+00 bond pdb=" C ILE D 136 " pdb=" O ILE D 136 " ideal model delta sigma weight residual 1.242 1.226 0.016 8.60e-03 1.35e+04 3.29e+00 ... (remaining 9337 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.87: 264 106.87 - 113.66: 5101 113.66 - 120.45: 3609 120.45 - 127.24: 3590 127.24 - 134.04: 83 Bond angle restraints: 12647 Sorted by residual: angle pdb=" N PRO A 78 " pdb=" CA PRO A 78 " pdb=" CB PRO A 78 " ideal model delta sigma weight residual 103.33 110.23 -6.90 1.10e+00 8.26e-01 3.93e+01 angle pdb=" CA ILE D 136 " pdb=" C ILE D 136 " pdb=" N PRO D 137 " ideal model delta sigma weight residual 120.83 117.08 3.75 6.10e-01 2.69e+00 3.79e+01 angle pdb=" N ILE B 503 " pdb=" CA ILE B 503 " pdb=" C ILE B 503 " ideal model delta sigma weight residual 110.23 116.24 -6.01 1.04e+00 9.25e-01 3.34e+01 angle pdb=" N GLY B 497 " pdb=" CA GLY B 497 " pdb=" C GLY B 497 " ideal model delta sigma weight residual 112.55 119.97 -7.42 1.44e+00 4.82e-01 2.65e+01 angle pdb=" N TYR E 44 " pdb=" CA TYR E 44 " pdb=" C TYR E 44 " ideal model delta sigma weight residual 110.80 120.50 -9.70 2.13e+00 2.20e-01 2.07e+01 ... (remaining 12642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4815 17.95 - 35.89: 522 35.89 - 53.84: 173 53.84 - 71.78: 53 71.78 - 89.73: 16 Dihedral angle restraints: 5579 sinusoidal: 2237 harmonic: 3342 Sorted by residual: dihedral pdb=" CA PRO B 142 " pdb=" C PRO B 142 " pdb=" N GLY B 143 " pdb=" CA GLY B 143 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TYR B 461 " pdb=" C TYR B 461 " pdb=" N GLY B 462 " pdb=" CA GLY B 462 " ideal model delta harmonic sigma weight residual 180.00 160.21 19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA LEU B 473 " pdb=" C LEU B 473 " pdb=" N TYR B 474 " pdb=" CA TYR B 474 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1106 0.057 - 0.114: 260 0.114 - 0.171: 43 0.171 - 0.228: 1 0.228 - 0.285: 3 Chirality restraints: 1413 Sorted by residual: chirality pdb=" CA TYR E 44 " pdb=" N TYR E 44 " pdb=" C TYR E 44 " pdb=" CB TYR E 44 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA GLU A 400 " pdb=" N GLU A 400 " pdb=" C GLU A 400 " pdb=" CB GLU A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO A 78 " pdb=" N PRO A 78 " pdb=" C PRO A 78 " pdb=" CB PRO A 78 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1410 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 42 " 0.012 2.00e-02 2.50e+03 1.61e-02 4.52e+00 pdb=" CG PHE D 42 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE D 42 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE D 42 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE D 42 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 42 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 42 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 135 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C PRO A 135 " 0.030 2.00e-02 2.50e+03 pdb=" O PRO A 135 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 136 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO B 502 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.024 5.00e-02 4.00e+02 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 2 2.17 - 2.85: 3240 2.85 - 3.53: 11357 3.53 - 4.22: 20123 4.22 - 4.90: 36240 Nonbonded interactions: 70962 Sorted by model distance: nonbonded pdb=" OG SER A 381 " pdb=" OE1 GLN A 469 " model vdw 1.486 2.440 nonbonded pdb=" OH TYR A 128 " pdb=" OD1 ASP A 143 " model vdw 2.143 2.440 nonbonded pdb=" O ARG B 399 " pdb=" OH TYR A 82 " model vdw 2.190 2.440 nonbonded pdb=" OD2 ASP D 76 " pdb=" NH1 ARG A 181 " model vdw 2.214 2.520 nonbonded pdb=" OD1 ASN B 245 " pdb=" OG SER B 402 " model vdw 2.219 2.440 ... (remaining 70957 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.80 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.010 Extract box with map and model: 4.100 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.020 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 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 : 0.006 0.094 9342 Z= 0.377 Angle : 0.838 9.697 12647 Z= 0.547 Chirality : 0.051 0.285 1413 Planarity : 0.004 0.043 1605 Dihedral : 18.001 89.730 3441 Min Nonbonded Distance : 1.486 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.43 % Favored : 91.87 % Rotamer: Outliers : 9.53 % Allowed : 5.64 % Favored : 84.84 % 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: -3.00 (0.24), residues: 1144 helix: -1.36 (0.23), residues: 504 sheet: -1.93 (0.51), residues: 109 loop : -2.61 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.004 0.001 HIS A 327 PHE 0.037 0.002 PHE D 42 TYR 0.025 0.002 TYR B 461 ARG 0.002 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 113 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8797 (mttt) REVERT: B 109 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8048 (mtmm) REVERT: B 136 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8932 (mtt180) REVERT: B 196 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8782 (tp) REVERT: B 197 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: B 288 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8645 (tp) REVERT: B 429 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: B 471 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8418 (tp) REVERT: B 475 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.7656 (mmt) REVERT: B 505 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: B 538 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8864 (mttp) REVERT: E 38 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8479 (pt) REVERT: D 118 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8057 (mtpt) REVERT: D 124 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7911 (t80) REVERT: A 58 GLU cc_start: 0.7939 (tp30) cc_final: 0.7275 (tp30) REVERT: A 77 HIS cc_start: 0.5934 (OUTLIER) cc_final: 0.4069 (t-90) REVERT: A 136 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8440 (ttt180) REVERT: A 234 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8238 (tttt) outliers start: 93 outliers final: 49 residues processed: 190 average time/residue: 0.2588 time to fit residues: 64.5378 Evaluate side-chains 165 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 99 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 134 TRP Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 467 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9342 Z= 0.361 Angle : 0.640 6.300 12647 Z= 0.333 Chirality : 0.046 0.243 1413 Planarity : 0.004 0.042 1605 Dihedral : 12.242 81.677 1439 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 5.12 % Allowed : 12.30 % Favored : 82.58 % 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: -2.25 (0.24), residues: 1144 helix: -0.65 (0.24), residues: 494 sheet: -1.52 (0.46), residues: 127 loop : -2.30 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 94 HIS 0.005 0.001 HIS B 47 PHE 0.020 0.002 PHE B 449 TYR 0.024 0.002 TYR E 44 ARG 0.004 0.000 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 112 time to evaluate : 0.976 Fit side-chains REVERT: B 46 HIS cc_start: 0.7345 (t-90) cc_final: 0.6720 (t-90) REVERT: B 109 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7909 (mtmm) REVERT: B 292 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8626 (mp) REVERT: B 429 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: B 505 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: B 530 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: E 42 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8323 (mmtm) REVERT: A 58 GLU cc_start: 0.7866 (tp30) cc_final: 0.7215 (tp30) REVERT: A 77 HIS cc_start: 0.5961 (OUTLIER) cc_final: 0.4113 (t-90) REVERT: A 234 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8257 (tttt) outliers start: 50 outliers final: 32 residues processed: 152 average time/residue: 0.2282 time to fit residues: 47.4105 Evaluate side-chains 145 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 105 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 134 TRP Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 467 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 HIS A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9342 Z= 0.236 Angle : 0.553 10.386 12647 Z= 0.286 Chirality : 0.043 0.213 1413 Planarity : 0.004 0.041 1605 Dihedral : 9.618 75.585 1344 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.79 % Allowed : 14.75 % Favored : 81.45 % 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: -1.79 (0.25), residues: 1144 helix: -0.15 (0.24), residues: 493 sheet: -1.39 (0.46), residues: 127 loop : -2.15 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 94 HIS 0.005 0.001 HIS E 24 PHE 0.013 0.001 PHE B 449 TYR 0.020 0.001 TYR E 44 ARG 0.002 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 107 time to evaluate : 1.149 Fit side-chains REVERT: B 198 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7763 (pp20) REVERT: B 289 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.7630 (tp30) REVERT: B 292 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8627 (mp) REVERT: B 345 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7971 (pt0) REVERT: B 429 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.7096 (tt0) REVERT: D 141 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7312 (mt0) REVERT: A 58 GLU cc_start: 0.7863 (tp30) cc_final: 0.7212 (tp30) REVERT: A 59 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7659 (mm-30) REVERT: A 77 HIS cc_start: 0.5896 (OUTLIER) cc_final: 0.3934 (t-90) outliers start: 37 outliers final: 22 residues processed: 135 average time/residue: 0.2271 time to fit residues: 42.3208 Evaluate side-chains 133 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 104 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9990 chunk 77 optimal weight: 0.0870 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 109 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9342 Z= 0.156 Angle : 0.496 8.504 12647 Z= 0.256 Chirality : 0.042 0.197 1413 Planarity : 0.003 0.041 1605 Dihedral : 7.745 71.333 1314 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.28 % Allowed : 15.37 % Favored : 81.35 % 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: -1.34 (0.25), residues: 1144 helix: 0.25 (0.25), residues: 496 sheet: -1.17 (0.47), residues: 129 loop : -1.95 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 94 HIS 0.003 0.001 HIS B 47 PHE 0.010 0.001 PHE A 209 TYR 0.020 0.001 TYR E 44 ARG 0.002 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 108 time to evaluate : 1.117 Fit side-chains REVERT: B 198 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7772 (pp20) REVERT: B 289 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.7631 (tp30) REVERT: B 292 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8661 (mp) REVERT: B 427 MET cc_start: 0.8628 (mtp) cc_final: 0.8315 (mtp) REVERT: E 36 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8247 (tp) REVERT: A 58 GLU cc_start: 0.7923 (tp30) cc_final: 0.7331 (tp30) REVERT: A 77 HIS cc_start: 0.5821 (OUTLIER) cc_final: 0.3817 (t-90) REVERT: A 274 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7764 (tm-30) outliers start: 32 outliers final: 21 residues processed: 133 average time/residue: 0.2222 time to fit residues: 40.7744 Evaluate side-chains 128 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.0570 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 HIS C 38 ASN A 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9342 Z= 0.383 Angle : 0.600 8.254 12647 Z= 0.309 Chirality : 0.046 0.200 1413 Planarity : 0.004 0.046 1605 Dihedral : 7.296 69.929 1306 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.41 % Allowed : 14.86 % Favored : 80.74 % 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 (0.25), residues: 1144 helix: 0.17 (0.24), residues: 505 sheet: -1.28 (0.46), residues: 121 loop : -1.89 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 94 HIS 0.004 0.001 HIS B 47 PHE 0.017 0.002 PHE D 101 TYR 0.020 0.002 TYR E 44 ARG 0.003 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 104 time to evaluate : 1.087 Fit side-chains REVERT: B 198 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7791 (pp20) REVERT: B 289 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.7641 (tp30) REVERT: B 292 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8580 (mp) REVERT: B 427 MET cc_start: 0.8677 (mtp) cc_final: 0.8324 (mtp) REVERT: B 472 MET cc_start: 0.9244 (mmm) cc_final: 0.8693 (mmm) REVERT: B 473 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8818 (pp) REVERT: E 36 ILE cc_start: 0.8556 (mm) cc_final: 0.8318 (tp) REVERT: D 121 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7005 (mp10) REVERT: D 141 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7266 (mt0) REVERT: A 58 GLU cc_start: 0.7988 (tp30) cc_final: 0.7362 (tp30) REVERT: A 77 HIS cc_start: 0.5895 (OUTLIER) cc_final: 0.3882 (t-90) REVERT: A 83 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8474 (p0) outliers start: 43 outliers final: 28 residues processed: 140 average time/residue: 0.2198 time to fit residues: 42.3815 Evaluate side-chains 139 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 103 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 134 TRP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 462 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.0470 chunk 26 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 0.0060 overall best weight: 0.5094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9342 Z= 0.137 Angle : 0.475 6.938 12647 Z= 0.245 Chirality : 0.041 0.178 1413 Planarity : 0.003 0.046 1605 Dihedral : 6.501 64.345 1300 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.69 % Allowed : 16.50 % Favored : 79.82 % 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: -0.94 (0.26), residues: 1144 helix: 0.61 (0.25), residues: 499 sheet: -1.10 (0.46), residues: 129 loop : -1.74 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 94 HIS 0.002 0.000 HIS B 47 PHE 0.012 0.001 PHE A 209 TYR 0.020 0.001 TYR E 44 ARG 0.002 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 1.050 Fit side-chains REVERT: B 92 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.6536 (ptm160) REVERT: B 198 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7812 (pp20) REVERT: B 289 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.7658 (tp30) REVERT: B 427 MET cc_start: 0.8624 (mtp) cc_final: 0.8249 (mtp) REVERT: B 472 MET cc_start: 0.9126 (mmm) cc_final: 0.8512 (mmm) REVERT: B 473 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8782 (pp) REVERT: E 36 ILE cc_start: 0.8413 (mm) cc_final: 0.8168 (tp) REVERT: D 141 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7297 (mt0) REVERT: A 58 GLU cc_start: 0.7898 (tp30) cc_final: 0.7386 (tp30) REVERT: A 77 HIS cc_start: 0.5950 (OUTLIER) cc_final: 0.3867 (t-90) REVERT: A 83 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8435 (p0) REVERT: A 274 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8010 (tm-30) outliers start: 36 outliers final: 23 residues processed: 138 average time/residue: 0.2205 time to fit residues: 41.9541 Evaluate side-chains 135 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.0980 chunk 62 optimal weight: 0.1980 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 50 optimal weight: 0.0570 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 ASN E 24 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9342 Z= 0.124 Angle : 0.462 6.481 12647 Z= 0.238 Chirality : 0.041 0.173 1413 Planarity : 0.003 0.046 1605 Dihedral : 5.771 58.305 1295 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.97 % Allowed : 17.73 % Favored : 79.30 % 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: -0.57 (0.26), residues: 1144 helix: 0.96 (0.25), residues: 498 sheet: -0.95 (0.47), residues: 127 loop : -1.58 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 94 HIS 0.002 0.000 HIS B 47 PHE 0.010 0.001 PHE A 209 TYR 0.022 0.001 TYR E 44 ARG 0.003 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.129 Fit side-chains REVERT: B 198 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7816 (pp20) REVERT: B 289 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.7773 (tp30) REVERT: B 427 MET cc_start: 0.8656 (mtp) cc_final: 0.8319 (mtp) REVERT: B 472 MET cc_start: 0.9083 (mmm) cc_final: 0.8465 (mmm) REVERT: B 473 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8729 (pp) REVERT: A 58 GLU cc_start: 0.7828 (tp30) cc_final: 0.7344 (tp30) REVERT: A 77 HIS cc_start: 0.5936 (OUTLIER) cc_final: 0.3870 (t-90) REVERT: A 83 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8426 (p0) REVERT: A 274 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7994 (tm-30) outliers start: 29 outliers final: 18 residues processed: 138 average time/residue: 0.2334 time to fit residues: 44.2714 Evaluate side-chains 132 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9342 Z= 0.273 Angle : 0.549 6.673 12647 Z= 0.283 Chirality : 0.044 0.223 1413 Planarity : 0.004 0.049 1605 Dihedral : 5.795 55.949 1289 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.97 % Allowed : 17.52 % Favored : 79.51 % 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: -0.68 (0.26), residues: 1144 helix: 0.77 (0.24), residues: 504 sheet: -1.12 (0.46), residues: 125 loop : -1.51 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 94 HIS 0.003 0.001 HIS B 47 PHE 0.015 0.002 PHE D 101 TYR 0.018 0.001 TYR E 44 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 0.998 Fit side-chains REVERT: B 198 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7826 (pp20) REVERT: B 289 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8105 (tp30) REVERT: B 418 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: B 427 MET cc_start: 0.8658 (mtp) cc_final: 0.8267 (mtp) REVERT: B 472 MET cc_start: 0.9188 (mmm) cc_final: 0.8637 (mmm) REVERT: B 473 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8770 (pp) REVERT: A 58 GLU cc_start: 0.7930 (tp30) cc_final: 0.7409 (tp30) REVERT: A 77 HIS cc_start: 0.5986 (OUTLIER) cc_final: 0.3881 (t-90) REVERT: A 83 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8470 (p0) outliers start: 29 outliers final: 22 residues processed: 127 average time/residue: 0.2141 time to fit residues: 37.7931 Evaluate side-chains 128 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 0.0060 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 0.0070 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 65 optimal weight: 0.0020 overall best weight: 0.4424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9342 Z= 0.134 Angle : 0.482 6.467 12647 Z= 0.249 Chirality : 0.041 0.204 1413 Planarity : 0.003 0.047 1605 Dihedral : 5.437 51.791 1289 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.87 % Allowed : 17.73 % Favored : 79.41 % 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: -0.39 (0.26), residues: 1144 helix: 1.05 (0.24), residues: 507 sheet: -0.98 (0.47), residues: 123 loop : -1.42 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 94 HIS 0.002 0.000 HIS B 47 PHE 0.011 0.001 PHE A 209 TYR 0.019 0.001 TYR E 44 ARG 0.003 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 1.083 Fit side-chains REVERT: B 472 MET cc_start: 0.9081 (mmm) cc_final: 0.8462 (mmm) REVERT: B 473 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8737 (pp) REVERT: A 58 GLU cc_start: 0.7847 (tp30) cc_final: 0.7266 (tp30) REVERT: A 77 HIS cc_start: 0.5953 (OUTLIER) cc_final: 0.3868 (t-90) REVERT: A 83 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8453 (p0) REVERT: A 274 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8018 (tm-30) outliers start: 28 outliers final: 20 residues processed: 135 average time/residue: 0.2211 time to fit residues: 41.5735 Evaluate side-chains 133 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN B 347 HIS ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 9342 Z= 0.429 Angle : 0.628 7.702 12647 Z= 0.325 Chirality : 0.048 0.262 1413 Planarity : 0.004 0.050 1605 Dihedral : 5.797 52.114 1286 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.97 % Allowed : 18.03 % Favored : 79.00 % Cbeta Deviations : 0.09 % 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: -0.80 (0.25), residues: 1144 helix: 0.61 (0.24), residues: 510 sheet: -1.05 (0.47), residues: 121 loop : -1.57 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 94 HIS 0.004 0.001 HIS B 47 PHE 0.022 0.002 PHE B 90 TYR 0.020 0.002 TYR D 26 ARG 0.003 0.000 ARG A 422 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 1.189 Fit side-chains REVERT: B 92 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.6894 (ptm160) REVERT: B 418 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: B 472 MET cc_start: 0.9235 (mmm) cc_final: 0.8731 (mmm) REVERT: A 58 GLU cc_start: 0.7970 (tp30) cc_final: 0.7417 (tp30) REVERT: A 77 HIS cc_start: 0.6040 (OUTLIER) cc_final: 0.4043 (t-90) REVERT: A 83 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8486 (p0) outliers start: 29 outliers final: 22 residues processed: 125 average time/residue: 0.2273 time to fit residues: 39.1339 Evaluate side-chains 128 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 64 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 HIS A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.107404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.085787 restraints weight = 13161.109| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.97 r_work: 0.2763 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9342 Z= 0.144 Angle : 0.503 10.619 12647 Z= 0.258 Chirality : 0.042 0.216 1413 Planarity : 0.003 0.044 1605 Dihedral : 5.415 51.967 1286 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.25 % Allowed : 18.85 % Favored : 78.89 % 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: -0.45 (0.26), residues: 1144 helix: 1.05 (0.24), residues: 500 sheet: -0.97 (0.48), residues: 123 loop : -1.50 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 94 HIS 0.002 0.000 HIS D 56 PHE 0.012 0.001 PHE A 209 TYR 0.017 0.001 TYR E 44 ARG 0.003 0.000 ARG A 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2062.45 seconds wall clock time: 37 minutes 49.41 seconds (2269.41 seconds total)