Starting phenix.real_space_refine on Fri Feb 16 21:52:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfv_30579/02_2024/7dfv_30579.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfv_30579/02_2024/7dfv_30579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfv_30579/02_2024/7dfv_30579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfv_30579/02_2024/7dfv_30579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfv_30579/02_2024/7dfv_30579.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfv_30579/02_2024/7dfv_30579.pdb" } resolution = 2.99 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= 1.000 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10564 2.51 5 N 2880 2.21 5 O 3040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 123": "NH1" <-> "NH2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C GLU 586": "OE1" <-> "OE2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D GLU 519": "OE1" <-> "OE2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A GLU 586": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16580 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4163 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4127 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 14, 'TRANS': 501} Chain: "D" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4163 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 4127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4127 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 14, 'TRANS': 501} Time building chain proxies: 9.24, per 1000 atoms: 0.56 Number of scatterers: 16580 At special positions: 0 Unit cell: (106.496, 108.692, 128.454, 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 96 16.00 O 3040 8.00 N 2880 7.00 C 10564 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=0, symmetry=0 Time building additional restraints: 6.46 Conformation dependent library (CDL) restraints added in 2.9 seconds 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 14 sheets defined 59.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 99 through 111 removed outlier: 4.243A pdb=" N HIS B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.518A pdb=" N GLU B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 Processing helix chain 'B' and resid 152 through 170 removed outlier: 4.026A pdb=" N LEU B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 removed outlier: 3.513A pdb=" N LYS B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 200 removed outlier: 3.719A pdb=" N PHE B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.598A pdb=" N GLU B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 231 through 248 removed outlier: 3.770A pdb=" N MET B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 274 removed outlier: 3.643A pdb=" N LEU B 272 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 305 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 316 through 321 removed outlier: 3.507A pdb=" N CYS B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 344 removed outlier: 3.714A pdb=" N ALA B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 375 through 383 removed outlier: 4.152A pdb=" N LEU B 379 " --> pdb=" O GLN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 401 through 408 removed outlier: 3.967A pdb=" N LEU B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 433 Processing helix chain 'B' and resid 442 through 453 Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 471 through 484 Proline residue: B 480 - end of helix Processing helix chain 'B' and resid 487 through 499 removed outlier: 4.323A pdb=" N ILE B 493 " --> pdb=" O LYS B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 515 Processing helix chain 'B' and resid 520 through 528 Processing helix chain 'B' and resid 533 through 544 Processing helix chain 'B' and resid 557 through 568 Processing helix chain 'B' and resid 592 through 596 removed outlier: 3.735A pdb=" N ASP B 596 " --> pdb=" O LEU B 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 99 through 111 removed outlier: 4.090A pdb=" N HIS C 103 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 137 removed outlier: 3.623A pdb=" N ILE C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 231 through 249 Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.751A pdb=" N GLY C 258 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 274 removed outlier: 3.910A pdb=" N HIS C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 272 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 305 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'C' and resid 327 through 344 removed outlier: 3.584A pdb=" N ALA C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 375 through 383 removed outlier: 3.674A pdb=" N LEU C 379 " --> pdb=" O GLN C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 409 removed outlier: 4.153A pdb=" N LEU C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 434 removed outlier: 3.592A pdb=" N GLY C 434 " --> pdb=" O MET C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 453 Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 471 through 485 Proline residue: C 480 - end of helix Processing helix chain 'C' and resid 487 through 499 removed outlier: 4.346A pdb=" N ILE C 493 " --> pdb=" O LYS C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 515 Processing helix chain 'C' and resid 520 through 529 Processing helix chain 'C' and resid 533 through 544 removed outlier: 3.553A pdb=" N HIS C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.974A pdb=" N PHE C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 594 removed outlier: 3.960A pdb=" N VAL C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 99 through 111 removed outlier: 4.243A pdb=" N HIS D 103 " --> pdb=" O THR D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 126 through 137 removed outlier: 3.517A pdb=" N GLU D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 151 Processing helix chain 'D' and resid 152 through 170 removed outlier: 4.026A pdb=" N LEU D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY D 170 " --> pdb=" O ARG D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 188 removed outlier: 3.512A pdb=" N LYS D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 200 removed outlier: 3.720A pdb=" N PHE D 196 " --> pdb=" O PHE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 220 removed outlier: 3.598A pdb=" N GLU D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 231 through 248 removed outlier: 3.770A pdb=" N MET D 235 " --> pdb=" O ASN D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 274 removed outlier: 3.643A pdb=" N LEU D 272 " --> pdb=" O MET D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 316 through 321 removed outlier: 3.508A pdb=" N CYS D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 344 removed outlier: 3.714A pdb=" N ALA D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 361 Processing helix chain 'D' and resid 375 through 383 removed outlier: 4.151A pdb=" N LEU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 401 through 408 removed outlier: 3.966A pdb=" N LEU D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 433 Processing helix chain 'D' and resid 442 through 453 Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 471 through 484 Proline residue: D 480 - end of helix Processing helix chain 'D' and resid 487 through 499 removed outlier: 4.323A pdb=" N ILE D 493 " --> pdb=" O LYS D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 515 Processing helix chain 'D' and resid 520 through 528 Processing helix chain 'D' and resid 533 through 544 Processing helix chain 'D' and resid 557 through 568 Processing helix chain 'D' and resid 592 through 596 removed outlier: 3.735A pdb=" N ASP D 596 " --> pdb=" O LEU D 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 99 through 111 removed outlier: 4.090A pdb=" N HIS A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.623A pdb=" N ILE A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 189 through 200 Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 231 through 249 Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.751A pdb=" N GLY A 258 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.911A pdb=" N HIS A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 272 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 305 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 327 through 344 removed outlier: 3.584A pdb=" N ALA A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.674A pdb=" N LEU A 379 " --> pdb=" O GLN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 409 removed outlier: 4.153A pdb=" N LEU A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.592A pdb=" N GLY A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 453 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 485 Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 487 through 499 removed outlier: 4.346A pdb=" N ILE A 493 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 515 Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 533 through 544 removed outlier: 3.554A pdb=" N HIS A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.974A pdb=" N PHE A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.960A pdb=" N VAL A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 85 through 90 removed outlier: 6.833A pdb=" N GLN B 86 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS B 139 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N MET B 174 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA B 141 " --> pdb=" O MET B 174 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE B 176 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL B 143 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 310 through 314 Processing sheet with id=AA3, first strand: chain 'B' and resid 548 through 549 Processing sheet with id=AA4, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AA5, first strand: chain 'C' and resid 310 through 314 removed outlier: 6.303A pdb=" N VAL C 366 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE C 396 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU C 368 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR C 398 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU C 370 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 283 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR C 399 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE C 285 " --> pdb=" O THR C 399 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N MET C 282 " --> pdb=" O HIS C 412 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR C 414 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY C 284 " --> pdb=" O TYR C 414 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 548 through 550 Processing sheet with id=AA7, first strand: chain 'C' and resid 573 through 574 Processing sheet with id=AA8, first strand: chain 'D' and resid 85 through 90 removed outlier: 6.833A pdb=" N GLN D 86 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS D 139 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N MET D 174 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA D 141 " --> pdb=" O MET D 174 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE D 176 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL D 143 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 310 through 314 Processing sheet with id=AB1, first strand: chain 'D' and resid 548 through 549 Processing sheet with id=AB2, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AB3, first strand: chain 'A' and resid 310 through 314 removed outlier: 6.303A pdb=" N VAL A 366 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE A 396 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 368 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR A 398 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 370 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 283 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR A 399 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE A 285 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N MET A 282 " --> pdb=" O HIS A 412 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR A 414 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY A 284 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 548 through 550 Processing sheet with id=AB5, first strand: chain 'A' and resid 573 through 574 816 hydrogen bonds defined for protein. 2358 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: 5.67 Time building geometry restraints manager: 6.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2776 1.31 - 1.44: 4326 1.44 - 1.56: 9646 1.56 - 1.68: 0 1.68 - 1.81: 156 Bond restraints: 16904 Sorted by residual: bond pdb=" C PRO B 288 " pdb=" O PRO B 288 " ideal model delta sigma weight residual 1.240 1.191 0.050 1.12e-02 7.97e+03 1.98e+01 bond pdb=" C PRO D 288 " pdb=" O PRO D 288 " ideal model delta sigma weight residual 1.240 1.191 0.049 1.12e-02 7.97e+03 1.94e+01 bond pdb=" C LEU B 269 " pdb=" O LEU B 269 " ideal model delta sigma weight residual 1.237 1.194 0.042 1.19e-02 7.06e+03 1.26e+01 bond pdb=" C LEU D 269 " pdb=" O LEU D 269 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.19e-02 7.06e+03 1.23e+01 bond pdb=" C GLY C 287 " pdb=" N PRO C 288 " ideal model delta sigma weight residual 1.329 1.370 -0.040 1.18e-02 7.18e+03 1.18e+01 ... (remaining 16899 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.49: 243 105.49 - 112.67: 8862 112.67 - 119.85: 5847 119.85 - 127.02: 7614 127.02 - 134.20: 178 Bond angle restraints: 22744 Sorted by residual: angle pdb=" N CYS B 590 " pdb=" CA CYS B 590 " pdb=" C CYS B 590 " ideal model delta sigma weight residual 114.75 105.77 8.98 1.26e+00 6.30e-01 5.08e+01 angle pdb=" N CYS D 590 " pdb=" CA CYS D 590 " pdb=" C CYS D 590 " ideal model delta sigma weight residual 114.75 105.77 8.98 1.26e+00 6.30e-01 5.07e+01 angle pdb=" C THR B 398 " pdb=" CA THR B 398 " pdb=" CB THR B 398 " ideal model delta sigma weight residual 109.48 119.86 -10.38 1.68e+00 3.54e-01 3.82e+01 angle pdb=" C THR D 398 " pdb=" CA THR D 398 " pdb=" CB THR D 398 " ideal model delta sigma weight residual 109.48 119.84 -10.36 1.68e+00 3.54e-01 3.80e+01 angle pdb=" CA PRO D 288 " pdb=" C PRO D 288 " pdb=" N PRO D 289 " ideal model delta sigma weight residual 117.93 124.59 -6.66 1.20e+00 6.94e-01 3.08e+01 ... (remaining 22739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 9193 16.97 - 33.94: 833 33.94 - 50.91: 138 50.91 - 67.88: 42 67.88 - 84.85: 14 Dihedral angle restraints: 10220 sinusoidal: 4260 harmonic: 5960 Sorted by residual: dihedral pdb=" C THR B 398 " pdb=" N THR B 398 " pdb=" CA THR B 398 " pdb=" CB THR B 398 " ideal model delta harmonic sigma weight residual -122.00 -133.46 11.46 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" C THR D 398 " pdb=" N THR D 398 " pdb=" CA THR D 398 " pdb=" CB THR D 398 " ideal model delta harmonic sigma weight residual -122.00 -133.42 11.42 0 2.50e+00 1.60e-01 2.09e+01 dihedral pdb=" CA LEU D 370 " pdb=" C LEU D 370 " pdb=" N ASP D 371 " pdb=" CA ASP D 371 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 10217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2084 0.067 - 0.134: 361 0.134 - 0.201: 41 0.201 - 0.268: 10 0.268 - 0.335: 6 Chirality restraints: 2502 Sorted by residual: chirality pdb=" CA PHE C 442 " pdb=" N PHE C 442 " pdb=" C PHE C 442 " pdb=" CB PHE C 442 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.33 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA PHE A 442 " pdb=" N PHE A 442 " pdb=" C PHE A 442 " pdb=" CB PHE A 442 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ASN C 411 " pdb=" N ASN C 411 " pdb=" C ASN C 411 " pdb=" CB ASN C 411 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 2499 not shown) Planarity restraints: 2910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 266 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C MET B 266 " -0.049 2.00e-02 2.50e+03 pdb=" O MET B 266 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP B 267 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 266 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C MET D 266 " -0.049 2.00e-02 2.50e+03 pdb=" O MET D 266 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP D 267 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 530 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C LYS A 530 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS A 530 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE A 531 " -0.015 2.00e-02 2.50e+03 ... (remaining 2907 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1413 2.74 - 3.28: 16178 3.28 - 3.82: 26641 3.82 - 4.36: 33137 4.36 - 4.90: 57304 Nonbonded interactions: 134673 Sorted by model distance: nonbonded pdb=" O GLU B 474 " pdb=" OG1 THR B 478 " model vdw 2.195 2.440 nonbonded pdb=" O GLU D 474 " pdb=" OG1 THR D 478 " model vdw 2.196 2.440 nonbonded pdb=" OG SER B 471 " pdb=" OE1 GLU B 474 " model vdw 2.207 2.440 nonbonded pdb=" OG SER D 471 " pdb=" OE1 GLU D 474 " model vdw 2.208 2.440 nonbonded pdb=" OH TYR B 224 " pdb=" OD2 ASP B 242 " model vdw 2.218 2.440 ... (remaining 134668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 85 through 600) selection = chain 'C' selection = (chain 'D' and resid 85 through 600) } 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: 2.660 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: 10.570 Check model and map are aligned: 0.220 Set scattering table: 0.160 Process input model: 45.690 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.090 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.007 0.055 16904 Z= 0.449 Angle : 0.845 10.381 22744 Z= 0.547 Chirality : 0.055 0.335 2502 Planarity : 0.004 0.045 2910 Dihedral : 13.607 84.855 6380 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.89 % Allowed : 1.44 % Favored : 97.67 % Cbeta Deviations : 0.21 % 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: -0.59 (0.18), residues: 2064 helix: 0.32 (0.15), residues: 1134 sheet: -0.16 (0.37), residues: 214 loop : -1.51 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 286 HIS 0.010 0.001 HIS D 346 PHE 0.023 0.002 PHE A 442 TYR 0.018 0.002 TYR C 511 ARG 0.005 0.001 ARG D 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 198 time to evaluate : 1.884 Fit side-chains revert: symmetry clash REVERT: B 485 SER cc_start: 0.8498 (t) cc_final: 0.7946 (p) REVERT: C 363 ASP cc_start: 0.7195 (p0) cc_final: 0.6935 (p0) REVERT: D 485 SER cc_start: 0.8563 (t) cc_final: 0.8096 (p) REVERT: A 363 ASP cc_start: 0.7135 (p0) cc_final: 0.6892 (p0) REVERT: A 591 GLU cc_start: 0.7618 (pm20) cc_final: 0.7301 (pm20) outliers start: 16 outliers final: 2 residues processed: 210 average time/residue: 1.4500 time to fit residues: 334.9808 Evaluate side-chains 129 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 439 HIS Chi-restraints excluded: chain A residue 439 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 187 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 HIS B 302 ASN B 334 GLN C 92 HIS D 92 HIS D 302 ASN D 334 GLN A 92 HIS A 346 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16904 Z= 0.224 Angle : 0.544 7.517 22744 Z= 0.291 Chirality : 0.043 0.201 2502 Planarity : 0.004 0.037 2910 Dihedral : 4.861 32.183 2232 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.94 % Allowed : 7.53 % Favored : 90.53 % 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: -0.06 (0.19), residues: 2064 helix: 0.74 (0.16), residues: 1168 sheet: 0.02 (0.38), residues: 214 loop : -1.36 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 286 HIS 0.006 0.001 HIS B 346 PHE 0.012 0.001 PHE C 389 TYR 0.012 0.001 TYR C 498 ARG 0.004 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 550 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6710 (tp30) REVERT: C 169 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8598 (mm) REVERT: C 363 ASP cc_start: 0.7458 (p0) cc_final: 0.7222 (p0) REVERT: C 430 MET cc_start: 0.8470 (tpp) cc_final: 0.8250 (mmm) REVERT: D 485 SER cc_start: 0.8313 (t) cc_final: 0.7634 (p) REVERT: D 550 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6701 (tp30) REVERT: A 169 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8606 (mm) REVERT: A 363 ASP cc_start: 0.7387 (p0) cc_final: 0.7073 (p0) outliers start: 35 outliers final: 17 residues processed: 167 average time/residue: 1.4143 time to fit residues: 261.9330 Evaluate side-chains 141 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 439 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 185 optimal weight: 0.0070 chunk 63 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN B 334 GLN C 346 HIS C 408 HIS D 302 ASN D 334 GLN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16904 Z= 0.214 Angle : 0.509 6.060 22744 Z= 0.271 Chirality : 0.042 0.182 2502 Planarity : 0.003 0.035 2910 Dihedral : 4.624 28.665 2232 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.60 % Allowed : 9.86 % Favored : 87.54 % 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: 0.20 (0.19), residues: 2064 helix: 1.03 (0.16), residues: 1154 sheet: 0.07 (0.38), residues: 214 loop : -1.34 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 286 HIS 0.005 0.001 HIS B 346 PHE 0.011 0.001 PHE C 389 TYR 0.012 0.001 TYR C 498 ARG 0.007 0.000 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 125 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: B 362 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7805 (mtm110) REVERT: B 550 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6621 (tp30) REVERT: C 363 ASP cc_start: 0.7412 (p0) cc_final: 0.7054 (p0) REVERT: C 430 MET cc_start: 0.8370 (tpp) cc_final: 0.8155 (mmm) REVERT: D 209 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7429 (tp30) REVERT: D 362 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7810 (mtm110) REVERT: D 485 SER cc_start: 0.8216 (t) cc_final: 0.7459 (p) REVERT: D 550 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6640 (tp30) REVERT: A 363 ASP cc_start: 0.7427 (p0) cc_final: 0.7088 (p0) REVERT: A 591 GLU cc_start: 0.7560 (pm20) cc_final: 0.7273 (pm20) outliers start: 47 outliers final: 18 residues processed: 161 average time/residue: 1.3955 time to fit residues: 249.0062 Evaluate side-chains 138 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 362 ARG Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 20 optimal weight: 0.0020 chunk 89 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 178 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 overall best weight: 0.3526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN B 334 GLN B 336 GLN C 336 GLN C 346 HIS D 302 ASN D 334 GLN D 336 GLN A 336 GLN A 346 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16904 Z= 0.144 Angle : 0.460 6.395 22744 Z= 0.244 Chirality : 0.041 0.193 2502 Planarity : 0.003 0.030 2910 Dihedral : 4.268 19.146 2228 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.21 % Allowed : 11.24 % Favored : 86.54 % 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: 0.51 (0.20), residues: 2064 helix: 1.34 (0.16), residues: 1154 sheet: 0.18 (0.39), residues: 214 loop : -1.31 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 286 HIS 0.005 0.001 HIS D 346 PHE 0.009 0.001 PHE D 250 TYR 0.011 0.001 TYR C 498 ARG 0.004 0.000 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 158 GLU cc_start: 0.7842 (pt0) cc_final: 0.7639 (pt0) REVERT: B 209 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7466 (tp30) REVERT: B 262 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7582 (mmm) REVERT: B 550 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6530 (tp30) REVERT: C 363 ASP cc_start: 0.7377 (p0) cc_final: 0.6993 (p0) REVERT: C 430 MET cc_start: 0.8354 (tpp) cc_final: 0.8118 (mmm) REVERT: D 158 GLU cc_start: 0.7844 (pt0) cc_final: 0.7638 (pt0) REVERT: D 209 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7493 (tp30) REVERT: D 262 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7578 (mmm) REVERT: D 550 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6540 (tp30) REVERT: A 363 ASP cc_start: 0.7395 (p0) cc_final: 0.6990 (p0) REVERT: A 591 GLU cc_start: 0.7475 (pm20) cc_final: 0.7187 (pm20) outliers start: 40 outliers final: 19 residues processed: 161 average time/residue: 1.4505 time to fit residues: 259.0538 Evaluate side-chains 138 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 178 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN C 336 GLN C 346 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN A 336 GLN A 346 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16904 Z= 0.391 Angle : 0.602 8.508 22744 Z= 0.315 Chirality : 0.046 0.211 2502 Planarity : 0.004 0.037 2910 Dihedral : 4.772 21.843 2228 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.93 % Allowed : 12.35 % 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: 0.04 (0.19), residues: 2064 helix: 0.96 (0.16), residues: 1154 sheet: -0.05 (0.39), residues: 208 loop : -1.49 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 286 HIS 0.008 0.001 HIS D 346 PHE 0.015 0.002 PHE C 531 TYR 0.015 0.002 TYR C 498 ARG 0.005 0.001 ARG A 535 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 116 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7387 (tp30) REVERT: B 485 SER cc_start: 0.8202 (t) cc_final: 0.7499 (p) REVERT: C 363 ASP cc_start: 0.7637 (p0) cc_final: 0.7237 (p0) REVERT: C 556 MET cc_start: 0.8065 (ttp) cc_final: 0.7844 (ttp) REVERT: C 591 GLU cc_start: 0.7522 (pm20) cc_final: 0.7178 (pm20) REVERT: D 209 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: D 485 SER cc_start: 0.8324 (t) cc_final: 0.7660 (p) REVERT: D 550 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6912 (tp30) REVERT: A 363 ASP cc_start: 0.7618 (p0) cc_final: 0.7220 (p0) REVERT: A 578 THR cc_start: 0.7364 (p) cc_final: 0.7084 (t) REVERT: A 591 GLU cc_start: 0.7623 (pm20) cc_final: 0.7329 (pm20) outliers start: 53 outliers final: 30 residues processed: 154 average time/residue: 1.3188 time to fit residues: 226.7004 Evaluate side-chains 147 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 207 TYR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN C 346 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16904 Z= 0.281 Angle : 0.550 8.589 22744 Z= 0.288 Chirality : 0.044 0.184 2502 Planarity : 0.004 0.040 2910 Dihedral : 4.637 20.561 2228 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.99 % Allowed : 13.12 % Favored : 83.89 % 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: 0.07 (0.19), residues: 2064 helix: 1.00 (0.16), residues: 1154 sheet: -0.12 (0.39), residues: 208 loop : -1.48 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 286 HIS 0.007 0.001 HIS D 346 PHE 0.011 0.001 PHE A 442 TYR 0.014 0.001 TYR A 498 ARG 0.004 0.000 ARG C 535 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 118 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7401 (tp30) REVERT: B 262 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7795 (mmm) REVERT: B 362 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.6858 (ttm110) REVERT: B 485 SER cc_start: 0.8201 (t) cc_final: 0.7489 (p) REVERT: B 550 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6777 (tp30) REVERT: C 363 ASP cc_start: 0.7616 (p0) cc_final: 0.7205 (p0) REVERT: C 591 GLU cc_start: 0.7495 (pm20) cc_final: 0.7151 (pm20) REVERT: D 209 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7424 (tp30) REVERT: D 262 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7793 (mmm) REVERT: D 362 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.6860 (ttm110) REVERT: D 485 SER cc_start: 0.8217 (t) cc_final: 0.7517 (p) REVERT: D 550 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6762 (tp30) REVERT: A 363 ASP cc_start: 0.7655 (p0) cc_final: 0.7227 (p0) REVERT: A 578 THR cc_start: 0.7449 (p) cc_final: 0.7163 (t) REVERT: A 591 GLU cc_start: 0.7479 (pm20) cc_final: 0.7183 (pm20) outliers start: 54 outliers final: 29 residues processed: 158 average time/residue: 1.3648 time to fit residues: 239.6243 Evaluate side-chains 149 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 112 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 362 ARG Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 198 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN B 336 GLN C 346 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN A 346 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16904 Z= 0.194 Angle : 0.509 9.211 22744 Z= 0.265 Chirality : 0.042 0.237 2502 Planarity : 0.003 0.038 2910 Dihedral : 4.402 19.945 2228 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.88 % Allowed : 13.73 % Favored : 83.39 % 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: 0.36 (0.19), residues: 2064 helix: 1.31 (0.16), residues: 1136 sheet: 0.01 (0.38), residues: 216 loop : -1.45 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 154 HIS 0.007 0.001 HIS C 346 PHE 0.009 0.001 PHE A 509 TYR 0.013 0.001 TYR A 498 ARG 0.005 0.000 ARG A 535 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 121 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7387 (tp30) REVERT: B 262 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7646 (mmm) REVERT: B 485 SER cc_start: 0.8178 (t) cc_final: 0.7391 (p) REVERT: B 550 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6651 (tp30) REVERT: C 363 ASP cc_start: 0.7602 (p0) cc_final: 0.7152 (p0) REVERT: C 591 GLU cc_start: 0.7468 (pm20) cc_final: 0.7154 (pm20) REVERT: D 209 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7414 (tp30) REVERT: D 262 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7643 (mmm) REVERT: D 485 SER cc_start: 0.8188 (t) cc_final: 0.7415 (p) REVERT: D 550 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6642 (tp30) REVERT: A 363 ASP cc_start: 0.7580 (p0) cc_final: 0.7137 (p0) REVERT: A 578 THR cc_start: 0.7371 (p) cc_final: 0.7072 (t) REVERT: A 591 GLU cc_start: 0.7445 (pm20) cc_final: 0.7135 (pm20) outliers start: 52 outliers final: 29 residues processed: 159 average time/residue: 1.3351 time to fit residues: 236.3798 Evaluate side-chains 148 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 113 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 GLN C 346 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 358 GLN A 346 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16904 Z= 0.227 Angle : 0.531 10.028 22744 Z= 0.276 Chirality : 0.043 0.240 2502 Planarity : 0.003 0.038 2910 Dihedral : 4.414 19.900 2228 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.77 % Allowed : 14.12 % Favored : 83.11 % 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: 0.33 (0.19), residues: 2064 helix: 1.30 (0.16), residues: 1136 sheet: -0.05 (0.39), residues: 208 loop : -1.45 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 154 HIS 0.008 0.001 HIS A 346 PHE 0.010 0.001 PHE A 442 TYR 0.013 0.001 TYR A 498 ARG 0.005 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 116 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7383 (tp30) REVERT: B 262 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7778 (mmm) REVERT: B 358 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.7686 (tp-100) REVERT: B 485 SER cc_start: 0.8187 (t) cc_final: 0.7395 (p) REVERT: B 550 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6683 (tp30) REVERT: C 363 ASP cc_start: 0.7642 (p0) cc_final: 0.7215 (p0) REVERT: C 591 GLU cc_start: 0.7412 (pm20) cc_final: 0.7125 (pm20) REVERT: D 209 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7419 (tp30) REVERT: D 262 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7780 (mmm) REVERT: D 358 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.7688 (tp-100) REVERT: D 485 SER cc_start: 0.8198 (t) cc_final: 0.7416 (p) REVERT: D 550 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6666 (tp30) REVERT: A 363 ASP cc_start: 0.7629 (p0) cc_final: 0.7176 (p0) REVERT: A 578 THR cc_start: 0.7383 (p) cc_final: 0.7080 (t) REVERT: A 591 GLU cc_start: 0.7477 (pm20) cc_final: 0.7157 (pm20) outliers start: 50 outliers final: 29 residues processed: 155 average time/residue: 1.3396 time to fit residues: 230.9825 Evaluate side-chains 149 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 112 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 358 GLN Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 1.9990 chunk 190 optimal weight: 0.4980 chunk 173 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 174 optimal weight: 0.1980 chunk 184 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN B 358 GLN C 346 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 336 GLN D 358 GLN A 346 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16904 Z= 0.176 Angle : 0.503 10.874 22744 Z= 0.263 Chirality : 0.042 0.225 2502 Planarity : 0.003 0.038 2910 Dihedral : 4.299 20.048 2228 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.33 % Allowed : 14.78 % Favored : 82.89 % 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: 0.46 (0.19), residues: 2064 helix: 1.39 (0.16), residues: 1136 sheet: 0.06 (0.38), residues: 216 loop : -1.39 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 154 HIS 0.008 0.001 HIS A 346 PHE 0.010 0.001 PHE A 496 TYR 0.013 0.001 TYR A 498 ARG 0.005 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 118 time to evaluate : 1.936 Fit side-chains REVERT: B 158 GLU cc_start: 0.7903 (pt0) cc_final: 0.7686 (pt0) REVERT: B 209 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7354 (tp30) REVERT: B 262 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7736 (mmm) REVERT: B 358 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8123 (tp-100) REVERT: B 550 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6629 (tp30) REVERT: C 363 ASP cc_start: 0.7596 (p0) cc_final: 0.7151 (p0) REVERT: C 591 GLU cc_start: 0.7292 (pm20) cc_final: 0.7013 (pm20) REVERT: D 209 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7405 (tp30) REVERT: D 262 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7749 (mmm) REVERT: D 358 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8136 (tp-100) REVERT: D 550 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6623 (tp30) REVERT: A 363 ASP cc_start: 0.7611 (p0) cc_final: 0.7136 (p0) REVERT: A 578 THR cc_start: 0.7356 (p) cc_final: 0.7052 (t) REVERT: A 591 GLU cc_start: 0.7471 (pm20) cc_final: 0.7138 (pm20) outliers start: 42 outliers final: 25 residues processed: 148 average time/residue: 1.4978 time to fit residues: 246.0142 Evaluate side-chains 146 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 358 GLN Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 205 optimal weight: 0.0370 chunk 188 optimal weight: 0.7980 chunk 163 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN B 358 GLN C 346 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 358 GLN A 346 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16904 Z= 0.178 Angle : 0.518 12.386 22744 Z= 0.266 Chirality : 0.042 0.252 2502 Planarity : 0.004 0.081 2910 Dihedral : 4.235 20.144 2228 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.05 % Allowed : 15.45 % Favored : 82.50 % 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: 0.51 (0.19), residues: 2064 helix: 1.43 (0.16), residues: 1136 sheet: 0.09 (0.37), residues: 216 loop : -1.37 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 154 HIS 0.008 0.001 HIS A 346 PHE 0.010 0.001 PHE A 496 TYR 0.012 0.001 TYR C 498 ARG 0.005 0.000 ARG B 230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 118 time to evaluate : 1.973 Fit side-chains REVERT: B 209 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7354 (tp30) REVERT: B 262 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7741 (mmm) REVERT: B 358 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7558 (tp-100) REVERT: B 450 MET cc_start: 0.7789 (ttp) cc_final: 0.7471 (ttt) REVERT: B 550 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6610 (tp30) REVERT: C 363 ASP cc_start: 0.7604 (p0) cc_final: 0.7148 (p0) REVERT: C 591 GLU cc_start: 0.7295 (pm20) cc_final: 0.6988 (pm20) REVERT: D 209 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: D 262 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7738 (mmm) REVERT: D 358 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.7563 (tp-100) REVERT: D 550 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6600 (tp30) REVERT: A 174 MET cc_start: 0.8771 (mtp) cc_final: 0.8560 (mtt) REVERT: A 363 ASP cc_start: 0.7615 (p0) cc_final: 0.7151 (p0) REVERT: A 578 THR cc_start: 0.7336 (p) cc_final: 0.7028 (t) REVERT: A 591 GLU cc_start: 0.7406 (pm20) cc_final: 0.7078 (pm20) outliers start: 37 outliers final: 27 residues processed: 145 average time/residue: 1.3527 time to fit residues: 218.1075 Evaluate side-chains 147 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 112 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 358 GLN Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 168 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN B 358 GLN C 346 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 358 GLN A 346 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102908 restraints weight = 23972.661| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.83 r_work: 0.3197 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16904 Z= 0.192 Angle : 0.518 11.284 22744 Z= 0.267 Chirality : 0.042 0.246 2502 Planarity : 0.004 0.072 2910 Dihedral : 4.238 20.108 2228 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.21 % Allowed : 15.56 % Favored : 82.23 % 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: 0.50 (0.19), residues: 2064 helix: 1.42 (0.16), residues: 1136 sheet: 0.09 (0.37), residues: 216 loop : -1.37 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 154 HIS 0.008 0.001 HIS A 346 PHE 0.010 0.001 PHE A 496 TYR 0.012 0.001 TYR C 498 ARG 0.005 0.000 ARG B 230 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4937.89 seconds wall clock time: 89 minutes 15.19 seconds (5355.19 seconds total)