Starting phenix.real_space_refine on Tue Feb 13 13:44:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg0_34730/02_2024/8hg0_34730.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg0_34730/02_2024/8hg0_34730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg0_34730/02_2024/8hg0_34730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg0_34730/02_2024/8hg0_34730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg0_34730/02_2024/8hg0_34730.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg0_34730/02_2024/8hg0_34730.pdb" } resolution = 3.51 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= -0.003 sd= 0.017 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 Zn 1 6.06 5 S 38 5.16 5 C 4132 2.51 5 N 1064 2.21 5 O 1235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 24": "OE1" <-> "OE2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 214": "OD1" <-> "OD2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6470 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4884 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 570} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.04, per 1000 atoms: 0.62 Number of scatterers: 6470 At special positions: 0 Unit cell: (77.35, 90.95, 119.85, 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) Zn 1 29.99 S 38 16.00 O 1235 8.00 N 1064 7.00 C 4132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 299 " " NAG A 702 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 374 " 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 55.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 21 through 54 removed outlier: 3.625A pdb=" N THR A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP A 39 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 82 removed outlier: 3.524A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 removed outlier: 3.560A pdb=" N LEU A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 110 through 130 removed outlier: 3.825A pdb=" N ARG A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.526A pdb=" N SER A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.550A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.649A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.253A pdb=" N MET A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 252 removed outlier: 4.256A pdb=" N GLU A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.596A pdb=" N TYR A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.671A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 299 through 302 removed outlier: 4.144A pdb=" N TRP A 302 " --> pdb=" O ASN A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.786A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.835A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 329' Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.580A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 414 removed outlier: 3.629A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.610A pdb=" N LEU A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.851A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.244A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.533A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 532 removed outlier: 4.336A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.625A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.917A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 600 Proline residue: A 590 - end of helix removed outlier: 3.811A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 598 " --> pdb=" O TRP A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.210A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.511A pdb=" N LEU A 142 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.694A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.450A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.606A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.818A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 264 hydrogen bonds defined for protein. 759 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: 1.73 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2068 1.35 - 1.46: 1734 1.46 - 1.58: 2786 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 6648 Sorted by residual: bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" CA LEU B 518 " pdb=" CB LEU B 518 " ideal model delta sigma weight residual 1.535 1.519 0.016 1.32e-02 5.74e+03 1.49e+00 bond pdb=" CG LYS B 417 " pdb=" CD LYS B 417 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" C LYS A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 1.334 1.352 -0.018 1.51e-02 4.39e+03 1.40e+00 ... (remaining 6643 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.96: 200 106.96 - 113.74: 3522 113.74 - 120.51: 2747 120.51 - 127.28: 2463 127.28 - 134.05: 88 Bond angle restraints: 9020 Sorted by residual: angle pdb=" CB LYS B 417 " pdb=" CG LYS B 417 " pdb=" CD LYS B 417 " ideal model delta sigma weight residual 111.30 120.67 -9.37 2.30e+00 1.89e-01 1.66e+01 angle pdb=" N ILE A 544 " pdb=" CA ILE A 544 " pdb=" C ILE A 544 " ideal model delta sigma weight residual 112.83 108.82 4.01 9.90e-01 1.02e+00 1.64e+01 angle pdb=" N SER A 104 " pdb=" CA SER A 104 " pdb=" C SER A 104 " ideal model delta sigma weight residual 112.13 108.27 3.86 1.37e+00 5.33e-01 7.94e+00 angle pdb=" N SER B 375 " pdb=" CA SER B 375 " pdb=" C SER B 375 " ideal model delta sigma weight residual 114.56 111.11 3.45 1.27e+00 6.20e-01 7.36e+00 angle pdb=" CB MET A 455 " pdb=" CG MET A 455 " pdb=" SD MET A 455 " ideal model delta sigma weight residual 112.70 120.76 -8.06 3.00e+00 1.11e-01 7.21e+00 ... (remaining 9015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.96: 3494 20.96 - 41.92: 399 41.92 - 62.88: 71 62.88 - 83.84: 4 83.84 - 104.80: 9 Dihedral angle restraints: 3977 sinusoidal: 1650 harmonic: 2327 Sorted by residual: dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -143.61 57.61 1 1.00e+01 1.00e-02 4.46e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -128.35 42.35 1 1.00e+01 1.00e-02 2.51e+01 dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" O4 NAG A 701 " ideal model delta sinusoidal sigma weight residual 175.11 70.31 104.80 1 3.00e+01 1.11e-03 1.34e+01 ... (remaining 3974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 681 0.036 - 0.072: 191 0.072 - 0.107: 63 0.107 - 0.143: 9 0.143 - 0.179: 1 Chirality restraints: 945 Sorted by residual: chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 432 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CA ILE A 468 " pdb=" N ILE A 468 " pdb=" C ILE A 468 " pdb=" CB ILE A 468 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 942 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO A 258 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.040 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO A 146 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 235 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.027 5.00e-02 4.00e+02 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 96 2.66 - 3.22: 6013 3.22 - 3.78: 9451 3.78 - 4.34: 13113 4.34 - 4.90: 21292 Nonbonded interactions: 49965 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 703 " model vdw 2.098 2.230 nonbonded pdb=" O THR A 123 " pdb=" OG1 THR A 126 " model vdw 2.252 2.440 nonbonded pdb=" OD1 ASP B 467 " pdb=" OG SER B 469 " model vdw 2.270 2.440 nonbonded pdb=" O THR A 119 " pdb=" OG1 THR A 123 " model vdw 2.300 2.440 nonbonded pdb=" O THR A 126 " pdb=" OG1 THR A 130 " model vdw 2.302 2.440 ... (remaining 49960 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.730 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: 18.110 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.400 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.003 0.054 6648 Z= 0.200 Angle : 0.612 9.367 9020 Z= 0.346 Chirality : 0.038 0.179 945 Planarity : 0.005 0.062 1160 Dihedral : 17.579 104.802 2467 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.78 % Favored : 98.09 % Rotamer: Outliers : 1.15 % Allowed : 26.19 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.30), residues: 786 helix: 0.27 (0.28), residues: 334 sheet: 1.49 (0.84), residues: 49 loop : -0.24 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 610 HIS 0.003 0.001 HIS A 241 PHE 0.019 0.001 PHE A 428 TYR 0.015 0.001 TYR A 429 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 498 CYS cc_start: 0.7594 (t) cc_final: 0.7364 (p) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.1944 time to fit residues: 15.9234 Evaluate side-chains 50 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.0570 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 52 ASN A 97 GLN A 103 GLN A 118 ASN A 194 ASN A 239 GLN A 374 HIS A 522 GLN B 409 GLN B 498 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6648 Z= 0.184 Angle : 0.566 7.858 9020 Z= 0.290 Chirality : 0.041 0.194 945 Planarity : 0.005 0.058 1160 Dihedral : 7.048 57.701 938 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 4.32 % Allowed : 24.03 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.55 (0.31), residues: 786 helix: 0.89 (0.27), residues: 378 sheet: 1.32 (0.80), residues: 48 loop : -0.23 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 461 HIS 0.004 0.000 HIS A 241 PHE 0.010 0.001 PHE A 369 TYR 0.019 0.001 TYR A 51 ARG 0.004 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 47 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8341 (mmm) cc_final: 0.8042 (tpp) REVERT: A 498 CYS cc_start: 0.7465 (t) cc_final: 0.6890 (p) outliers start: 30 outliers final: 11 residues processed: 73 average time/residue: 0.2035 time to fit residues: 20.1694 Evaluate side-chains 54 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 0.0070 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6648 Z= 0.220 Angle : 0.540 7.890 9020 Z= 0.277 Chirality : 0.041 0.192 945 Planarity : 0.004 0.060 1160 Dihedral : 4.635 25.585 934 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.69 % Rotamer: Outliers : 3.60 % Allowed : 23.74 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.81 (0.31), residues: 786 helix: 1.29 (0.28), residues: 371 sheet: 1.22 (0.77), residues: 49 loop : -0.29 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 PHE 0.009 0.001 PHE A 523 TYR 0.008 0.001 TYR A 202 ARG 0.006 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 41 time to evaluate : 0.813 Fit side-chains REVERT: A 80 MET cc_start: 0.7958 (mtp) cc_final: 0.7758 (ttt) REVERT: A 462 MET cc_start: 0.8375 (mmm) cc_final: 0.8109 (tpp) outliers start: 25 outliers final: 14 residues processed: 61 average time/residue: 0.1819 time to fit residues: 15.4419 Evaluate side-chains 54 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6648 Z= 0.169 Angle : 0.503 8.236 9020 Z= 0.256 Chirality : 0.040 0.192 945 Planarity : 0.004 0.060 1160 Dihedral : 4.055 17.673 932 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 3.74 % Allowed : 24.46 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.87 (0.31), residues: 786 helix: 1.40 (0.28), residues: 372 sheet: 1.01 (0.75), residues: 49 loop : -0.29 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 PHE 0.009 0.001 PHE A 369 TYR 0.019 0.001 TYR A 429 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 43 time to evaluate : 0.782 Fit side-chains REVERT: A 249 MET cc_start: 0.8585 (mmm) cc_final: 0.8367 (mmp) REVERT: A 462 MET cc_start: 0.8394 (mmm) cc_final: 0.8187 (tpp) outliers start: 26 outliers final: 15 residues processed: 64 average time/residue: 0.1968 time to fit residues: 17.3238 Evaluate side-chains 55 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.0020 chunk 64 optimal weight: 0.4980 chunk 52 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.0170 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 overall best weight: 0.3026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6648 Z= 0.131 Angle : 0.495 8.805 9020 Z= 0.249 Chirality : 0.039 0.195 945 Planarity : 0.004 0.058 1160 Dihedral : 3.757 15.100 931 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 2.88 % Allowed : 24.89 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.31), residues: 786 helix: 1.48 (0.28), residues: 374 sheet: 0.94 (0.74), residues: 49 loop : -0.27 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.000 HIS A 241 PHE 0.009 0.001 PHE A 438 TYR 0.007 0.001 TYR A 51 ARG 0.004 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 43 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: A 462 MET cc_start: 0.8440 (mmm) cc_final: 0.8227 (tpp) outliers start: 20 outliers final: 11 residues processed: 60 average time/residue: 0.2205 time to fit residues: 18.5992 Evaluate side-chains 51 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6648 Z= 0.296 Angle : 0.568 8.584 9020 Z= 0.290 Chirality : 0.041 0.190 945 Planarity : 0.004 0.059 1160 Dihedral : 4.137 21.790 931 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.93 % Favored : 96.95 % Rotamer: Outliers : 4.32 % Allowed : 23.88 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.03 (0.32), residues: 786 helix: 1.54 (0.28), residues: 373 sheet: 0.90 (0.72), residues: 49 loop : -0.19 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 606 HIS 0.004 0.001 HIS A 378 PHE 0.015 0.001 PHE A 523 TYR 0.015 0.001 TYR A 429 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 41 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8469 (mmm) cc_final: 0.8198 (tpp) REVERT: A 474 MET cc_start: 0.8629 (mmt) cc_final: 0.8341 (mpp) outliers start: 30 outliers final: 22 residues processed: 63 average time/residue: 0.1742 time to fit residues: 15.3036 Evaluate side-chains 60 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 38 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 chunk 75 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6648 Z= 0.152 Angle : 0.528 9.262 9020 Z= 0.260 Chirality : 0.040 0.194 945 Planarity : 0.004 0.059 1160 Dihedral : 3.894 17.247 931 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 4.17 % Allowed : 24.32 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.31), residues: 786 helix: 1.47 (0.28), residues: 376 sheet: 0.79 (0.71), residues: 49 loop : -0.25 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.000 HIS A 241 PHE 0.009 0.001 PHE A 438 TYR 0.008 0.001 TYR A 51 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 39 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.8508 (mmm) cc_final: 0.8227 (mmp) outliers start: 29 outliers final: 22 residues processed: 62 average time/residue: 0.1845 time to fit residues: 16.0724 Evaluate side-chains 59 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 37 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 0.0770 chunk 42 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6648 Z= 0.162 Angle : 0.539 10.851 9020 Z= 0.265 Chirality : 0.040 0.205 945 Planarity : 0.004 0.058 1160 Dihedral : 3.817 17.555 931 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 3.60 % Allowed : 24.89 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.99 (0.31), residues: 786 helix: 1.48 (0.28), residues: 381 sheet: 0.91 (0.71), residues: 49 loop : -0.23 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 478 HIS 0.002 0.000 HIS A 241 PHE 0.008 0.001 PHE A 438 TYR 0.018 0.001 TYR A 429 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 39 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 162 LEU cc_start: 0.9539 (tp) cc_final: 0.9326 (pp) REVERT: A 249 MET cc_start: 0.8488 (mmm) cc_final: 0.8253 (mmt) REVERT: A 474 MET cc_start: 0.8417 (mpp) cc_final: 0.8111 (mpp) outliers start: 25 outliers final: 21 residues processed: 59 average time/residue: 0.2187 time to fit residues: 18.2320 Evaluate side-chains 58 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 37 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0370 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6648 Z= 0.187 Angle : 0.542 9.518 9020 Z= 0.269 Chirality : 0.040 0.206 945 Planarity : 0.004 0.058 1160 Dihedral : 3.870 19.860 931 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 4.17 % Allowed : 24.32 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.01 (0.31), residues: 786 helix: 1.49 (0.28), residues: 381 sheet: 1.02 (0.71), residues: 49 loop : -0.23 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.003 0.000 HIS A 378 PHE 0.010 0.001 PHE A 523 TYR 0.010 0.001 TYR A 51 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 40 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 474 MET cc_start: 0.8376 (mpp) cc_final: 0.8037 (mpp) REVERT: A 498 CYS cc_start: 0.7759 (t) cc_final: 0.7269 (t) outliers start: 29 outliers final: 25 residues processed: 63 average time/residue: 0.1705 time to fit residues: 15.0784 Evaluate side-chains 64 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 39 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0470 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 0.0270 chunk 49 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6648 Z= 0.142 Angle : 0.545 11.114 9020 Z= 0.264 Chirality : 0.040 0.201 945 Planarity : 0.004 0.058 1160 Dihedral : 3.689 16.319 931 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 3.45 % Allowed : 25.04 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.99 (0.31), residues: 786 helix: 1.50 (0.28), residues: 381 sheet: 1.04 (0.71), residues: 49 loop : -0.28 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.002 0.000 HIS A 241 PHE 0.009 0.001 PHE A 438 TYR 0.017 0.001 TYR A 429 ARG 0.003 0.000 ARG B 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 41 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 162 LEU cc_start: 0.9536 (tp) cc_final: 0.9311 (pp) REVERT: A 474 MET cc_start: 0.8338 (mpp) cc_final: 0.8020 (mpp) REVERT: A 498 CYS cc_start: 0.7684 (t) cc_final: 0.7145 (t) outliers start: 24 outliers final: 21 residues processed: 59 average time/residue: 0.1759 time to fit residues: 14.7400 Evaluate side-chains 60 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 39 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.0370 chunk 41 optimal weight: 5.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.039811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.029949 restraints weight = 39301.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.031050 restraints weight = 22154.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.031812 restraints weight = 15368.695| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6648 Z= 0.193 Angle : 0.567 11.089 9020 Z= 0.277 Chirality : 0.040 0.199 945 Planarity : 0.004 0.058 1160 Dihedral : 3.810 18.739 931 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.07 % Rotamer: Outliers : 3.17 % Allowed : 25.76 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.02 (0.31), residues: 786 helix: 1.52 (0.28), residues: 381 sheet: 1.09 (0.72), residues: 49 loop : -0.25 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.000 HIS A 378 PHE 0.010 0.001 PHE A 523 TYR 0.008 0.001 TYR A 51 ARG 0.003 0.000 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1765.67 seconds wall clock time: 33 minutes 41.95 seconds (2021.95 seconds total)