Starting phenix.real_space_refine on Sun May 11 16:49:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uph_42448/05_2025/8uph_42448.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uph_42448/05_2025/8uph_42448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uph_42448/05_2025/8uph_42448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uph_42448/05_2025/8uph_42448.map" model { file = "/net/cci-nas-00/data/ceres_data/8uph_42448/05_2025/8uph_42448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uph_42448/05_2025/8uph_42448.cif" } resolution = 4.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 19 5.16 5 C 5140 2.51 5 N 1473 2.21 5 O 1489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8121 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4101 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 501} Chain: "B" Number of atoms: 3934 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 3924 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 516, 3924 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 480} bond proxies already assigned to first conformer: 3997 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'BLA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'BLA': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS B 315 " occ=0.52 ... (18 atoms not shown) pdb=" NE2BHIS B 315 " occ=0.48 Time building chain proxies: 7.68, per 1000 atoms: 0.95 Number of scatterers: 8121 At special positions: 0 Unit cell: (81.024, 116.472, 163.736, 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 19 16.00 O 1489 8.00 N 1473 7.00 C 5140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.4 seconds 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 11 sheets defined 45.6% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 removed outlier: 3.584A pdb=" N ARG A 15 " --> pdb=" O GLN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 54 through 59 removed outlier: 3.909A pdb=" N LEU A 58 " --> pdb=" O PRO A 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 54 through 59' Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.600A pdb=" N VAL A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 74 removed outlier: 3.961A pdb=" N GLN A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 82 removed outlier: 3.580A pdb=" N LEU A 78 " --> pdb=" O GLN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 130 removed outlier: 4.099A pdb=" N THR A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 154 Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 242 through 253 removed outlier: 3.603A pdb=" N MET A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 330 removed outlier: 3.888A pdb=" N VAL A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 3.637A pdb=" N GLY A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 340 Processing helix chain 'A' and resid 340 through 346 removed outlier: 3.716A pdb=" N VAL A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 346' Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 399 through 403 removed outlier: 4.079A pdb=" N ALA A 403 " --> pdb=" O PRO A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 546 removed outlier: 3.900A pdb=" N LEU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Proline residue: A 528 - end of helix removed outlier: 3.831A pdb=" N MET A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU A 541 " --> pdb=" O GLY A 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 removed outlier: 3.536A pdb=" N GLU B 16 " --> pdb=" O GLN B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.897A pdb=" N LEU B 21 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY B 22 " --> pdb=" O HIS B 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 18 through 22' Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 62 through 66 removed outlier: 3.792A pdb=" N GLN B 65 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 66 " --> pdb=" O ALA B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 66' Processing helix chain 'B' and resid 74 through 82 Processing helix chain 'B' and resid 116 through 130 removed outlier: 4.009A pdb=" N THR B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 154 removed outlier: 3.583A pdb=" N LEU B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR B 148 " --> pdb=" O THR B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 194 through 204 removed outlier: 3.863A pdb=" N ARG B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 253 removed outlier: 3.723A pdb=" N LEU B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR B 248 " --> pdb=" O ILE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 327 removed outlier: 3.789A pdb=" N LEU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 299 " --> pdb=" O GLN B 295 " (cutoff:3.500A) Proline residue: B 322 - end of helix Processing helix chain 'B' and resid 332 through 340 Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.535A pdb=" N LEU B 347 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.539A pdb=" N VAL B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU B 374 " --> pdb=" O MET B 370 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 375 " --> pdb=" O ASP B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 removed outlier: 4.596A pdb=" N LEU B 397 " --> pdb=" O ARG B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 removed outlier: 3.988A pdb=" N ALA B 402 " --> pdb=" O TYR B 398 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 398 through 403' Processing helix chain 'B' and resid 476 through 524 removed outlier: 3.549A pdb=" N ALA B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLY B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU B 494 " --> pdb=" O ILE B 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.658A pdb=" N VAL A 220 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 43 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU A 41 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA A 32 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL A 43 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 30 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 removed outlier: 3.645A pdb=" N ARG A 207 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.650A pdb=" N LEU A 425 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 412 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 391 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 433 through 438 removed outlier: 4.409A pdb=" N ARG A 433 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 467 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 435 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 465 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 446 through 447 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 33 removed outlier: 3.502A pdb=" N VAL B 29 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 105 " --> pdb=" O HIS B 98 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS B 98 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 107 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 96 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 84 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 188 removed outlier: 5.786A pdb=" N VAL B 171 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG B 162 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 173 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 157 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP B 269 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS B 264 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B 270 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 259 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 362 through 365 removed outlier: 3.757A pdb=" N GLY B 352 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 410 " --> pdb=" O ARG B 428 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 433 through 438 removed outlier: 3.848A pdb=" N ARG B 433 " --> pdb=" O VAL B 467 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 446 through 447 405 hydrogen bonds defined for protein. 1135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1515 1.32 - 1.44: 1985 1.44 - 1.56: 4772 1.56 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 8304 Sorted by residual: bond pdb=" C1D BLA A 801 " pdb=" CHD BLA A 801 " ideal model delta sigma weight residual 1.440 1.339 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C1D BLA B 801 " pdb=" CHD BLA B 801 " ideal model delta sigma weight residual 1.440 1.339 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C3C BLA A 801 " pdb=" CAC BLA A 801 " ideal model delta sigma weight residual 1.458 1.360 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C3C BLA A 801 " pdb=" C4C BLA A 801 " ideal model delta sigma weight residual 1.471 1.375 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C3C BLA B 801 " pdb=" C4C BLA B 801 " ideal model delta sigma weight residual 1.471 1.389 0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 8299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 10987 1.90 - 3.79: 280 3.79 - 5.69: 34 5.69 - 7.58: 14 7.58 - 9.48: 4 Bond angle restraints: 11319 Sorted by residual: angle pdb=" CA ARG B 502 " pdb=" CB ARG B 502 " pdb=" CG ARG B 502 " ideal model delta sigma weight residual 114.10 123.58 -9.48 2.00e+00 2.50e-01 2.25e+01 angle pdb=" C GLU B 501 " pdb=" N ARG B 502 " pdb=" CA ARG B 502 " ideal model delta sigma weight residual 121.58 114.87 6.71 1.95e+00 2.63e-01 1.18e+01 angle pdb=" C1C BLA A 801 " pdb=" C2C BLA A 801 " pdb=" CMC BLA A 801 " ideal model delta sigma weight residual 121.37 130.29 -8.92 3.00e+00 1.11e-01 8.85e+00 angle pdb=" C GLY A 518 " pdb=" N HIS A 519 " pdb=" CA HIS A 519 " ideal model delta sigma weight residual 121.58 116.26 5.32 1.95e+00 2.63e-01 7.43e+00 angle pdb=" C GLN B 65 " pdb=" N VAL B 66 " pdb=" CA VAL B 66 " ideal model delta sigma weight residual 122.66 120.10 2.56 9.70e-01 1.06e+00 6.96e+00 ... (remaining 11314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 4525 17.42 - 34.85: 411 34.85 - 52.27: 73 52.27 - 69.69: 12 69.69 - 87.11: 11 Dihedral angle restraints: 5032 sinusoidal: 2014 harmonic: 3018 Sorted by residual: dihedral pdb=" CA ARG B 502 " pdb=" C ARG B 502 " pdb=" N LEU B 503 " pdb=" CA LEU B 503 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LYS A 475 " pdb=" C LYS A 475 " pdb=" N ARG A 476 " pdb=" CA ARG A 476 " ideal model delta harmonic sigma weight residual -180.00 -155.41 -24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA LEU B 489 " pdb=" C LEU B 489 " pdb=" N ILE B 490 " pdb=" CA ILE B 490 " ideal model delta harmonic sigma weight residual 180.00 159.01 20.99 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 5029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1032 0.050 - 0.100: 192 0.100 - 0.150: 43 0.150 - 0.200: 0 0.200 - 0.250: 1 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA ARG B 502 " pdb=" N ARG B 502 " pdb=" C ARG B 502 " pdb=" CB ARG B 502 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ASP B 265 " pdb=" N ASP B 265 " pdb=" C ASP B 265 " pdb=" CB ASP B 265 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CB ILE A 490 " pdb=" CA ILE A 490 " pdb=" CG1 ILE A 490 " pdb=" CG2 ILE A 490 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1265 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C BLA A 801 " -0.127 2.00e-02 2.50e+03 4.54e-01 5.14e+03 pdb=" C1D BLA A 801 " 0.011 2.00e-02 2.50e+03 pdb=" C2C BLA A 801 " 0.163 2.00e-02 2.50e+03 pdb=" C3C BLA A 801 " -0.237 2.00e-02 2.50e+03 pdb=" C4C BLA A 801 " 0.119 2.00e-02 2.50e+03 pdb=" CAC BLA A 801 " -0.880 2.00e-02 2.50e+03 pdb=" CHD BLA A 801 " 0.602 2.00e-02 2.50e+03 pdb=" CMC BLA A 801 " 0.809 2.00e-02 2.50e+03 pdb=" NC BLA A 801 " -0.075 2.00e-02 2.50e+03 pdb=" OC BLA A 801 " -0.385 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA B 801 " -0.130 2.00e-02 2.50e+03 3.68e-01 3.39e+03 pdb=" C1D BLA B 801 " 0.123 2.00e-02 2.50e+03 pdb=" C2C BLA B 801 " 0.131 2.00e-02 2.50e+03 pdb=" C3C BLA B 801 " -0.183 2.00e-02 2.50e+03 pdb=" C4C BLA B 801 " 0.036 2.00e-02 2.50e+03 pdb=" CAC BLA B 801 " -0.663 2.00e-02 2.50e+03 pdb=" CHD BLA B 801 " 0.513 2.00e-02 2.50e+03 pdb=" CMC BLA B 801 " 0.663 2.00e-02 2.50e+03 pdb=" NC BLA B 801 " -0.310 2.00e-02 2.50e+03 pdb=" OC BLA B 801 " -0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA A 801 " -0.281 2.00e-02 2.50e+03 3.34e-01 2.79e+03 pdb=" OB BLA A 801 " -0.172 2.00e-02 2.50e+03 pdb=" C1B BLA A 801 " -0.168 2.00e-02 2.50e+03 pdb=" C2B BLA A 801 " -0.149 2.00e-02 2.50e+03 pdb=" C3B BLA A 801 " 0.167 2.00e-02 2.50e+03 pdb=" C4A BLA A 801 " 0.567 2.00e-02 2.50e+03 pdb=" C4B BLA A 801 " -0.103 2.00e-02 2.50e+03 pdb=" CAB BLA A 801 " 0.645 2.00e-02 2.50e+03 pdb=" CHB BLA A 801 " -0.090 2.00e-02 2.50e+03 pdb=" CMB BLA A 801 " -0.415 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1476 2.77 - 3.30: 8226 3.30 - 3.83: 13593 3.83 - 4.37: 14603 4.37 - 4.90: 24498 Nonbonded interactions: 62396 Sorted by model distance: nonbonded pdb=" O ARG A 127 " pdb=" OG SER A 130 " model vdw 2.236 3.040 nonbonded pdb=" O GLY A 330 " pdb=" NH1 ARG A 495 " model vdw 2.252 3.120 nonbonded pdb=" O GLU B 505 " pdb=" OG SER B 508 " model vdw 2.252 3.040 nonbonded pdb=" O ALA A 516 " pdb=" OG1 THR A 520 " model vdw 2.262 3.040 nonbonded pdb=" O PHE B 385 " pdb=" NH1 ARG B 415 " model vdw 2.274 3.120 ... (remaining 62391 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 314 or resid 316 through 524 or resid 801)) selection = (chain 'B' and (resid 9 through 314 or resid 316 through 524 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 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: 5.290 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.020 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.005 0.101 8306 Z= 0.258 Angle : 0.714 9.477 11319 Z= 0.352 Chirality : 0.040 0.250 1268 Planarity : 0.021 0.454 1488 Dihedral : 14.178 87.112 3084 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.29 % Favored : 97.62 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.18 (0.25), residues: 1053 helix: 0.39 (0.26), residues: 393 sheet: 0.35 (0.38), residues: 170 loop : -0.62 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 72 HIS 0.015 0.001 HIS B 519 PHE 0.020 0.001 PHE B 517 TYR 0.013 0.001 TYR B 27 ARG 0.006 0.000 ARG A 530 Details of bonding type rmsd hydrogen bonds : bond 0.21020 ( 405) hydrogen bonds : angle 8.53805 ( 1135) covalent geometry : bond 0.00449 ( 8304) covalent geometry : angle 0.71437 (11319) Misc. bond : bond 0.08193 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 345 LEU cc_start: 0.9388 (mt) cc_final: 0.9114 (mt) REVERT: A 362 LEU cc_start: 0.9222 (tp) cc_final: 0.8897 (tt) REVERT: B 252 MET cc_start: 0.9233 (tpp) cc_final: 0.8682 (tpp) REVERT: B 290 CYS cc_start: 0.9408 (m) cc_final: 0.9135 (m) outliers start: 1 outliers final: 1 residues processed: 64 average time/residue: 0.2214 time to fit residues: 19.5132 Evaluate side-chains 50 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.037104 restraints weight = 123390.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.038957 restraints weight = 48987.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.040220 restraints weight = 29503.548| |-----------------------------------------------------------------------------| r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8306 Z= 0.188 Angle : 0.682 9.772 11319 Z= 0.339 Chirality : 0.041 0.169 1268 Planarity : 0.006 0.049 1488 Dihedral : 6.765 76.230 1215 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.24 (0.25), residues: 1053 helix: 0.54 (0.26), residues: 394 sheet: 0.06 (0.37), residues: 192 loop : -0.78 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 72 HIS 0.015 0.002 HIS B 519 PHE 0.018 0.002 PHE B 517 TYR 0.012 0.002 TYR B 161 ARG 0.005 0.001 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.05735 ( 405) hydrogen bonds : angle 6.53206 ( 1135) covalent geometry : bond 0.00391 ( 8304) covalent geometry : angle 0.68152 (11319) Misc. bond : bond 0.00090 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.8953 (mmm) cc_final: 0.8721 (mmm) REVERT: A 284 TYR cc_start: 0.8902 (t80) cc_final: 0.8648 (t80) REVERT: A 345 LEU cc_start: 0.9428 (mt) cc_final: 0.9091 (mt) REVERT: A 362 LEU cc_start: 0.9153 (tp) cc_final: 0.8795 (tt) REVERT: B 180 MET cc_start: 0.7831 (ptp) cc_final: 0.7448 (mpp) REVERT: B 290 CYS cc_start: 0.9508 (m) cc_final: 0.9254 (m) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2206 time to fit residues: 16.5966 Evaluate side-chains 42 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 51 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 86 optimal weight: 0.2980 chunk 76 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.058376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.037506 restraints weight = 111699.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.039329 restraints weight = 44233.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.040526 restraints weight = 26743.549| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8306 Z= 0.150 Angle : 0.644 9.131 11319 Z= 0.320 Chirality : 0.040 0.158 1268 Planarity : 0.005 0.049 1488 Dihedral : 6.581 84.036 1215 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.12 % Allowed : 3.56 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.25 (0.25), residues: 1053 helix: 0.56 (0.26), residues: 387 sheet: 0.29 (0.37), residues: 179 loop : -0.89 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 72 HIS 0.014 0.001 HIS B 519 PHE 0.018 0.001 PHE B 517 TYR 0.011 0.001 TYR B 161 ARG 0.006 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.05416 ( 405) hydrogen bonds : angle 6.22557 ( 1135) covalent geometry : bond 0.00313 ( 8304) covalent geometry : angle 0.64360 (11319) Misc. bond : bond 0.00170 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.8931 (t80) cc_final: 0.8671 (t80) REVERT: A 345 LEU cc_start: 0.9487 (mt) cc_final: 0.9281 (mt) REVERT: A 362 LEU cc_start: 0.9160 (tp) cc_final: 0.8810 (tt) REVERT: A 370 MET cc_start: 0.9306 (pmm) cc_final: 0.9101 (pmm) REVERT: B 180 MET cc_start: 0.8018 (ptp) cc_final: 0.7520 (mpp) REVERT: B 186 MET cc_start: 0.9076 (mmp) cc_final: 0.8840 (mmm) REVERT: B 290 CYS cc_start: 0.9513 (m) cc_final: 0.9242 (m) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.2523 time to fit residues: 19.0021 Evaluate side-chains 41 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 39 optimal weight: 0.0770 chunk 36 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.059291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.037975 restraints weight = 104452.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.039768 restraints weight = 43919.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.041005 restraints weight = 27192.736| |-----------------------------------------------------------------------------| r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8306 Z= 0.122 Angle : 0.624 9.104 11319 Z= 0.307 Chirality : 0.040 0.155 1268 Planarity : 0.005 0.046 1488 Dihedral : 6.567 85.660 1215 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.24 (0.25), residues: 1053 helix: 0.62 (0.26), residues: 387 sheet: 0.08 (0.37), residues: 185 loop : -0.84 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 72 HIS 0.013 0.001 HIS B 519 PHE 0.018 0.001 PHE B 517 TYR 0.010 0.001 TYR B 161 ARG 0.006 0.000 ARG B 502 Details of bonding type rmsd hydrogen bonds : bond 0.04999 ( 405) hydrogen bonds : angle 6.01094 ( 1135) covalent geometry : bond 0.00254 ( 8304) covalent geometry : angle 0.62403 (11319) Misc. bond : bond 0.00094 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.8956 (t80) cc_final: 0.8751 (t80) REVERT: A 339 LYS cc_start: 0.9399 (ptpp) cc_final: 0.9159 (ptpp) REVERT: A 345 LEU cc_start: 0.9492 (mt) cc_final: 0.9214 (mt) REVERT: A 362 LEU cc_start: 0.9173 (tp) cc_final: 0.8824 (tt) REVERT: A 370 MET cc_start: 0.9306 (pmm) cc_final: 0.9083 (pmm) REVERT: B 180 MET cc_start: 0.8084 (ptp) cc_final: 0.7600 (mpp) REVERT: B 186 MET cc_start: 0.9097 (mmp) cc_final: 0.8852 (mmm) REVERT: B 290 CYS cc_start: 0.9505 (m) cc_final: 0.9230 (m) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2465 time to fit residues: 19.1783 Evaluate side-chains 44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 58 optimal weight: 5.9990 chunk 65 optimal weight: 0.0570 chunk 92 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.8700 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.059251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.038534 restraints weight = 81337.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.040139 restraints weight = 38660.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.041236 restraints weight = 25117.203| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8306 Z= 0.132 Angle : 0.630 8.827 11319 Z= 0.312 Chirality : 0.040 0.152 1268 Planarity : 0.005 0.049 1488 Dihedral : 6.547 88.988 1215 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.28 (0.25), residues: 1053 helix: 0.66 (0.26), residues: 380 sheet: -0.00 (0.37), residues: 185 loop : -0.89 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 72 HIS 0.012 0.001 HIS B 519 PHE 0.013 0.001 PHE B 517 TYR 0.011 0.001 TYR B 161 ARG 0.007 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.05067 ( 405) hydrogen bonds : angle 5.95104 ( 1135) covalent geometry : bond 0.00276 ( 8304) covalent geometry : angle 0.63011 (11319) Misc. bond : bond 0.00081 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.8953 (t80) cc_final: 0.8708 (t80) REVERT: A 339 LYS cc_start: 0.9365 (ptpp) cc_final: 0.9116 (ptpp) REVERT: A 345 LEU cc_start: 0.9491 (mt) cc_final: 0.9219 (mt) REVERT: A 362 LEU cc_start: 0.9147 (tp) cc_final: 0.8798 (tt) REVERT: A 370 MET cc_start: 0.9321 (pmm) cc_final: 0.9098 (pmm) REVERT: B 159 MET cc_start: 0.8797 (mpp) cc_final: 0.8495 (mpp) REVERT: B 180 MET cc_start: 0.8114 (ptp) cc_final: 0.7609 (mpp) REVERT: B 186 MET cc_start: 0.9088 (mmp) cc_final: 0.8827 (mmm) REVERT: B 290 CYS cc_start: 0.9501 (m) cc_final: 0.9228 (m) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2602 time to fit residues: 20.4276 Evaluate side-chains 44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 63 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3191 r_free = 0.3191 target = 0.058749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.037594 restraints weight = 107467.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.039256 restraints weight = 45006.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.040476 restraints weight = 28070.349| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8306 Z= 0.145 Angle : 0.636 8.561 11319 Z= 0.314 Chirality : 0.040 0.154 1268 Planarity : 0.005 0.050 1488 Dihedral : 6.395 84.017 1215 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.27 (0.25), residues: 1053 helix: 0.60 (0.26), residues: 388 sheet: 0.06 (0.37), residues: 179 loop : -0.86 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 72 HIS 0.012 0.001 HIS B 519 PHE 0.013 0.001 PHE B 517 TYR 0.013 0.002 TYR A 398 ARG 0.007 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.05000 ( 405) hydrogen bonds : angle 5.89388 ( 1135) covalent geometry : bond 0.00311 ( 8304) covalent geometry : angle 0.63641 (11319) Misc. bond : bond 0.00082 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.829 Fit side-chains REVERT: A 284 TYR cc_start: 0.9005 (t80) cc_final: 0.8726 (t80) REVERT: A 345 LEU cc_start: 0.9512 (mt) cc_final: 0.9246 (mt) REVERT: A 362 LEU cc_start: 0.9153 (tp) cc_final: 0.8800 (tt) REVERT: A 370 MET cc_start: 0.9279 (pmm) cc_final: 0.9053 (pmm) REVERT: B 159 MET cc_start: 0.8830 (mpp) cc_final: 0.8495 (mpp) REVERT: B 180 MET cc_start: 0.8120 (ptp) cc_final: 0.7574 (mpp) REVERT: B 186 MET cc_start: 0.9122 (mmp) cc_final: 0.8841 (mmm) REVERT: B 290 CYS cc_start: 0.9538 (m) cc_final: 0.9251 (m) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2491 time to fit residues: 18.2716 Evaluate side-chains 44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 94 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.059147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.037532 restraints weight = 144429.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.039430 restraints weight = 50832.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.040751 restraints weight = 29598.817| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8306 Z= 0.124 Angle : 0.625 8.736 11319 Z= 0.307 Chirality : 0.040 0.150 1268 Planarity : 0.005 0.044 1488 Dihedral : 6.296 88.707 1215 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.21 (0.25), residues: 1053 helix: 0.68 (0.26), residues: 387 sheet: 0.07 (0.37), residues: 179 loop : -0.83 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 72 HIS 0.012 0.001 HIS B 519 PHE 0.015 0.001 PHE B 517 TYR 0.010 0.001 TYR B 161 ARG 0.008 0.000 ARG A 530 Details of bonding type rmsd hydrogen bonds : bond 0.04849 ( 405) hydrogen bonds : angle 5.79337 ( 1135) covalent geometry : bond 0.00259 ( 8304) covalent geometry : angle 0.62474 (11319) Misc. bond : bond 0.00067 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9018 (t80) cc_final: 0.8730 (t80) REVERT: A 362 LEU cc_start: 0.9166 (tp) cc_final: 0.8821 (tt) REVERT: A 370 MET cc_start: 0.9280 (pmm) cc_final: 0.9052 (pmm) REVERT: B 159 MET cc_start: 0.8803 (mpp) cc_final: 0.8458 (mpp) REVERT: B 180 MET cc_start: 0.8118 (ptp) cc_final: 0.7610 (mpp) REVERT: B 186 MET cc_start: 0.9138 (mmp) cc_final: 0.8855 (mmm) REVERT: B 290 CYS cc_start: 0.9514 (m) cc_final: 0.9225 (m) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2406 time to fit residues: 18.1551 Evaluate side-chains 44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 1 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 0.0770 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.059008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.037460 restraints weight = 131517.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.039326 restraints weight = 48705.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.040615 restraints weight = 28728.536| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8306 Z= 0.133 Angle : 0.624 8.596 11319 Z= 0.308 Chirality : 0.041 0.197 1268 Planarity : 0.005 0.047 1488 Dihedral : 6.230 87.252 1215 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.21 (0.25), residues: 1053 helix: 0.73 (0.26), residues: 387 sheet: 0.02 (0.37), residues: 179 loop : -0.85 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 72 HIS 0.011 0.001 HIS B 519 PHE 0.015 0.001 PHE B 517 TYR 0.010 0.001 TYR B 161 ARG 0.005 0.000 ARG B 502 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 405) hydrogen bonds : angle 5.77308 ( 1135) covalent geometry : bond 0.00280 ( 8304) covalent geometry : angle 0.62436 (11319) Misc. bond : bond 0.00065 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.919 Fit side-chains REVERT: A 284 TYR cc_start: 0.9038 (t80) cc_final: 0.8763 (t80) REVERT: A 345 LEU cc_start: 0.9469 (mt) cc_final: 0.9160 (mt) REVERT: A 362 LEU cc_start: 0.9155 (tp) cc_final: 0.8811 (tt) REVERT: A 370 MET cc_start: 0.9254 (pmm) cc_final: 0.9035 (pmm) REVERT: B 180 MET cc_start: 0.8137 (ptp) cc_final: 0.7634 (mpp) REVERT: B 186 MET cc_start: 0.9138 (mmp) cc_final: 0.8838 (mmm) REVERT: B 290 CYS cc_start: 0.9527 (m) cc_final: 0.9243 (m) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2552 time to fit residues: 18.7434 Evaluate side-chains 44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.059285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.038023 restraints weight = 114503.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.039858 restraints weight = 45294.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.041112 restraints weight = 27457.157| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8306 Z= 0.123 Angle : 0.622 8.666 11319 Z= 0.308 Chirality : 0.041 0.172 1268 Planarity : 0.005 0.046 1488 Dihedral : 6.338 88.580 1215 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.19 (0.25), residues: 1053 helix: 0.75 (0.26), residues: 386 sheet: 0.03 (0.37), residues: 178 loop : -0.85 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 72 HIS 0.011 0.001 HIS B 519 PHE 0.015 0.001 PHE B 517 TYR 0.010 0.001 TYR B 161 ARG 0.006 0.000 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.04837 ( 405) hydrogen bonds : angle 5.71723 ( 1135) covalent geometry : bond 0.00257 ( 8304) covalent geometry : angle 0.62217 (11319) Misc. bond : bond 0.00060 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9015 (t80) cc_final: 0.8737 (t80) REVERT: A 362 LEU cc_start: 0.9129 (tp) cc_final: 0.8773 (tt) REVERT: A 370 MET cc_start: 0.9248 (pmm) cc_final: 0.9031 (pmm) REVERT: B 180 MET cc_start: 0.8130 (ptp) cc_final: 0.7660 (mpp) REVERT: B 186 MET cc_start: 0.9137 (mmp) cc_final: 0.8854 (mmm) REVERT: B 290 CYS cc_start: 0.9514 (m) cc_final: 0.9231 (m) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2656 time to fit residues: 19.9699 Evaluate side-chains 47 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 0.0970 chunk 82 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 75 optimal weight: 0.0870 chunk 90 optimal weight: 2.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.060040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.039038 restraints weight = 106015.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.040820 restraints weight = 43389.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.042047 restraints weight = 26439.040| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8306 Z= 0.110 Angle : 0.625 8.834 11319 Z= 0.309 Chirality : 0.041 0.163 1268 Planarity : 0.005 0.046 1488 Dihedral : 6.293 84.106 1215 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.13 (0.25), residues: 1053 helix: 0.78 (0.26), residues: 386 sheet: 0.12 (0.37), residues: 178 loop : -0.82 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 72 HIS 0.011 0.001 HIS B 519 PHE 0.016 0.001 PHE B 517 TYR 0.010 0.001 TYR B 161 ARG 0.010 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 405) hydrogen bonds : angle 5.65944 ( 1135) covalent geometry : bond 0.00227 ( 8304) covalent geometry : angle 0.62545 (11319) Misc. bond : bond 0.00049 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.8977 (t80) cc_final: 0.8699 (t80) REVERT: A 345 LEU cc_start: 0.9452 (mt) cc_final: 0.9149 (mt) REVERT: A 362 LEU cc_start: 0.9146 (tp) cc_final: 0.8790 (tt) REVERT: A 370 MET cc_start: 0.9214 (pmm) cc_final: 0.8991 (pmm) REVERT: B 180 MET cc_start: 0.8140 (ptp) cc_final: 0.7694 (mpp) REVERT: B 252 MET cc_start: 0.9377 (tpp) cc_final: 0.8753 (tpp) REVERT: B 290 CYS cc_start: 0.9488 (m) cc_final: 0.9218 (m) REVERT: B 370 MET cc_start: 0.9321 (tpt) cc_final: 0.8966 (tpp) REVERT: B 489 LEU cc_start: 0.9517 (tt) cc_final: 0.9014 (mt) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2187 time to fit residues: 18.0956 Evaluate side-chains 47 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 103 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.056990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.036107 restraints weight = 111426.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.037713 restraints weight = 46444.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.038831 restraints weight = 28892.076| |-----------------------------------------------------------------------------| r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8306 Z= 0.235 Angle : 0.709 7.952 11319 Z= 0.356 Chirality : 0.042 0.152 1268 Planarity : 0.006 0.045 1488 Dihedral : 6.337 74.766 1215 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.42 (0.25), residues: 1053 helix: 0.67 (0.26), residues: 387 sheet: -0.44 (0.38), residues: 170 loop : -0.93 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 72 HIS 0.012 0.002 HIS B 519 PHE 0.016 0.002 PHE B 485 TYR 0.019 0.002 TYR B 27 ARG 0.010 0.001 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.05400 ( 405) hydrogen bonds : angle 5.91150 ( 1135) covalent geometry : bond 0.00491 ( 8304) covalent geometry : angle 0.70906 (11319) Misc. bond : bond 0.00095 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3874.32 seconds wall clock time: 68 minutes 10.18 seconds (4090.18 seconds total)