Starting phenix.real_space_refine on Thu Jul 2 14:38:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zyg_15022/07_2026/7zyg_15022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyg_15022/07_2026/7zyg_15022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zyg_15022/07_2026/7zyg_15022.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zyg_15022/07_2026/7zyg_15022.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zyg_15022/07_2026/7zyg_15022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyg_15022/07_2026/7zyg_15022.map" model { file = "/net/cci-nas-00/data/ceres_data/7zyg_15022/07_2026/7zyg_15022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyg_15022/07_2026/7zyg_15022.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 41 5.16 5 C 5606 2.51 5 N 1512 2.21 5 O 1724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8914 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4056 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 476} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 4016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4016 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 480} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 165 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 3, 'TRANS': 19} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "D" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 301 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain breaks: 1 Chain: "E" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 314 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.15, per 1000 atoms: 0.24 Number of scatterers: 8914 At special positions: 0 Unit cell: (88.4, 89.7, 146.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 31 15.00 O 1724 8.00 N 1512 7.00 C 5606 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=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 475.7 milliseconds 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 36.9% alpha, 21.3% beta 7 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 58 through 78 Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 127 through 135 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.582A pdb=" N ASN A 178 " --> pdb=" O ASN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.812A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.601A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.552A pdb=" N LYS A 443 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 480 through 495 Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 29 through 48 Processing helix chain 'B' and resid 87 through 96 Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.705A pdb=" N ILE B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 217 removed outlier: 3.623A pdb=" N ILE B 207 " --> pdb=" O GLU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 285 through 289 removed outlier: 3.755A pdb=" N ASP B 288 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE B 289 " --> pdb=" O LYS B 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 285 through 289' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 484 through 500 Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.513A pdb=" N TRP B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.549A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 removed outlier: 3.515A pdb=" N SER B 531 " --> pdb=" O GLN B 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 299 removed outlier: 3.814A pdb=" N PHE F 298 " --> pdb=" O ARG F 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 109 removed outlier: 6.593A pdb=" N VAL A 85 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU A 107 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU A 83 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ARG A 35 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N HIS A 163 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N PHE A 199 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N MET A 203 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU A 168 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 262 removed outlier: 4.720A pdb=" N PHE A 410 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG A 399 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU A 347 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR A 401 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU A 345 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 303 Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 329 Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA7, first strand: chain 'A' and resid 419 through 420 removed outlier: 6.509A pdb=" N GLU A 419 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.760A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 10 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL B 57 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU B 12 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE B 59 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET B 14 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG B 130 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N TYR B 225 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE B 163 " --> pdb=" O TYR B 225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 247 through 252 removed outlier: 6.499A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU B 268 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N ASN B 359 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG B 394 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 342 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA B 396 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE B 340 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N PHE B 340 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ARG B 250 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL B 342 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR B 252 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLY B 344 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 467 removed outlier: 3.628A pdb=" N THR B 472 " --> pdb=" O ASP B 467 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2603 1.34 - 1.45: 1360 1.45 - 1.57: 5061 1.57 - 1.69: 57 1.69 - 1.81: 69 Bond restraints: 9150 Sorted by residual: bond pdb=" C3' DG E 0 " pdb=" C2' DG E 0 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.24e+00 bond pdb=" O3 PO4 B 801 " pdb=" P PO4 B 801 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.70e+00 bond pdb=" O4 PO4 B 801 " pdb=" P PO4 B 801 " ideal model delta sigma weight residual 1.568 1.511 0.057 2.00e-02 2.50e+03 8.20e+00 bond pdb=" O2 PO4 B 801 " pdb=" P PO4 B 801 " ideal model delta sigma weight residual 1.567 1.510 0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" O1 PO4 B 801 " pdb=" P PO4 B 801 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.68e+00 ... (remaining 9145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 11949 1.06 - 2.12: 346 2.12 - 3.17: 152 3.17 - 4.23: 11 4.23 - 5.29: 7 Bond angle restraints: 12465 Sorted by residual: angle pdb=" O4' DT E 4 " pdb=" C4' DT E 4 " pdb=" C3' DT E 4 " ideal model delta sigma weight residual 106.00 103.53 2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT E 14 " pdb=" C4 DT E 14 " pdb=" O4 DT E 14 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT D 7 " pdb=" C4 DT D 7 " pdb=" O4 DT D 7 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT D 13 " pdb=" C4 DT D 13 " pdb=" O4 DT D 13 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT D 15 " pdb=" C4 DT D 15 " pdb=" O4 DT D 15 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 ... (remaining 12460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 5273 30.32 - 60.63: 255 60.63 - 90.95: 22 90.95 - 121.27: 0 121.27 - 151.58: 2 Dihedral angle restraints: 5552 sinusoidal: 2508 harmonic: 3044 Sorted by residual: dihedral pdb=" C4' DT E 4 " pdb=" C3' DT E 4 " pdb=" O3' DT E 4 " pdb=" P DC E 5 " ideal model delta sinusoidal sigma weight residual 220.00 68.42 151.58 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" C4' DG E 0 " pdb=" C3' DG E 0 " pdb=" O3' DG E 0 " pdb=" P DA E 1 " ideal model delta sinusoidal sigma weight residual 220.00 77.10 142.90 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" CA ASP B 280 " pdb=" CB ASP B 280 " pdb=" CG ASP B 280 " pdb=" OD1 ASP B 280 " ideal model delta sinusoidal sigma weight residual -30.00 -87.47 57.47 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 5549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 877 0.030 - 0.060: 326 0.060 - 0.089: 103 0.089 - 0.119: 81 0.119 - 0.149: 12 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CB ILE A 223 " pdb=" CA ILE A 223 " pdb=" CG1 ILE A 223 " pdb=" CG2 ILE A 223 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA ASP A 212 " pdb=" N ASP A 212 " pdb=" C ASP A 212 " pdb=" CB ASP A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ASP A 496 " pdb=" N ASP A 496 " pdb=" C ASP A 496 " pdb=" CB ASP A 496 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1396 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 58 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO A 59 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 59 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 59 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 194 " 0.016 5.00e-02 4.00e+02 2.49e-02 9.90e-01 pdb=" N PRO C 195 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO C 195 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 195 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 363 " 0.016 5.00e-02 4.00e+02 2.43e-02 9.47e-01 pdb=" N PRO A 364 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " 0.014 5.00e-02 4.00e+02 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1937 2.79 - 3.32: 7948 3.32 - 3.85: 14173 3.85 - 4.37: 16695 4.37 - 4.90: 28595 Nonbonded interactions: 69348 Sorted by model distance: nonbonded pdb=" ND2 ASN A 171 " pdb=" O LYS A 206 " model vdw 2.263 3.120 nonbonded pdb=" OH TYR A 369 " pdb=" O SER B 436 " model vdw 2.320 3.040 nonbonded pdb=" OG SER A 270 " pdb=" O GLU A 371 " model vdw 2.328 3.040 nonbonded pdb=" O MET B 20 " pdb=" OG SER B 29 " model vdw 2.333 3.040 nonbonded pdb=" OG SER A 78 " pdb=" OD2 ASP A 81 " model vdw 2.354 3.040 ... (remaining 69343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.920 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.710 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 0.059 9150 Z= 0.212 Angle : 0.500 5.289 12465 Z= 0.331 Chirality : 0.042 0.149 1399 Planarity : 0.003 0.047 1498 Dihedral : 16.314 151.584 3568 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.26), residues: 1027 helix: 1.30 (0.29), residues: 327 sheet: 0.34 (0.41), residues: 154 loop : -0.10 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 502 TYR 0.008 0.001 TYR A 71 PHE 0.010 0.001 PHE B 107 TRP 0.005 0.001 TRP B 513 HIS 0.004 0.000 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.21 ( 9150) covalent geometry : angle 0.49992 / 0.33 (12465) hydrogen bonds : bond 0.23099 / 15.28 ( 371) hydrogen bonds : angle 7.69696 / 5.36 ( 1033) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8382 (tppt) cc_final: 0.8093 (ttmm) REVERT: A 132 GLN cc_start: 0.9470 (mt0) cc_final: 0.9219 (mp10) REVERT: A 143 LEU cc_start: 0.9278 (tt) cc_final: 0.9077 (tp) REVERT: A 374 LEU cc_start: 0.9071 (mm) cc_final: 0.8779 (mm) REVERT: B 15 ASP cc_start: 0.8763 (t0) cc_final: 0.8388 (t0) REVERT: B 20 MET cc_start: 0.8676 (mtp) cc_final: 0.8171 (mtt) REVERT: B 53 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7339 (mm-30) REVERT: B 83 LEU cc_start: 0.9362 (tp) cc_final: 0.9155 (tm) REVERT: B 93 ASP cc_start: 0.8882 (m-30) cc_final: 0.8622 (m-30) REVERT: B 111 LEU cc_start: 0.9476 (tp) cc_final: 0.9156 (tm) REVERT: B 115 MET cc_start: 0.9476 (mtm) cc_final: 0.9150 (mtm) REVERT: B 157 CYS cc_start: 0.9046 (m) cc_final: 0.8602 (m) REVERT: B 210 MET cc_start: 0.9686 (tmm) cc_final: 0.9366 (tmm) REVERT: B 229 GLU cc_start: 0.9022 (pt0) cc_final: 0.8493 (pp20) REVERT: B 241 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7997 (mt-10) REVERT: B 414 HIS cc_start: 0.8245 (p-80) cc_final: 0.7952 (p-80) REVERT: B 415 ASN cc_start: 0.8736 (m-40) cc_final: 0.8407 (m-40) REVERT: B 541 GLU cc_start: 0.8792 (tt0) cc_final: 0.8479 (tm-30) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.5283 time to fit residues: 93.5030 Evaluate side-chains 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.107291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.066640 restraints weight = 15288.424| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.62 r_work: 0.2546 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9150 Z= 0.138 Angle : 0.601 8.670 12465 Z= 0.314 Chirality : 0.045 0.350 1399 Planarity : 0.003 0.039 1498 Dihedral : 17.117 157.504 1437 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.51 % Allowed : 10.16 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1027 helix: 1.66 (0.29), residues: 334 sheet: 0.27 (0.40), residues: 154 loop : -0.10 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 295 TYR 0.009 0.001 TYR A 71 PHE 0.027 0.001 PHE B 107 TRP 0.003 0.001 TRP A 148 HIS 0.003 0.001 HIS B 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 9150) covalent geometry : angle 0.60051 / 0.31 (12465) hydrogen bonds : bond 0.05916 / 3.91 ( 371) hydrogen bonds : angle 5.31527 / 3.66 ( 1033) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8384 (tppt) cc_final: 0.8074 (ttmm) REVERT: A 172 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 205 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8161 (mm) REVERT: A 294 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8355 (mp0) REVERT: A 332 GLU cc_start: 0.8797 (mp0) cc_final: 0.8418 (pm20) REVERT: A 341 ASP cc_start: 0.8890 (m-30) cc_final: 0.8642 (m-30) REVERT: B 15 ASP cc_start: 0.8758 (t0) cc_final: 0.8517 (t0) REVERT: B 20 MET cc_start: 0.8902 (mtp) cc_final: 0.8363 (mtt) REVERT: B 53 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7394 (mm-30) REVERT: B 83 LEU cc_start: 0.9309 (tp) cc_final: 0.9080 (tm) REVERT: B 93 ASP cc_start: 0.8895 (m-30) cc_final: 0.8634 (m-30) REVERT: B 155 LYS cc_start: 0.9534 (mmmt) cc_final: 0.9276 (mmpt) REVERT: B 157 CYS cc_start: 0.9102 (m) cc_final: 0.8732 (m) REVERT: B 210 MET cc_start: 0.9690 (tmm) cc_final: 0.9371 (tmm) REVERT: B 229 GLU cc_start: 0.8901 (pt0) cc_final: 0.8641 (pt0) REVERT: B 241 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8295 (mt-10) REVERT: B 414 HIS cc_start: 0.8412 (p-80) cc_final: 0.8130 (p-80) REVERT: B 415 ASN cc_start: 0.8820 (m-40) cc_final: 0.8516 (m-40) REVERT: B 541 GLU cc_start: 0.9166 (tt0) cc_final: 0.8742 (tm-30) outliers start: 14 outliers final: 3 residues processed: 139 average time/residue: 0.5197 time to fit residues: 77.5002 Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 165 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 0.0040 chunk 59 optimal weight: 7.9990 chunk 39 optimal weight: 0.0670 chunk 53 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 overall best weight: 0.8134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.066874 restraints weight = 15303.511| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.62 r_work: 0.2549 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9150 Z= 0.134 Angle : 0.576 8.593 12465 Z= 0.300 Chirality : 0.044 0.297 1399 Planarity : 0.003 0.038 1498 Dihedral : 17.332 155.544 1437 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.51 % Allowed : 11.68 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.26), residues: 1027 helix: 1.71 (0.29), residues: 334 sheet: 0.24 (0.41), residues: 155 loop : -0.19 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 295 TYR 0.009 0.001 TYR A 88 PHE 0.036 0.001 PHE B 107 TRP 0.003 0.000 TRP B 513 HIS 0.003 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9150) covalent geometry : angle 0.57607 / 0.30 (12465) hydrogen bonds : bond 0.04345 / 2.90 ( 371) hydrogen bonds : angle 5.01470 / 3.45 ( 1033) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8421 (tppt) cc_final: 0.8126 (ttmm) REVERT: A 132 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.9106 (mp10) REVERT: A 172 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8097 (tm-30) REVERT: A 341 ASP cc_start: 0.8925 (m-30) cc_final: 0.8604 (m-30) REVERT: B 15 ASP cc_start: 0.8721 (t0) cc_final: 0.8510 (t0) REVERT: B 20 MET cc_start: 0.8897 (mtp) cc_final: 0.8325 (mtt) REVERT: B 53 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7438 (mm-30) REVERT: B 83 LEU cc_start: 0.9309 (tp) cc_final: 0.9095 (tm) REVERT: B 93 ASP cc_start: 0.8891 (m-30) cc_final: 0.8621 (m-30) REVERT: B 157 CYS cc_start: 0.9153 (m) cc_final: 0.8752 (m) REVERT: B 210 MET cc_start: 0.9691 (tmm) cc_final: 0.9382 (tmm) REVERT: B 229 GLU cc_start: 0.8890 (pt0) cc_final: 0.8608 (pt0) REVERT: B 241 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8314 (mt-10) REVERT: B 414 HIS cc_start: 0.8413 (p-80) cc_final: 0.8123 (p-80) REVERT: B 415 ASN cc_start: 0.8812 (m-40) cc_final: 0.8499 (m-40) REVERT: B 541 GLU cc_start: 0.9181 (tt0) cc_final: 0.8781 (tm-30) REVERT: C 184 SER cc_start: 0.7951 (t) cc_final: 0.7644 (t) outliers start: 14 outliers final: 2 residues processed: 132 average time/residue: 0.5358 time to fit residues: 75.9181 Evaluate side-chains 118 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 0.0570 chunk 60 optimal weight: 0.7980 overall best weight: 1.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.106044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.065119 restraints weight = 15567.808| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.62 r_work: 0.2518 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9150 Z= 0.205 Angle : 0.591 11.370 12465 Z= 0.305 Chirality : 0.045 0.396 1399 Planarity : 0.003 0.035 1498 Dihedral : 17.394 155.842 1437 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.73 % Allowed : 12.65 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 1027 helix: 1.72 (0.29), residues: 335 sheet: 0.26 (0.40), residues: 161 loop : -0.24 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 295 TYR 0.009 0.001 TYR A 88 PHE 0.034 0.001 PHE B 107 TRP 0.003 0.001 TRP B 513 HIS 0.005 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 ( 9150) covalent geometry : angle 0.59072 / 0.31 (12465) hydrogen bonds : bond 0.04363 / 2.92 ( 371) hydrogen bonds : angle 4.90902 / 3.39 ( 1033) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8444 (tppt) cc_final: 0.8150 (ttmm) REVERT: A 172 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8099 (tm-30) REVERT: A 265 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9104 (ptmm) REVERT: A 294 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8389 (mp0) REVERT: A 332 GLU cc_start: 0.8807 (mp0) cc_final: 0.8421 (pm20) REVERT: A 341 ASP cc_start: 0.8995 (m-30) cc_final: 0.8665 (m-30) REVERT: B 20 MET cc_start: 0.8935 (mtp) cc_final: 0.8292 (mtt) REVERT: B 52 ASP cc_start: 0.8730 (m-30) cc_final: 0.8473 (m-30) REVERT: B 53 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7385 (mm-30) REVERT: B 83 LEU cc_start: 0.9324 (tp) cc_final: 0.9062 (tm) REVERT: B 93 ASP cc_start: 0.8894 (m-30) cc_final: 0.8618 (m-30) REVERT: B 157 CYS cc_start: 0.9166 (m) cc_final: 0.8795 (m) REVERT: B 210 MET cc_start: 0.9695 (tmm) cc_final: 0.9385 (tmm) REVERT: B 229 GLU cc_start: 0.8881 (pt0) cc_final: 0.8614 (pt0) REVERT: B 241 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8363 (mt-10) REVERT: B 414 HIS cc_start: 0.8420 (p-80) cc_final: 0.8113 (p-80) REVERT: B 415 ASN cc_start: 0.8824 (m-40) cc_final: 0.8505 (m-40) REVERT: B 541 GLU cc_start: 0.9183 (tt0) cc_final: 0.8771 (tm-30) REVERT: C 184 SER cc_start: 0.8041 (t) cc_final: 0.7739 (t) outliers start: 16 outliers final: 5 residues processed: 131 average time/residue: 0.5298 time to fit residues: 74.7383 Evaluate side-chains 126 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 515 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 89 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.066350 restraints weight = 15326.821| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.59 r_work: 0.2539 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9150 Z= 0.138 Angle : 0.569 9.905 12465 Z= 0.293 Chirality : 0.045 0.335 1399 Planarity : 0.003 0.035 1498 Dihedral : 17.387 156.010 1437 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.95 % Allowed : 12.86 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.26), residues: 1027 helix: 1.83 (0.29), residues: 334 sheet: 0.25 (0.41), residues: 155 loop : -0.19 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 295 TYR 0.009 0.001 TYR A 88 PHE 0.035 0.001 PHE B 107 TRP 0.004 0.000 TRP B 513 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 9150) covalent geometry : angle 0.56852 / 0.29 (12465) hydrogen bonds : bond 0.03849 / 2.57 ( 371) hydrogen bonds : angle 4.79897 / 3.31 ( 1033) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8447 (tppt) cc_final: 0.8150 (ttmm) REVERT: A 172 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 265 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9108 (ptmm) REVERT: A 294 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8369 (mm-30) REVERT: A 332 GLU cc_start: 0.8850 (mp0) cc_final: 0.8443 (pm20) REVERT: A 341 ASP cc_start: 0.8927 (m-30) cc_final: 0.8586 (m-30) REVERT: B 15 ASP cc_start: 0.8903 (t0) cc_final: 0.8572 (t0) REVERT: B 52 ASP cc_start: 0.8734 (m-30) cc_final: 0.8483 (m-30) REVERT: B 53 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7477 (mm-30) REVERT: B 83 LEU cc_start: 0.9348 (tp) cc_final: 0.9101 (tm) REVERT: B 84 MET cc_start: 0.8261 (ptp) cc_final: 0.8048 (ptp) REVERT: B 93 ASP cc_start: 0.8899 (m-30) cc_final: 0.8613 (m-30) REVERT: B 157 CYS cc_start: 0.9189 (m) cc_final: 0.8817 (m) REVERT: B 210 MET cc_start: 0.9701 (tmm) cc_final: 0.9394 (tmm) REVERT: B 229 GLU cc_start: 0.8887 (pt0) cc_final: 0.8598 (pt0) REVERT: B 241 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8343 (mt-10) REVERT: B 414 HIS cc_start: 0.8390 (p-80) cc_final: 0.8076 (p-80) REVERT: B 415 ASN cc_start: 0.8823 (m-40) cc_final: 0.8504 (m-40) REVERT: B 541 GLU cc_start: 0.9177 (tt0) cc_final: 0.8785 (tm-30) REVERT: C 184 SER cc_start: 0.8095 (t) cc_final: 0.7815 (t) outliers start: 18 outliers final: 7 residues processed: 133 average time/residue: 0.5158 time to fit residues: 73.9927 Evaluate side-chains 127 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 357 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.105415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.064663 restraints weight = 15466.646| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.59 r_work: 0.2505 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9150 Z= 0.224 Angle : 0.596 11.098 12465 Z= 0.308 Chirality : 0.045 0.382 1399 Planarity : 0.003 0.034 1498 Dihedral : 17.450 155.554 1437 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.73 % Allowed : 13.62 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.26), residues: 1027 helix: 1.81 (0.29), residues: 335 sheet: 0.24 (0.40), residues: 161 loop : -0.24 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 295 TYR 0.010 0.001 TYR A 71 PHE 0.033 0.001 PHE B 107 TRP 0.004 0.001 TRP B 513 HIS 0.005 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 ( 9150) covalent geometry : angle 0.59578 / 0.31 (12465) hydrogen bonds : bond 0.04250 / 2.85 ( 371) hydrogen bonds : angle 4.79085 / 3.30 ( 1033) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8419 (tppt) cc_final: 0.8124 (ttmm) REVERT: A 172 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8078 (tm-30) REVERT: A 265 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9076 (ptmm) REVERT: A 294 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8325 (mm-30) REVERT: A 332 GLU cc_start: 0.8838 (mp0) cc_final: 0.8422 (pm20) REVERT: A 341 ASP cc_start: 0.8981 (m-30) cc_final: 0.8674 (m-30) REVERT: B 15 ASP cc_start: 0.8935 (t0) cc_final: 0.8697 (t0) REVERT: B 52 ASP cc_start: 0.8719 (m-30) cc_final: 0.8516 (m-30) REVERT: B 53 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7511 (mm-30) REVERT: B 83 LEU cc_start: 0.9329 (tp) cc_final: 0.9095 (tm) REVERT: B 84 MET cc_start: 0.8179 (ptp) cc_final: 0.7843 (ptp) REVERT: B 93 ASP cc_start: 0.8877 (m-30) cc_final: 0.8592 (m-30) REVERT: B 157 CYS cc_start: 0.9171 (m) cc_final: 0.8791 (m) REVERT: B 210 MET cc_start: 0.9703 (tmm) cc_final: 0.9396 (tmm) REVERT: B 229 GLU cc_start: 0.8871 (pt0) cc_final: 0.8578 (pt0) REVERT: B 241 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8370 (mt-10) REVERT: B 414 HIS cc_start: 0.8426 (p-80) cc_final: 0.8112 (p-80) REVERT: B 415 ASN cc_start: 0.8820 (m-40) cc_final: 0.8496 (m-40) REVERT: B 541 GLU cc_start: 0.9174 (tt0) cc_final: 0.8768 (tm-30) REVERT: C 184 SER cc_start: 0.8145 (t) cc_final: 0.7880 (t) outliers start: 16 outliers final: 8 residues processed: 128 average time/residue: 0.5505 time to fit residues: 75.4398 Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 19 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 100 optimal weight: 0.0170 chunk 66 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.066513 restraints weight = 15364.792| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.60 r_work: 0.2542 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9150 Z= 0.120 Angle : 0.571 9.576 12465 Z= 0.296 Chirality : 0.044 0.291 1399 Planarity : 0.003 0.035 1498 Dihedral : 17.412 156.191 1437 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.41 % Allowed : 14.27 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1027 helix: 1.86 (0.29), residues: 334 sheet: 0.24 (0.41), residues: 157 loop : -0.20 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 400 TYR 0.014 0.001 TYR A 88 PHE 0.035 0.001 PHE B 107 TRP 0.004 0.000 TRP B 513 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9150) covalent geometry : angle 0.57093 / 0.30 (12465) hydrogen bonds : bond 0.03612 / 2.41 ( 371) hydrogen bonds : angle 4.71742 / 3.26 ( 1033) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8399 (tppt) cc_final: 0.8088 (ttmm) REVERT: A 172 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8061 (tm-30) REVERT: A 294 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8335 (mm-30) REVERT: A 332 GLU cc_start: 0.8852 (mp0) cc_final: 0.8429 (pm20) REVERT: A 341 ASP cc_start: 0.8921 (m-30) cc_final: 0.8564 (m-30) REVERT: B 52 ASP cc_start: 0.8697 (m-30) cc_final: 0.8484 (m-30) REVERT: B 53 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7507 (mm-30) REVERT: B 83 LEU cc_start: 0.9320 (tp) cc_final: 0.9110 (tm) REVERT: B 84 MET cc_start: 0.8196 (ptp) cc_final: 0.7856 (ptp) REVERT: B 93 ASP cc_start: 0.8863 (m-30) cc_final: 0.8578 (m-30) REVERT: B 115 MET cc_start: 0.9619 (mtm) cc_final: 0.9379 (pmm) REVERT: B 157 CYS cc_start: 0.9172 (m) cc_final: 0.8798 (m) REVERT: B 210 MET cc_start: 0.9708 (tmm) cc_final: 0.9401 (tmm) REVERT: B 229 GLU cc_start: 0.8863 (pt0) cc_final: 0.8592 (pt0) REVERT: B 241 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8328 (mt-10) REVERT: B 414 HIS cc_start: 0.8409 (p-80) cc_final: 0.8089 (p-80) REVERT: B 415 ASN cc_start: 0.8810 (m-40) cc_final: 0.8494 (m-40) REVERT: B 474 GLU cc_start: 0.7362 (pm20) cc_final: 0.7120 (pm20) REVERT: B 541 GLU cc_start: 0.9170 (tt0) cc_final: 0.8763 (tm-30) REVERT: C 184 SER cc_start: 0.8021 (t) cc_final: 0.7769 (t) outliers start: 13 outliers final: 7 residues processed: 136 average time/residue: 0.5473 time to fit residues: 79.8804 Evaluate side-chains 128 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 357 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.065479 restraints weight = 15502.138| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.61 r_work: 0.2522 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9150 Z= 0.174 Angle : 0.590 7.904 12465 Z= 0.306 Chirality : 0.044 0.253 1399 Planarity : 0.004 0.080 1498 Dihedral : 17.441 155.607 1437 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.41 % Allowed : 15.57 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.26), residues: 1027 helix: 1.87 (0.29), residues: 334 sheet: 0.17 (0.41), residues: 157 loop : -0.20 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 502 TYR 0.011 0.001 TYR A 88 PHE 0.038 0.001 PHE B 107 TRP 0.004 0.001 TRP B 513 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 9150) covalent geometry : angle 0.59015 / 0.31 (12465) hydrogen bonds : bond 0.03821 / 2.56 ( 371) hydrogen bonds : angle 4.69778 / 3.23 ( 1033) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8412 (tppt) cc_final: 0.8105 (ttmm) REVERT: A 172 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8087 (tm-30) REVERT: A 265 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.9091 (ptmm) REVERT: A 294 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8337 (mm-30) REVERT: A 332 GLU cc_start: 0.8856 (mp0) cc_final: 0.8434 (pm20) REVERT: A 341 ASP cc_start: 0.8964 (m-30) cc_final: 0.8618 (m-30) REVERT: B 52 ASP cc_start: 0.8699 (m-30) cc_final: 0.8464 (m-30) REVERT: B 53 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7433 (mm-30) REVERT: B 83 LEU cc_start: 0.9335 (tp) cc_final: 0.9090 (tm) REVERT: B 84 MET cc_start: 0.8184 (ptp) cc_final: 0.7947 (ptp) REVERT: B 93 ASP cc_start: 0.8874 (m-30) cc_final: 0.8588 (m-30) REVERT: B 157 CYS cc_start: 0.9184 (m) cc_final: 0.8805 (m) REVERT: B 210 MET cc_start: 0.9707 (tmm) cc_final: 0.9396 (tmm) REVERT: B 229 GLU cc_start: 0.8869 (pt0) cc_final: 0.8575 (pt0) REVERT: B 241 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8365 (mt-10) REVERT: B 414 HIS cc_start: 0.8417 (p-80) cc_final: 0.8114 (p-80) REVERT: B 415 ASN cc_start: 0.8823 (m-40) cc_final: 0.8530 (m-40) REVERT: B 474 GLU cc_start: 0.7368 (pm20) cc_final: 0.7099 (pm20) REVERT: B 541 GLU cc_start: 0.9168 (tt0) cc_final: 0.8772 (tm-30) REVERT: C 184 SER cc_start: 0.8080 (t) cc_final: 0.7794 (t) REVERT: C 185 LEU cc_start: 0.9397 (tp) cc_final: 0.9190 (tp) outliers start: 13 outliers final: 8 residues processed: 127 average time/residue: 0.5743 time to fit residues: 78.0001 Evaluate side-chains 127 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 357 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.066583 restraints weight = 15315.425| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.62 r_work: 0.2544 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9150 Z= 0.125 Angle : 0.586 9.160 12465 Z= 0.302 Chirality : 0.044 0.257 1399 Planarity : 0.004 0.077 1498 Dihedral : 17.406 156.154 1437 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.30 % Allowed : 15.57 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.26), residues: 1027 helix: 1.88 (0.29), residues: 334 sheet: 0.19 (0.41), residues: 157 loop : -0.19 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 502 TYR 0.011 0.001 TYR A 141 PHE 0.035 0.001 PHE B 107 TRP 0.005 0.001 TRP B 513 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9150) covalent geometry : angle 0.58583 / 0.30 (12465) hydrogen bonds : bond 0.03472 / 2.32 ( 371) hydrogen bonds : angle 4.67852 / 3.23 ( 1033) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8396 (tppt) cc_final: 0.8075 (ttmm) REVERT: A 107 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7283 (mp0) REVERT: A 172 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8042 (tm-30) REVERT: A 250 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8902 (tp30) REVERT: A 294 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8337 (mm-30) REVERT: A 332 GLU cc_start: 0.8864 (mp0) cc_final: 0.8443 (pm20) REVERT: A 341 ASP cc_start: 0.8933 (m-30) cc_final: 0.8595 (m-30) REVERT: B 52 ASP cc_start: 0.8708 (m-30) cc_final: 0.8461 (m-30) REVERT: B 53 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7499 (mm-30) REVERT: B 68 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9162 (pp) REVERT: B 83 LEU cc_start: 0.9353 (tp) cc_final: 0.9117 (tm) REVERT: B 84 MET cc_start: 0.8275 (ptp) cc_final: 0.8024 (ptp) REVERT: B 93 ASP cc_start: 0.8878 (m-30) cc_final: 0.8581 (m-30) REVERT: B 157 CYS cc_start: 0.9207 (m) cc_final: 0.8824 (m) REVERT: B 210 MET cc_start: 0.9708 (tmm) cc_final: 0.9403 (tmm) REVERT: B 223 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7263 (mp0) REVERT: B 229 GLU cc_start: 0.8880 (pt0) cc_final: 0.8588 (pt0) REVERT: B 241 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8341 (mt-10) REVERT: B 414 HIS cc_start: 0.8389 (p-80) cc_final: 0.8082 (p-80) REVERT: B 415 ASN cc_start: 0.8818 (m-40) cc_final: 0.8534 (m-40) REVERT: B 474 GLU cc_start: 0.7408 (pm20) cc_final: 0.7135 (pm20) REVERT: B 541 GLU cc_start: 0.9168 (tt0) cc_final: 0.8780 (tm-30) REVERT: C 184 SER cc_start: 0.8101 (t) cc_final: 0.7827 (t) outliers start: 12 outliers final: 6 residues processed: 129 average time/residue: 0.5530 time to fit residues: 76.5567 Evaluate side-chains 130 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 357 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.064402 restraints weight = 15486.245| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 3.59 r_work: 0.2501 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9150 Z= 0.236 Angle : 0.639 9.145 12465 Z= 0.330 Chirality : 0.045 0.246 1399 Planarity : 0.004 0.084 1498 Dihedral : 17.492 155.425 1437 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.41 % Allowed : 15.46 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.26), residues: 1027 helix: 1.90 (0.29), residues: 333 sheet: 0.21 (0.41), residues: 159 loop : -0.24 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 502 TYR 0.011 0.001 TYR A 71 PHE 0.042 0.001 PHE B 107 TRP 0.003 0.001 TRP B 276 HIS 0.005 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 ( 9150) covalent geometry : angle 0.63870 / 0.33 (12465) hydrogen bonds : bond 0.04203 / 2.83 ( 371) hydrogen bonds : angle 4.72658 / 3.27 ( 1033) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8372 (tppt) cc_final: 0.8137 (ttmm) REVERT: A 107 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7332 (mp0) REVERT: A 172 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8075 (tm-30) REVERT: A 250 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8919 (tp30) REVERT: A 265 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.9075 (ptmm) REVERT: A 294 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8321 (mm-30) REVERT: A 332 GLU cc_start: 0.8850 (mp0) cc_final: 0.8443 (pm20) REVERT: A 341 ASP cc_start: 0.9018 (m-30) cc_final: 0.8725 (m-30) REVERT: B 52 ASP cc_start: 0.8686 (m-30) cc_final: 0.8478 (m-30) REVERT: B 53 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7476 (mm-30) REVERT: B 83 LEU cc_start: 0.9345 (tp) cc_final: 0.9110 (tm) REVERT: B 93 ASP cc_start: 0.8874 (m-30) cc_final: 0.8575 (m-30) REVERT: B 157 CYS cc_start: 0.9190 (m) cc_final: 0.8806 (m) REVERT: B 210 MET cc_start: 0.9705 (tmm) cc_final: 0.9396 (tmm) REVERT: B 223 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7248 (mp0) REVERT: B 229 GLU cc_start: 0.8867 (pt0) cc_final: 0.8559 (pt0) REVERT: B 241 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8347 (mt-10) REVERT: B 414 HIS cc_start: 0.8424 (p-80) cc_final: 0.8125 (p-80) REVERT: B 415 ASN cc_start: 0.8821 (m-40) cc_final: 0.8537 (m-40) REVERT: B 474 GLU cc_start: 0.7360 (pm20) cc_final: 0.7054 (pm20) REVERT: B 541 GLU cc_start: 0.9172 (tt0) cc_final: 0.8769 (tm-30) REVERT: C 184 SER cc_start: 0.8157 (t) cc_final: 0.7887 (t) outliers start: 13 outliers final: 8 residues processed: 129 average time/residue: 0.5544 time to fit residues: 76.7811 Evaluate side-chains 129 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 357 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.066025 restraints weight = 15180.740| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.57 r_work: 0.2531 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9150 Z= 0.138 Angle : 0.601 9.960 12465 Z= 0.313 Chirality : 0.044 0.256 1399 Planarity : 0.004 0.084 1498 Dihedral : 17.459 156.482 1437 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.19 % Allowed : 15.57 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1027 helix: 1.89 (0.29), residues: 334 sheet: 0.14 (0.41), residues: 157 loop : -0.18 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 502 TYR 0.011 0.001 TYR A 141 PHE 0.035 0.001 PHE B 107 TRP 0.004 0.001 TRP B 513 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9150) covalent geometry : angle 0.60116 / 0.31 (12465) hydrogen bonds : bond 0.03667 / 2.46 ( 371) hydrogen bonds : angle 4.70161 / 3.27 ( 1033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3303.66 seconds wall clock time: 57 minutes 8.05 seconds (3428.05 seconds total)