Starting phenix.real_space_refine on Fri Sep 11 10:33:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zyg_15022/09_2026/7zyg_15022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyg_15022/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zyg_15022/09_2026/7zyg_15022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyg_15022/09_2026/7zyg_15022.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zyg_15022/09_2026/7zyg_15022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyg_15022/09_2026/7zyg_15022.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zyg_15022/09_2026/7zyg_15022.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zyg_15022/09_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-2.2.1-6174/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: 1.62, per 1000 atoms: 0.18 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: 0.68 Conformation dependent library (CDL) restraints added in 312.7 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: 0.85 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: 1.44 Time building geometry restraints manager: 0.92 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: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.780 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- 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 : 0.501 5.289 12465 Z= 0.333 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 0.50098 / 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 : 0.347 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: 0.4657 time to fit residues: 82.6057 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 : 0.350 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.107306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.066672 restraints weight = 15291.922| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.61 r_work: 0.2547 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1209 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= 0.143 Angle : 0.613 8.777 12465 Z= 0.321 Chirality : 0.046 0.339 1399 Planarity : 0.003 0.038 1498 Dihedral : 17.094 156.602 1437 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: 0.76 (0.26), residues: 1027 helix: 1.68 (0.29), residues: 334 sheet: 0.27 (0.40), residues: 154 loop : -0.11 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 295 TYR 0.009 0.001 TYR A 71 PHE 0.028 0.001 PHE B 107 TRP 0.003 0.001 TRP A 148 HIS 0.004 0.001 HIS B 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 9150) covalent geometry : angle 0.61260 / 0.32 (12465) hydrogen bonds : bond 0.05510 / 3.64 ( 371) hydrogen bonds : angle 5.30583 / 3.65 ( 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 : 0.332 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8384 (tppt) cc_final: 0.8073 (ttmm) REVERT: A 172 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 205 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8171 (mm) REVERT: A 294 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8352 (mp0) REVERT: A 332 GLU cc_start: 0.8793 (mp0) cc_final: 0.8412 (pm20) REVERT: A 341 ASP cc_start: 0.8891 (m-30) cc_final: 0.8633 (m-30) REVERT: B 15 ASP cc_start: 0.8760 (t0) cc_final: 0.8520 (t0) REVERT: B 20 MET cc_start: 0.8911 (mtp) cc_final: 0.8369 (mtt) REVERT: B 53 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7390 (mm-30) REVERT: B 83 LEU cc_start: 0.9310 (tp) cc_final: 0.9089 (tm) REVERT: B 93 ASP cc_start: 0.8898 (m-30) cc_final: 0.8640 (m-30) REVERT: B 155 LYS cc_start: 0.9534 (mmmt) cc_final: 0.9272 (mmpt) REVERT: B 157 CYS cc_start: 0.9107 (m) cc_final: 0.8734 (m) REVERT: B 210 MET cc_start: 0.9689 (tmm) cc_final: 0.9369 (tmm) REVERT: B 229 GLU cc_start: 0.8897 (pt0) cc_final: 0.8638 (pt0) REVERT: B 241 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8293 (mt-10) REVERT: B 414 HIS cc_start: 0.8410 (p-80) cc_final: 0.8128 (p-80) REVERT: B 415 ASN cc_start: 0.8819 (m-40) cc_final: 0.8513 (m-40) REVERT: B 541 GLU cc_start: 0.9164 (tt0) cc_final: 0.8742 (tm-30) outliers start: 14 outliers final: 3 residues processed: 139 average time/residue: 0.4824 time to fit residues: 72.0048 Evaluate side-chains 122 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 0.0870 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 0.0030 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 0.0670 chunk 53 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 overall best weight: 0.4306 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.108395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.067668 restraints weight = 15296.730| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.64 r_work: 0.2565 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9150 Z= 0.115 Angle : 0.571 7.864 12465 Z= 0.298 Chirality : 0.045 0.314 1399 Planarity : 0.003 0.037 1498 Dihedral : 17.251 154.453 1437 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.41 % Allowed : 11.68 % Favored : 86.92 % 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: 1.73 (0.29), residues: 333 sheet: 0.27 (0.41), residues: 155 loop : -0.16 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 400 TYR 0.010 0.001 TYR A 88 PHE 0.035 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 0.00234 / 0.12 ( 9150) covalent geometry : angle 0.57078 / 0.30 (12465) hydrogen bonds : bond 0.04228 / 2.81 ( 371) hydrogen bonds : angle 5.02790 / 3.46 ( 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: 13 poor density : 126 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8422 (tppt) cc_final: 0.8132 (ttmm) REVERT: A 132 GLN cc_start: 0.9317 (OUTLIER) cc_final: 0.9106 (mp10) REVERT: A 172 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8078 (tm-30) REVERT: A 205 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8204 (mm) REVERT: A 288 LEU cc_start: 0.9432 (mt) cc_final: 0.9230 (mm) REVERT: A 341 ASP cc_start: 0.8887 (m-30) cc_final: 0.8606 (m-30) REVERT: B 20 MET cc_start: 0.8904 (mtp) cc_final: 0.8357 (mtt) REVERT: B 53 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7462 (mm-30) REVERT: B 93 ASP cc_start: 0.8887 (m-30) cc_final: 0.8617 (m-30) REVERT: B 115 MET cc_start: 0.9605 (mtm) cc_final: 0.9385 (mtm) REVERT: B 157 CYS cc_start: 0.9145 (m) cc_final: 0.8781 (m) REVERT: B 210 MET cc_start: 0.9692 (tmm) cc_final: 0.9385 (tmm) REVERT: B 229 GLU cc_start: 0.8888 (pt0) cc_final: 0.8609 (pt0) REVERT: B 241 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8290 (mt-10) REVERT: B 414 HIS cc_start: 0.8411 (p-80) cc_final: 0.8124 (p-80) REVERT: B 415 ASN cc_start: 0.8803 (m-40) cc_final: 0.8490 (m-40) REVERT: B 541 GLU cc_start: 0.9176 (tt0) cc_final: 0.8762 (tm-30) outliers start: 13 outliers final: 1 residues processed: 132 average time/residue: 0.4721 time to fit residues: 66.9478 Evaluate side-chains 116 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 165 LEU 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: 5.9990 chunk 67 optimal weight: 6.9990 chunk 63 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 ASN B 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.067440 restraints weight = 15440.737| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.61 r_work: 0.2561 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1611 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= 0.126 Angle : 0.565 12.131 12465 Z= 0.290 Chirality : 0.045 0.419 1399 Planarity : 0.003 0.037 1498 Dihedral : 17.273 154.307 1437 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.30 % Allowed : 13.08 % 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: 0.81 (0.26), residues: 1027 helix: 1.83 (0.29), residues: 334 sheet: 0.29 (0.41), residues: 157 loop : -0.16 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 400 TYR 0.009 0.001 TYR A 88 PHE 0.032 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 0.00273 / 0.13 ( 9150) covalent geometry : angle 0.56527 / 0.29 (12465) hydrogen bonds : bond 0.03806 / 2.54 ( 371) hydrogen bonds : angle 4.86221 / 3.35 ( 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: 12 poor density : 127 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8467 (tppt) cc_final: 0.8183 (ttmm) REVERT: A 172 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8029 (tm-30) REVERT: A 332 GLU cc_start: 0.8843 (mp0) cc_final: 0.8456 (pm20) REVERT: A 341 ASP cc_start: 0.8877 (m-30) cc_final: 0.8538 (m-30) REVERT: B 15 ASP cc_start: 0.8848 (t0) cc_final: 0.8453 (OUTLIER) REVERT: B 20 MET cc_start: 0.8746 (mtp) cc_final: 0.8496 (mtp) REVERT: B 53 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 68 LEU cc_start: 0.9364 (mt) cc_final: 0.9102 (pp) REVERT: B 93 ASP cc_start: 0.8891 (m-30) cc_final: 0.8617 (m-30) REVERT: B 115 MET cc_start: 0.9574 (mtm) cc_final: 0.9268 (mtm) REVERT: B 157 CYS cc_start: 0.9204 (m) cc_final: 0.8834 (m) REVERT: B 210 MET cc_start: 0.9703 (tmm) cc_final: 0.9402 (tmm) REVERT: B 229 GLU cc_start: 0.8876 (pt0) cc_final: 0.8593 (pt0) REVERT: B 241 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8322 (mt-10) REVERT: B 414 HIS cc_start: 0.8391 (p-80) cc_final: 0.8090 (p-80) REVERT: B 415 ASN cc_start: 0.8800 (m-40) cc_final: 0.8495 (m-40) REVERT: B 541 GLU cc_start: 0.9174 (tt0) cc_final: 0.8764 (tm-30) REVERT: C 184 SER cc_start: 0.8030 (t) cc_final: 0.7739 (t) outliers start: 12 outliers final: 6 residues processed: 131 average time/residue: 0.4651 time to fit residues: 65.8063 Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN 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: 2.9990 chunk 22 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.104746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.063917 restraints weight = 15460.030| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.58 r_work: 0.2491 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9150 Z= 0.270 Angle : 0.633 10.197 12465 Z= 0.322 Chirality : 0.046 0.320 1399 Planarity : 0.004 0.042 1498 Dihedral : 17.421 153.826 1437 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.73 % Allowed : 13.51 % Favored : 84.76 % 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: 1.84 (0.29), residues: 335 sheet: 0.28 (0.41), residues: 159 loop : -0.26 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 400 TYR 0.011 0.001 TYR A 71 PHE 0.036 0.002 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 0.00629 / 0.27 ( 9150) covalent geometry : angle 0.63339 / 0.32 (12465) hydrogen bonds : bond 0.04630 / 3.12 ( 371) hydrogen bonds : angle 4.83732 / 3.33 ( 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 135 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8419 (tppt) cc_final: 0.8130 (ttmm) REVERT: A 172 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8087 (tm-30) REVERT: A 265 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9093 (ptmm) REVERT: A 294 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8345 (mm-30) REVERT: A 332 GLU cc_start: 0.8850 (mp0) cc_final: 0.8452 (pm20) REVERT: A 341 ASP cc_start: 0.9020 (m-30) cc_final: 0.8677 (m-30) REVERT: B 15 ASP cc_start: 0.8909 (t0) cc_final: 0.8580 (t0) REVERT: B 20 MET cc_start: 0.8828 (mtp) cc_final: 0.8504 (mtt) REVERT: B 93 ASP cc_start: 0.8896 (m-30) cc_final: 0.8610 (m-30) REVERT: B 157 CYS cc_start: 0.9208 (m) cc_final: 0.8852 (m) REVERT: B 210 MET cc_start: 0.9706 (tmm) cc_final: 0.9394 (tmm) REVERT: B 229 GLU cc_start: 0.8879 (pt0) cc_final: 0.8589 (pt0) REVERT: B 241 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8410 (mt-10) REVERT: B 414 HIS cc_start: 0.8434 (p-80) cc_final: 0.8122 (p-80) REVERT: B 415 ASN cc_start: 0.8826 (m-40) cc_final: 0.8496 (m-40) REVERT: B 541 GLU cc_start: 0.9171 (tt0) cc_final: 0.8758 (tm-30) REVERT: C 184 SER cc_start: 0.8158 (t) cc_final: 0.7870 (t) outliers start: 16 outliers final: 6 residues processed: 126 average time/residue: 0.4919 time to fit residues: 66.5133 Evaluate side-chains 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.106824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.066107 restraints weight = 15368.648| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.60 r_work: 0.2532 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1775 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= 0.131 Angle : 0.573 12.196 12465 Z= 0.294 Chirality : 0.045 0.391 1399 Planarity : 0.003 0.041 1498 Dihedral : 17.376 154.999 1437 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.30 % Allowed : 14.81 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 335 sheet: 0.24 (0.41), residues: 157 loop : -0.22 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 400 TYR 0.009 0.001 TYR A 88 PHE 0.034 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 0.00287 / 0.13 ( 9150) covalent geometry : angle 0.57259 / 0.29 (12465) hydrogen bonds : bond 0.03749 / 2.51 ( 371) hydrogen bonds : angle 4.72677 / 3.25 ( 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 135 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8395 (tppt) cc_final: 0.8085 (ttmm) REVERT: A 172 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8026 (tm-30) REVERT: A 265 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.9090 (ptmm) REVERT: A 294 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8346 (mm-30) REVERT: A 332 GLU cc_start: 0.8869 (mp0) cc_final: 0.8471 (pm20) REVERT: A 341 ASP cc_start: 0.8936 (m-30) cc_final: 0.8636 (m-30) REVERT: B 15 ASP cc_start: 0.8910 (t0) cc_final: 0.8645 (t0) REVERT: B 20 MET cc_start: 0.8858 (mtp) cc_final: 0.8537 (mtt) REVERT: B 93 ASP cc_start: 0.8864 (m-30) cc_final: 0.8586 (m-30) REVERT: B 157 CYS cc_start: 0.9216 (m) cc_final: 0.8836 (m) REVERT: B 210 MET cc_start: 0.9710 (tmm) cc_final: 0.9401 (tmm) REVERT: B 229 GLU cc_start: 0.8866 (pt0) cc_final: 0.8600 (pt0) REVERT: B 241 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8350 (mt-10) REVERT: B 414 HIS cc_start: 0.8405 (p-80) cc_final: 0.8089 (p-80) REVERT: B 415 ASN cc_start: 0.8820 (m-40) cc_final: 0.8505 (m-40) REVERT: B 541 GLU cc_start: 0.9177 (tt0) cc_final: 0.8773 (tm-30) REVERT: C 184 SER cc_start: 0.7983 (t) cc_final: 0.7692 (t) outliers start: 12 outliers final: 7 residues processed: 130 average time/residue: 0.5110 time to fit residues: 71.2528 Evaluate side-chains 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 19 optimal weight: 30.0000 chunk 8 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 76 optimal weight: 0.0470 chunk 40 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 100 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.107762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.066840 restraints weight = 15406.131| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.64 r_work: 0.2551 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9150 Z= 0.114 Angle : 0.576 9.974 12465 Z= 0.297 Chirality : 0.044 0.325 1399 Planarity : 0.004 0.078 1498 Dihedral : 17.336 154.475 1437 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.30 % Allowed : 15.46 % 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: 0.84 (0.26), residues: 1027 helix: 1.93 (0.29), residues: 334 sheet: 0.24 (0.41), residues: 157 loop : -0.18 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 502 TYR 0.010 0.001 TYR A 88 PHE 0.036 0.001 PHE B 107 TRP 0.005 0.000 TRP B 513 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 9150) covalent geometry : angle 0.57628 / 0.30 (12465) hydrogen bonds : bond 0.03441 / 2.30 ( 371) hydrogen bonds : angle 4.69628 / 3.23 ( 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 141 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8422 (tppt) cc_final: 0.8119 (ttmm) REVERT: A 172 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8039 (tm-30) REVERT: A 294 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8364 (mm-30) REVERT: A 332 GLU cc_start: 0.8896 (mp0) cc_final: 0.8497 (pm20) REVERT: A 341 ASP cc_start: 0.8927 (m-30) cc_final: 0.8594 (m-30) REVERT: B 15 ASP cc_start: 0.8945 (t0) cc_final: 0.8644 (t0) REVERT: B 20 MET cc_start: 0.8857 (mtp) cc_final: 0.8512 (mtt) REVERT: B 93 ASP cc_start: 0.8880 (m-30) cc_final: 0.8599 (m-30) REVERT: B 115 MET cc_start: 0.9636 (mtm) cc_final: 0.9370 (mtm) REVERT: B 157 CYS cc_start: 0.9239 (m) cc_final: 0.8856 (m) REVERT: B 210 MET cc_start: 0.9709 (tmm) cc_final: 0.9404 (tmm) REVERT: B 229 GLU cc_start: 0.8880 (pt0) cc_final: 0.8589 (pt0) REVERT: B 241 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8349 (mt-10) REVERT: B 414 HIS cc_start: 0.8393 (p-80) cc_final: 0.8069 (p-80) REVERT: B 415 ASN cc_start: 0.8817 (m-40) cc_final: 0.8503 (m-40) REVERT: B 474 GLU cc_start: 0.7387 (pm20) cc_final: 0.7153 (pm20) REVERT: B 541 GLU cc_start: 0.9174 (tt0) cc_final: 0.8781 (tm-30) REVERT: C 184 SER cc_start: 0.8051 (t) cc_final: 0.7785 (t) outliers start: 12 outliers final: 7 residues processed: 135 average time/residue: 0.4985 time to fit residues: 72.4311 Evaluate side-chains 130 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 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=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: 2.9990 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.106898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.066097 restraints weight = 15458.640| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.61 r_work: 0.2534 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9150 Z= 0.154 Angle : 0.590 8.249 12465 Z= 0.305 Chirality : 0.044 0.287 1399 Planarity : 0.004 0.071 1498 Dihedral : 17.359 154.039 1437 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.30 % Allowed : 16.00 % Favored : 82.70 % 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: 0.85 (0.26), residues: 1027 helix: 1.97 (0.29), residues: 334 sheet: 0.19 (0.41), residues: 157 loop : -0.17 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 502 TYR 0.010 0.001 TYR A 88 PHE 0.041 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 0.00349 / 0.15 ( 9150) covalent geometry : angle 0.59043 / 0.30 (12465) hydrogen bonds : bond 0.03636 / 2.44 ( 371) hydrogen bonds : angle 4.66182 / 3.20 ( 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 136 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8430 (tppt) cc_final: 0.8130 (ttmm) REVERT: A 172 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8069 (tm-30) REVERT: A 332 GLU cc_start: 0.8893 (mp0) cc_final: 0.8499 (pm20) REVERT: A 341 ASP cc_start: 0.8932 (m-30) cc_final: 0.8597 (m-30) REVERT: B 15 ASP cc_start: 0.8916 (t0) cc_final: 0.8611 (t0) REVERT: B 20 MET cc_start: 0.8859 (mtp) cc_final: 0.8499 (mtt) REVERT: B 68 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9116 (pp) REVERT: B 93 ASP cc_start: 0.8879 (m-30) cc_final: 0.8591 (m-30) REVERT: B 157 CYS cc_start: 0.9237 (m) cc_final: 0.8850 (m) REVERT: B 210 MET cc_start: 0.9710 (tmm) cc_final: 0.9406 (tmm) REVERT: B 223 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7224 (mp0) REVERT: B 229 GLU cc_start: 0.8883 (pt0) cc_final: 0.8611 (pt0) REVERT: B 241 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8361 (mt-10) REVERT: B 414 HIS cc_start: 0.8398 (p-80) cc_final: 0.8075 (p-80) REVERT: B 415 ASN cc_start: 0.8824 (m-40) cc_final: 0.8507 (m-40) REVERT: B 474 GLU cc_start: 0.7395 (pm20) cc_final: 0.7160 (pm20) REVERT: B 541 GLU cc_start: 0.9173 (tt0) cc_final: 0.8801 (tm-30) REVERT: C 184 SER cc_start: 0.8128 (t) cc_final: 0.7828 (t) outliers start: 12 outliers final: 7 residues processed: 131 average time/residue: 0.4949 time to fit residues: 69.6525 Evaluate side-chains 128 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 100 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.107936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.067221 restraints weight = 15270.969| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.61 r_work: 0.2554 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9150 Z= 0.118 Angle : 0.586 8.526 12465 Z= 0.301 Chirality : 0.044 0.277 1399 Planarity : 0.004 0.080 1498 Dihedral : 17.343 154.445 1437 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: 0.88 (0.26), residues: 1027 helix: 2.00 (0.29), residues: 334 sheet: 0.21 (0.41), residues: 157 loop : -0.16 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 502 TYR 0.016 0.001 TYR A 88 PHE 0.041 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 0.00258 / 0.12 ( 9150) covalent geometry : angle 0.58649 / 0.30 (12465) hydrogen bonds : bond 0.03409 / 2.28 ( 371) hydrogen bonds : angle 4.64544 / 3.19 ( 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 137 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8410 (tppt) cc_final: 0.8102 (ttmm) REVERT: A 107 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7235 (mp0) REVERT: A 172 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 294 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8613 (mp0) REVERT: A 332 GLU cc_start: 0.8897 (mp0) cc_final: 0.8500 (pm20) REVERT: A 341 ASP cc_start: 0.8894 (m-30) cc_final: 0.8549 (m-30) REVERT: B 15 ASP cc_start: 0.8899 (t0) cc_final: 0.8604 (t0) REVERT: B 20 MET cc_start: 0.8849 (mtp) cc_final: 0.8496 (mtt) REVERT: B 93 ASP cc_start: 0.8884 (m-30) cc_final: 0.8594 (m-30) REVERT: B 115 MET cc_start: 0.9631 (mtm) cc_final: 0.9370 (mtm) REVERT: B 157 CYS cc_start: 0.9235 (m) cc_final: 0.8851 (m) REVERT: B 210 MET cc_start: 0.9710 (tmm) cc_final: 0.9402 (tmm) REVERT: B 223 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7195 (mp0) REVERT: B 229 GLU cc_start: 0.8867 (pt0) cc_final: 0.8573 (pt0) REVERT: B 241 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8332 (mt-10) REVERT: B 414 HIS cc_start: 0.8390 (p-80) cc_final: 0.8090 (p-80) REVERT: B 415 ASN cc_start: 0.8812 (m-40) cc_final: 0.8533 (m-40) REVERT: B 474 GLU cc_start: 0.7345 (pm20) cc_final: 0.7142 (pm20) REVERT: B 541 GLU cc_start: 0.9174 (tt0) cc_final: 0.8795 (tm-30) REVERT: C 184 SER cc_start: 0.8093 (t) cc_final: 0.7826 (t) REVERT: C 191 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8816 (pmtt) outliers start: 13 outliers final: 7 residues processed: 133 average time/residue: 0.4960 time to fit residues: 70.7490 Evaluate side-chains 130 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 294 GLU 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 Chi-restraints excluded: chain C residue 191 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 50 optimal weight: 0.2980 chunk 23 optimal weight: 0.0470 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.108140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.067275 restraints weight = 15395.421| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.66 r_work: 0.2554 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9150 Z= 0.129 Angle : 0.605 8.396 12465 Z= 0.310 Chirality : 0.044 0.276 1399 Planarity : 0.004 0.086 1498 Dihedral : 17.341 154.314 1437 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.08 % Allowed : 16.11 % Favored : 82.81 % 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: 0.85 (0.26), residues: 1027 helix: 1.92 (0.29), residues: 334 sheet: 0.22 (0.41), residues: 157 loop : -0.14 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 502 TYR 0.015 0.001 TYR B 74 PHE 0.042 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 0.00282 / 0.13 ( 9150) covalent geometry : angle 0.60515 / 0.31 (12465) hydrogen bonds : bond 0.03511 / 2.37 ( 371) hydrogen bonds : angle 4.69108 / 3.21 ( 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 135 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8381 (tppt) cc_final: 0.8036 (ttmm) REVERT: A 107 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7202 (mp0) REVERT: A 172 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8017 (tm-30) REVERT: A 289 TYR cc_start: 0.8170 (t80) cc_final: 0.7871 (t80) REVERT: A 294 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8531 (mp0) REVERT: A 332 GLU cc_start: 0.8893 (mp0) cc_final: 0.8508 (pm20) REVERT: A 341 ASP cc_start: 0.8895 (m-30) cc_final: 0.8527 (m-30) REVERT: B 15 ASP cc_start: 0.8889 (t0) cc_final: 0.8604 (t0) REVERT: B 20 MET cc_start: 0.8858 (mtp) cc_final: 0.8499 (mtt) REVERT: B 93 ASP cc_start: 0.8873 (m-30) cc_final: 0.8594 (m-30) REVERT: B 157 CYS cc_start: 0.9231 (m) cc_final: 0.8840 (m) REVERT: B 210 MET cc_start: 0.9714 (tmm) cc_final: 0.9410 (tmm) REVERT: B 223 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7225 (mp0) REVERT: B 229 GLU cc_start: 0.8868 (pt0) cc_final: 0.8577 (pt0) REVERT: B 241 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8321 (mt-10) REVERT: B 414 HIS cc_start: 0.8400 (p-80) cc_final: 0.8097 (p-80) REVERT: B 415 ASN cc_start: 0.8800 (m-40) cc_final: 0.8519 (m-40) REVERT: B 541 GLU cc_start: 0.9176 (tt0) cc_final: 0.8795 (tm-30) REVERT: C 184 SER cc_start: 0.8077 (t) cc_final: 0.7791 (t) REVERT: C 191 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8831 (pmtt) outliers start: 10 outliers final: 7 residues processed: 132 average time/residue: 0.4813 time to fit residues: 68.0323 Evaluate side-chains 129 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 294 GLU 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 Chi-restraints excluded: chain C residue 191 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 74 optimal weight: 0.1980 chunk 52 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 37 optimal weight: 0.0000 chunk 42 optimal weight: 3.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.108734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.068044 restraints weight = 15181.947| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.63 r_work: 0.2568 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9150 Z= 0.117 Angle : 0.607 10.916 12465 Z= 0.313 Chirality : 0.044 0.278 1399 Planarity : 0.004 0.082 1498 Dihedral : 17.317 154.277 1437 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.08 % Allowed : 16.11 % Favored : 82.81 % 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: 0.89 (0.26), residues: 1027 helix: 1.96 (0.29), residues: 334 sheet: 0.23 (0.41), residues: 157 loop : -0.13 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 502 TYR 0.012 0.001 TYR A 88 PHE 0.043 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 0.00253 / 0.12 ( 9150) covalent geometry : angle 0.60719 / 0.31 (12465) hydrogen bonds : bond 0.03295 / 2.21 ( 371) hydrogen bonds : angle 4.65601 / 3.21 ( 1033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2968.93 seconds wall clock time: 51 minutes 19.17 seconds (3079.17 seconds total)