Starting phenix.real_space_refine on Tue Mar 3 22:27:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zyg_15022/03_2026/7zyg_15022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyg_15022/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zyg_15022/03_2026/7zyg_15022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyg_15022/03_2026/7zyg_15022.map" model { file = "/net/cci-nas-00/data/ceres_data/7zyg_15022/03_2026/7zyg_15022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyg_15022/03_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-5986/lib/python3.9/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: 1.98, per 1000 atoms: 0.22 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: 0.73 Conformation dependent library (CDL) restraints added in 316.7 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: 0.97 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: 1.27 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=" 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 bond pdb=" N ASP A 212 " pdb=" CA ASP A 212 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.11e+00 ... (remaining 9145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 12055 1.06 - 2.12: 282 2.12 - 3.17: 112 3.17 - 4.23: 9 4.23 - 5.29: 7 Bond angle restraints: 12465 Sorted by residual: angle pdb=" C LEU A 495 " pdb=" N ASP A 496 " pdb=" CA ASP A 496 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.94e+00 angle pdb=" C PHE A 211 " pdb=" N ASP A 212 " pdb=" CA ASP A 212 " ideal model delta sigma weight residual 121.54 126.13 -4.59 1.91e+00 2.74e-01 5.77e+00 angle pdb=" N VAL A 231 " pdb=" CA VAL A 231 " pdb=" C VAL A 231 " ideal model delta sigma weight residual 113.07 109.99 3.08 1.36e+00 5.41e-01 5.11e+00 angle pdb=" C SER A 222 " pdb=" N ILE A 223 " pdb=" CA ILE A 223 " ideal model delta sigma weight residual 121.97 126.03 -4.06 1.80e+00 3.09e-01 5.09e+00 angle pdb=" N ASN A 174 " pdb=" CA ASN A 174 " pdb=" C ASN A 174 " ideal model delta sigma weight residual 109.81 114.77 -4.96 2.21e+00 2.05e-01 5.05e+00 ... (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: 925 0.030 - 0.060: 308 0.060 - 0.089: 86 0.089 - 0.119: 69 0.119 - 0.149: 11 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: 5.970 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.640 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:8.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.002 0.059 9150 Z= 0.115 Angle : 0.463 5.289 12465 Z= 0.250 Chirality : 0.039 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 covalent geometry : bond 0.00239 ( 9150) covalent geometry : angle 0.46300 (12465) hydrogen bonds : bond 0.23099 ( 371) hydrogen bonds : angle 7.69696 ( 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 : 0.346 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: 0.5304 time to fit residues: 93.5288 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 : 0.354 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.107505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.066758 restraints weight = 15297.513| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.63 r_work: 0.2550 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9150 Z= 0.138 Angle : 0.581 10.383 12465 Z= 0.303 Chirality : 0.044 0.333 1399 Planarity : 0.003 0.038 1498 Dihedral : 17.026 152.157 1437 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.73 % Allowed : 10.05 % Favored : 88.22 % 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: 1.65 (0.29), residues: 334 sheet: 0.32 (0.41), residues: 157 loop : -0.13 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 295 TYR 0.011 0.001 TYR A 88 PHE 0.029 0.001 PHE B 107 TRP 0.002 0.000 TRP A 148 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9150) covalent geometry : angle 0.58099 (12465) hydrogen bonds : bond 0.04719 ( 371) hydrogen bonds : angle 5.16789 ( 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 152 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8400 (tppt) cc_final: 0.8096 (ttmm) REVERT: A 172 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 294 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8374 (mp0) REVERT: A 332 GLU cc_start: 0.8820 (mp0) cc_final: 0.8465 (pm20) REVERT: A 341 ASP cc_start: 0.8906 (m-30) cc_final: 0.8653 (m-30) REVERT: B 15 ASP cc_start: 0.8742 (t0) cc_final: 0.8497 (t0) REVERT: B 20 MET cc_start: 0.8899 (mtp) cc_final: 0.8347 (mtt) REVERT: B 53 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7425 (mm-30) REVERT: B 83 LEU cc_start: 0.9298 (tp) cc_final: 0.9065 (tm) REVERT: B 93 ASP cc_start: 0.8897 (m-30) cc_final: 0.8613 (m-30) REVERT: B 157 CYS cc_start: 0.9129 (m) cc_final: 0.8747 (m) REVERT: B 210 MET cc_start: 0.9690 (tmm) cc_final: 0.9376 (tmm) REVERT: B 229 GLU cc_start: 0.8882 (pt0) cc_final: 0.8602 (pt0) REVERT: B 241 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8302 (mt-10) REVERT: B 414 HIS cc_start: 0.8407 (p-80) cc_final: 0.8119 (p-80) REVERT: B 415 ASN cc_start: 0.8818 (m-40) cc_final: 0.8514 (m-40) REVERT: B 541 GLU cc_start: 0.9175 (tt0) cc_final: 0.8749 (tm-30) outliers start: 16 outliers final: 3 residues processed: 140 average time/residue: 0.5464 time to fit residues: 81.6752 Evaluate side-chains 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 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: 1.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.105506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.064735 restraints weight = 15397.848| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 3.59 r_work: 0.2508 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9150 Z= 0.219 Angle : 0.573 5.667 12465 Z= 0.300 Chirality : 0.043 0.221 1399 Planarity : 0.003 0.035 1498 Dihedral : 17.077 151.570 1437 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.38 % Allowed : 10.92 % Favored : 86.70 % 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: 0.70 (0.26), residues: 1027 helix: 1.69 (0.29), residues: 335 sheet: 0.24 (0.40), residues: 159 loop : -0.20 (0.27), residues: 533 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 0.030 0.001 PHE B 107 TRP 0.004 0.000 TRP B 513 HIS 0.005 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 9150) covalent geometry : angle 0.57319 (12465) hydrogen bonds : bond 0.04466 ( 371) hydrogen bonds : angle 4.94493 ( 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 146 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8404 (tppt) cc_final: 0.8101 (ttmm) REVERT: A 172 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 265 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9101 (ptmm) REVERT: A 294 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8409 (mp0) REVERT: A 332 GLU cc_start: 0.8841 (mp0) cc_final: 0.8398 (pm20) REVERT: A 335 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8680 (mm-30) REVERT: A 341 ASP cc_start: 0.8983 (m-30) cc_final: 0.8664 (m-30) REVERT: B 20 MET cc_start: 0.8925 (mtp) cc_final: 0.8283 (mtt) REVERT: B 52 ASP cc_start: 0.8724 (m-30) cc_final: 0.8494 (m-30) REVERT: B 53 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7433 (mm-30) REVERT: B 83 LEU cc_start: 0.9317 (tp) cc_final: 0.9062 (tm) REVERT: B 93 ASP cc_start: 0.8882 (m-30) cc_final: 0.8592 (m-30) REVERT: B 157 CYS cc_start: 0.9155 (m) cc_final: 0.8772 (m) REVERT: B 210 MET cc_start: 0.9699 (tmm) cc_final: 0.9391 (tmm) REVERT: B 229 GLU cc_start: 0.8877 (pt0) cc_final: 0.8610 (pt0) REVERT: B 241 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8353 (mt-10) REVERT: B 414 HIS cc_start: 0.8411 (p-80) cc_final: 0.8113 (p-80) REVERT: B 415 ASN cc_start: 0.8823 (m-40) cc_final: 0.8517 (m-40) REVERT: B 432 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8649 (mm-40) REVERT: B 541 GLU cc_start: 0.9156 (tt0) cc_final: 0.8745 (tm-30) REVERT: C 184 SER cc_start: 0.8036 (t) cc_final: 0.7734 (t) outliers start: 22 outliers final: 8 residues processed: 134 average time/residue: 0.5420 time to fit residues: 77.8700 Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 A residue 335 GLU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 515 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 0.0270 chunk 60 optimal weight: 0.7980 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3449 r_free = 0.3449 target = 0.106437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.065572 restraints weight = 15498.518| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.62 r_work: 0.2525 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9150 Z= 0.159 Angle : 0.550 7.010 12465 Z= 0.287 Chirality : 0.042 0.181 1399 Planarity : 0.003 0.036 1498 Dihedral : 17.034 151.772 1437 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.62 % Allowed : 13.08 % Favored : 85.30 % 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: 1.79 (0.29), residues: 334 sheet: 0.28 (0.41), residues: 157 loop : -0.20 (0.27), residues: 536 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 0.032 0.001 PHE B 107 TRP 0.004 0.000 TRP B 513 HIS 0.005 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9150) covalent geometry : angle 0.54951 (12465) hydrogen bonds : bond 0.03833 ( 371) hydrogen bonds : angle 4.78957 ( 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 140 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8413 (tppt) cc_final: 0.8113 (ttmm) REVERT: A 172 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8042 (tm-30) REVERT: A 265 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9103 (ptmm) REVERT: A 332 GLU cc_start: 0.8859 (mp0) cc_final: 0.8447 (pm20) REVERT: A 341 ASP cc_start: 0.8986 (m-30) cc_final: 0.8710 (m-30) REVERT: B 15 ASP cc_start: 0.8913 (t0) cc_final: 0.8604 (t0) REVERT: B 20 MET cc_start: 0.8779 (mtp) cc_final: 0.8540 (mtt) REVERT: B 53 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7497 (mm-30) REVERT: B 83 LEU cc_start: 0.9311 (tp) cc_final: 0.9094 (tm) REVERT: B 84 MET cc_start: 0.8219 (ptp) cc_final: 0.7865 (ptp) REVERT: B 93 ASP cc_start: 0.8869 (m-30) cc_final: 0.8588 (m-30) REVERT: B 115 MET cc_start: 0.9617 (mtm) cc_final: 0.9416 (mtm) REVERT: B 157 CYS cc_start: 0.9177 (m) cc_final: 0.8790 (m) REVERT: B 210 MET cc_start: 0.9708 (tmm) cc_final: 0.9402 (tmm) REVERT: B 229 GLU cc_start: 0.8868 (pt0) cc_final: 0.8584 (pt0) REVERT: B 241 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8353 (mt-10) REVERT: B 414 HIS cc_start: 0.8401 (p-80) cc_final: 0.8097 (p-80) REVERT: B 415 ASN cc_start: 0.8821 (m-40) cc_final: 0.8520 (m-40) REVERT: B 541 GLU cc_start: 0.9170 (tt0) cc_final: 0.8767 (tm-30) REVERT: C 184 SER cc_start: 0.8052 (t) cc_final: 0.7770 (t) outliers start: 15 outliers final: 7 residues processed: 133 average time/residue: 0.5503 time to fit residues: 78.4431 Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 89 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.106825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.065731 restraints weight = 15385.884| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.62 r_work: 0.2529 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9150 Z= 0.152 Angle : 0.546 6.391 12465 Z= 0.285 Chirality : 0.042 0.157 1399 Planarity : 0.003 0.036 1498 Dihedral : 17.011 151.479 1437 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.84 % Allowed : 13.95 % Favored : 84.22 % 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: 0.82 (0.26), residues: 1027 helix: 1.92 (0.29), residues: 334 sheet: 0.26 (0.41), residues: 157 loop : -0.20 (0.27), residues: 536 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 0.004 0.001 TRP B 513 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9150) covalent geometry : angle 0.54585 (12465) hydrogen bonds : bond 0.03637 ( 371) hydrogen bonds : angle 4.67226 ( 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: 17 poor density : 129 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8446 (tppt) cc_final: 0.8134 (ttmm) REVERT: A 172 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8049 (tm-30) REVERT: A 265 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9113 (ptmm) REVERT: A 294 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8557 (mp0) REVERT: A 332 GLU cc_start: 0.8875 (mp0) cc_final: 0.8479 (pm20) REVERT: A 341 ASP cc_start: 0.8980 (m-30) cc_final: 0.8706 (m-30) REVERT: B 15 ASP cc_start: 0.8882 (t0) cc_final: 0.8628 (t0) REVERT: B 20 MET cc_start: 0.8818 (mtp) cc_final: 0.8516 (mtt) REVERT: B 53 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7570 (mm-30) REVERT: B 68 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9133 (pp) REVERT: B 83 LEU cc_start: 0.9345 (tp) cc_final: 0.9138 (tm) REVERT: B 84 MET cc_start: 0.8279 (ptp) cc_final: 0.7923 (ptp) REVERT: B 93 ASP cc_start: 0.8874 (m-30) cc_final: 0.8592 (m-30) REVERT: B 157 CYS cc_start: 0.9214 (m) cc_final: 0.8828 (m) REVERT: B 210 MET cc_start: 0.9708 (tmm) cc_final: 0.9399 (tmm) REVERT: B 229 GLU cc_start: 0.8879 (pt0) cc_final: 0.8608 (pt0) REVERT: B 241 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8349 (mt-10) REVERT: B 414 HIS cc_start: 0.8388 (p-80) cc_final: 0.8072 (p-80) REVERT: B 415 ASN cc_start: 0.8837 (m-40) cc_final: 0.8528 (m-40) REVERT: B 541 GLU cc_start: 0.9169 (tt0) cc_final: 0.8783 (tm-30) REVERT: C 184 SER cc_start: 0.8138 (t) cc_final: 0.7859 (t) outliers start: 17 outliers final: 6 residues processed: 136 average time/residue: 0.5233 time to fit residues: 76.2437 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 : 0.344 ------------------------------------------------------------------------------- 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 A residue 294 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 275 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3445 r_free = 0.3445 target = 0.106124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.065359 restraints weight = 15443.710| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 3.60 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: 0.8164 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9150 Z= 0.174 Angle : 0.570 8.948 12465 Z= 0.296 Chirality : 0.043 0.263 1399 Planarity : 0.004 0.055 1498 Dihedral : 17.014 151.387 1437 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.62 % Allowed : 14.92 % Favored : 83.46 % 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: 0.82 (0.26), residues: 1027 helix: 1.93 (0.29), residues: 334 sheet: 0.24 (0.41), residues: 157 loop : -0.21 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 502 TYR 0.010 0.001 TYR A 88 PHE 0.035 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 covalent geometry : bond 0.00410 ( 9150) covalent geometry : angle 0.57047 (12465) hydrogen bonds : bond 0.03729 ( 371) hydrogen bonds : angle 4.67391 ( 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: 15 poor density : 121 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8414 (tppt) cc_final: 0.8173 (ttmm) REVERT: A 172 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 265 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9116 (ptmm) REVERT: A 294 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8602 (pm20) REVERT: A 332 GLU cc_start: 0.8868 (mp0) cc_final: 0.8527 (pm20) REVERT: A 341 ASP cc_start: 0.8988 (m-30) cc_final: 0.8697 (m-30) REVERT: B 15 ASP cc_start: 0.8918 (t0) cc_final: 0.8677 (t0) REVERT: B 20 MET cc_start: 0.8827 (mtp) cc_final: 0.8489 (mtt) REVERT: B 53 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7524 (mm-30) REVERT: B 68 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9174 (pp) REVERT: B 83 LEU cc_start: 0.9336 (tp) cc_final: 0.9114 (tm) REVERT: B 84 MET cc_start: 0.8227 (ptp) cc_final: 0.7882 (ptp) REVERT: B 93 ASP cc_start: 0.8869 (m-30) cc_final: 0.8572 (m-30) REVERT: B 115 MET cc_start: 0.9646 (mtm) cc_final: 0.9403 (mtm) REVERT: B 157 CYS cc_start: 0.9209 (m) cc_final: 0.8826 (m) REVERT: B 210 MET cc_start: 0.9709 (tmm) cc_final: 0.9397 (tmm) REVERT: B 229 GLU cc_start: 0.8871 (pt0) cc_final: 0.8582 (pt0) REVERT: B 241 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8340 (mt-10) REVERT: B 414 HIS cc_start: 0.8392 (p-80) cc_final: 0.8098 (p-80) REVERT: B 415 ASN cc_start: 0.8810 (m-40) cc_final: 0.8537 (m-40) REVERT: B 541 GLU cc_start: 0.9174 (tt0) cc_final: 0.8779 (tm-30) REVERT: C 184 SER cc_start: 0.8094 (t) cc_final: 0.7816 (t) outliers start: 15 outliers final: 7 residues processed: 130 average time/residue: 0.5531 time to fit residues: 76.9532 Evaluate side-chains 127 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 A residue 294 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 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: 20.0000 chunk 8 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.104350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.063483 restraints weight = 15572.633| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 3.61 r_work: 0.2483 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9150 Z= 0.256 Angle : 0.609 7.019 12465 Z= 0.316 Chirality : 0.044 0.159 1399 Planarity : 0.004 0.061 1498 Dihedral : 17.128 152.719 1437 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.62 % Allowed : 15.35 % 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: 0.76 (0.26), residues: 1027 helix: 1.86 (0.29), residues: 335 sheet: 0.25 (0.40), residues: 161 loop : -0.26 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 502 TYR 0.014 0.001 TYR A 71 PHE 0.033 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 covalent geometry : bond 0.00604 ( 9150) covalent geometry : angle 0.60890 (12465) hydrogen bonds : bond 0.04253 ( 371) hydrogen bonds : angle 4.70595 ( 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 132 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8340 (tppt) cc_final: 0.8091 (ttmm) REVERT: A 172 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8086 (tm-30) REVERT: A 265 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9102 (ptmm) REVERT: A 294 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8625 (pm20) REVERT: A 341 ASP cc_start: 0.9065 (m-30) cc_final: 0.8753 (m-30) REVERT: B 15 ASP cc_start: 0.8894 (t0) cc_final: 0.8658 (t0) REVERT: B 20 MET cc_start: 0.8802 (mtp) cc_final: 0.8445 (mtt) REVERT: B 53 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 93 ASP cc_start: 0.8867 (m-30) cc_final: 0.8573 (m-30) REVERT: B 115 MET cc_start: 0.9646 (mtm) cc_final: 0.9374 (mtm) REVERT: B 157 CYS cc_start: 0.9198 (m) cc_final: 0.8856 (m) REVERT: B 210 MET cc_start: 0.9702 (tmm) cc_final: 0.9385 (tmm) REVERT: B 229 GLU cc_start: 0.8869 (pt0) cc_final: 0.8572 (pt0) REVERT: B 241 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8366 (mt-10) REVERT: B 414 HIS cc_start: 0.8398 (p-80) cc_final: 0.8098 (p-80) REVERT: B 415 ASN cc_start: 0.8829 (m-40) cc_final: 0.8537 (m-40) REVERT: B 541 GLU cc_start: 0.9172 (tt0) cc_final: 0.8772 (tm-30) REVERT: C 184 SER cc_start: 0.8164 (t) cc_final: 0.7877 (t) outliers start: 15 outliers final: 9 residues processed: 128 average time/residue: 0.5484 time to fit residues: 75.2044 Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 A residue 294 GLU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 94 ILE 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: 0.8980 chunk 74 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.0270 chunk 68 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 GLN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.107613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.066624 restraints weight = 15472.246| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.65 r_work: 0.2547 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9150 Z= 0.121 Angle : 0.565 7.637 12465 Z= 0.295 Chirality : 0.042 0.155 1399 Planarity : 0.004 0.063 1498 Dihedral : 17.019 152.497 1437 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.73 % Allowed : 16.22 % Favored : 82.05 % 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: 1.94 (0.29), residues: 334 sheet: 0.26 (0.41), residues: 157 loop : -0.20 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 502 TYR 0.013 0.001 TYR A 88 PHE 0.035 0.001 PHE B 107 TRP 0.006 0.001 TRP B 513 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9150) covalent geometry : angle 0.56505 (12465) hydrogen bonds : bond 0.03233 ( 371) hydrogen bonds : angle 4.61614 ( 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 144 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8370 (tppt) cc_final: 0.8111 (ttmm) REVERT: A 172 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8045 (tm-30) REVERT: A 265 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.9101 (ptmm) REVERT: A 294 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8653 (pm20) REVERT: A 341 ASP cc_start: 0.8955 (m-30) cc_final: 0.8657 (m-30) REVERT: A 374 LEU cc_start: 0.9170 (mm) cc_final: 0.8845 (mm) REVERT: B 15 ASP cc_start: 0.8860 (t0) cc_final: 0.8581 (t0) REVERT: B 20 MET cc_start: 0.8820 (mtp) cc_final: 0.8445 (mtt) REVERT: B 68 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9174 (pp) REVERT: B 93 ASP cc_start: 0.8878 (m-30) cc_final: 0.8578 (m-30) REVERT: B 157 CYS cc_start: 0.9226 (m) cc_final: 0.8854 (m) REVERT: B 210 MET cc_start: 0.9708 (tmm) cc_final: 0.9393 (tmm) REVERT: B 229 GLU cc_start: 0.8864 (pt0) cc_final: 0.8575 (pt0) REVERT: B 241 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8341 (mt-10) REVERT: B 294 VAL cc_start: 0.8023 (OUTLIER) cc_final: 0.7764 (m) REVERT: B 414 HIS cc_start: 0.8392 (p-80) cc_final: 0.8083 (p-80) REVERT: B 415 ASN cc_start: 0.8839 (m-40) cc_final: 0.8591 (m-40) REVERT: B 541 GLU cc_start: 0.9169 (tt0) cc_final: 0.8786 (tm-30) REVERT: C 184 SER cc_start: 0.8028 (t) cc_final: 0.7731 (t) outliers start: 16 outliers final: 5 residues processed: 140 average time/residue: 0.5145 time to fit residues: 77.1622 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 : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 294 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 294 VAL 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: 0.9990 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 79 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.107892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.067132 restraints weight = 15303.857| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 3.62 r_work: 0.2555 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9150 Z= 0.120 Angle : 0.576 8.567 12465 Z= 0.296 Chirality : 0.042 0.155 1399 Planarity : 0.004 0.072 1498 Dihedral : 16.956 151.650 1437 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.97 % Allowed : 17.84 % Favored : 81.19 % 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: 0.90 (0.26), residues: 1027 helix: 2.00 (0.29), residues: 334 sheet: 0.28 (0.41), residues: 157 loop : -0.15 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 502 TYR 0.013 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 covalent geometry : bond 0.00274 ( 9150) covalent geometry : angle 0.57638 (12465) hydrogen bonds : bond 0.03171 ( 371) hydrogen bonds : angle 4.53379 ( 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: 9 poor density : 127 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8379 (tppt) cc_final: 0.8122 (ttmm) REVERT: A 107 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7276 (mp0) REVERT: A 172 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8005 (tm-30) REVERT: A 294 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8666 (pm20) REVERT: A 341 ASP cc_start: 0.8913 (m-30) cc_final: 0.8600 (m-30) REVERT: A 374 LEU cc_start: 0.9171 (mm) cc_final: 0.8878 (mm) REVERT: B 15 ASP cc_start: 0.8808 (t0) cc_final: 0.8564 (t0) REVERT: B 20 MET cc_start: 0.8787 (mtp) cc_final: 0.8412 (mtt) REVERT: B 93 ASP cc_start: 0.8883 (m-30) cc_final: 0.8575 (m-30) REVERT: B 115 MET cc_start: 0.9633 (mtm) cc_final: 0.9311 (mtm) REVERT: B 157 CYS cc_start: 0.9244 (m) cc_final: 0.8866 (m) REVERT: B 210 MET cc_start: 0.9709 (tmm) cc_final: 0.9392 (tmm) REVERT: B 229 GLU cc_start: 0.8859 (pt0) cc_final: 0.8567 (pt0) REVERT: B 241 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8296 (mt-10) REVERT: B 414 HIS cc_start: 0.8374 (p-80) cc_final: 0.8058 (p-80) REVERT: B 415 ASN cc_start: 0.8825 (m-40) cc_final: 0.8578 (m-40) REVERT: B 541 GLU cc_start: 0.9160 (tt0) cc_final: 0.8782 (tm-30) REVERT: C 184 SER cc_start: 0.8048 (t) cc_final: 0.7755 (t) outliers start: 9 outliers final: 6 residues processed: 133 average time/residue: 0.5064 time to fit residues: 72.4224 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 : 0.400 ------------------------------------------------------------------------------- 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 357 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 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: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.065404 restraints weight = 15442.093| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.61 r_work: 0.2519 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9150 Z= 0.206 Angle : 0.618 11.995 12465 Z= 0.318 Chirality : 0.043 0.159 1399 Planarity : 0.003 0.036 1498 Dihedral : 17.002 151.282 1437 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.97 % Allowed : 17.73 % Favored : 81.30 % 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: 0.83 (0.26), residues: 1027 helix: 1.93 (0.29), residues: 334 sheet: 0.21 (0.41), residues: 157 loop : -0.19 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 295 TYR 0.019 0.001 TYR B 74 PHE 0.036 0.001 PHE B 107 TRP 0.003 0.001 TRP B 513 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 9150) covalent geometry : angle 0.61836 (12465) hydrogen bonds : bond 0.03754 ( 371) hydrogen bonds : angle 4.60386 ( 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 127 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8347 (tppt) cc_final: 0.8095 (ttmm) REVERT: A 107 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7300 (mp0) REVERT: A 172 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8040 (tm-30) REVERT: A 265 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9190 (ptmm) REVERT: A 289 TYR cc_start: 0.8115 (t80) cc_final: 0.7886 (t80) REVERT: A 294 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8660 (pm20) REVERT: A 341 ASP cc_start: 0.8976 (m-30) cc_final: 0.8690 (m-30) REVERT: B 20 MET cc_start: 0.8813 (mtp) cc_final: 0.8452 (mtt) REVERT: B 93 ASP cc_start: 0.8884 (m-30) cc_final: 0.8584 (m-30) REVERT: B 115 MET cc_start: 0.9641 (mtm) cc_final: 0.9331 (mtm) REVERT: B 210 MET cc_start: 0.9708 (tmm) cc_final: 0.9393 (tmm) REVERT: B 229 GLU cc_start: 0.8860 (pt0) cc_final: 0.8567 (pt0) REVERT: B 241 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8313 (mt-10) REVERT: B 414 HIS cc_start: 0.8421 (p-80) cc_final: 0.8109 (p-80) REVERT: B 415 ASN cc_start: 0.8832 (m-40) cc_final: 0.8563 (m-40) REVERT: B 541 GLU cc_start: 0.9167 (tt0) cc_final: 0.8783 (tm-30) REVERT: C 184 SER cc_start: 0.8103 (t) cc_final: 0.7819 (t) outliers start: 9 outliers final: 6 residues processed: 124 average time/residue: 0.5441 time to fit residues: 72.3342 Evaluate side-chains 122 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 357 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 37 optimal weight: 0.0070 chunk 42 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.067095 restraints weight = 15203.862| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.60 r_work: 0.2552 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9150 Z= 0.128 Angle : 0.599 9.368 12465 Z= 0.305 Chirality : 0.043 0.255 1399 Planarity : 0.003 0.038 1498 Dihedral : 16.958 152.059 1437 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.97 % Allowed : 18.05 % Favored : 80.97 % 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: 0.87 (0.26), residues: 1027 helix: 1.99 (0.29), residues: 334 sheet: 0.22 (0.40), residues: 157 loop : -0.17 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 271 TYR 0.017 0.001 TYR B 74 PHE 0.035 0.001 PHE B 107 TRP 0.006 0.001 TRP B 513 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9150) covalent geometry : angle 0.59886 (12465) hydrogen bonds : bond 0.03227 ( 371) hydrogen bonds : angle 4.54422 ( 1033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3247.03 seconds wall clock time: 55 minutes 51.30 seconds (3351.30 seconds total)