Starting phenix.real_space_refine on Sat Dec 28 19:51:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zyg_15022/12_2024/7zyg_15022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyg_15022/12_2024/7zyg_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_15022/12_2024/7zyg_15022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyg_15022/12_2024/7zyg_15022.map" model { file = "/net/cci-nas-00/data/ceres_data/7zyg_15022/12_2024/7zyg_15022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyg_15022/12_2024/7zyg_15022.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'ARG:plan': 1, 'ASP:plan': 2} 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: 6.19, per 1000 atoms: 0.69 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.16 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: 3.07 Time building geometry restraints manager: 2.74 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: 10.650 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.440 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.830 ------------------------------------------------------------------------------- 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= 0.144 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (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 TRP 0.005 0.001 TRP B 513 HIS 0.004 0.000 HIS A 176 PHE 0.010 0.001 PHE B 107 TYR 0.008 0.001 TYR A 71 ARG 0.001 0.000 ARG B 502 *********************** 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 : 1.119 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: 1.1708 time to fit residues: 207.1995 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 : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9150 Z= 0.203 Angle : 0.578 10.174 12465 Z= 0.301 Chirality : 0.044 0.379 1399 Planarity : 0.003 0.037 1498 Dihedral : 17.022 152.165 1437 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1027 helix: 1.66 (0.29), residues: 334 sheet: 0.31 (0.41), residues: 157 loop : -0.13 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 148 HIS 0.004 0.001 HIS A 176 PHE 0.028 0.001 PHE B 107 TYR 0.011 0.001 TYR A 88 ARG 0.004 0.000 ARG F 295 *********************** 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 149 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8419 (tppt) cc_final: 0.8114 (ttmm) REVERT: A 172 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7994 (tm-30) REVERT: A 294 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8304 (mp0) REVERT: A 332 GLU cc_start: 0.8745 (mp0) cc_final: 0.8379 (pm20) REVERT: A 341 ASP cc_start: 0.8911 (m-30) cc_final: 0.8681 (m-30) REVERT: B 15 ASP cc_start: 0.8712 (t0) cc_final: 0.8464 (t0) REVERT: B 20 MET cc_start: 0.8966 (mtp) cc_final: 0.8486 (mtt) REVERT: B 53 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7393 (mm-30) REVERT: B 83 LEU cc_start: 0.9359 (tp) cc_final: 0.9134 (tm) REVERT: B 93 ASP cc_start: 0.8910 (m-30) cc_final: 0.8620 (m-30) REVERT: B 115 MET cc_start: 0.9456 (mtm) cc_final: 0.9237 (mtm) REVERT: B 157 CYS cc_start: 0.9165 (m) cc_final: 0.8756 (m) REVERT: B 210 MET cc_start: 0.9677 (tmm) cc_final: 0.9361 (tmm) REVERT: B 229 GLU cc_start: 0.8881 (pt0) cc_final: 0.8577 (pt0) REVERT: B 241 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8040 (mt-10) REVERT: B 414 HIS cc_start: 0.8231 (p-80) cc_final: 0.7934 (p-80) REVERT: B 415 ASN cc_start: 0.8730 (m-40) cc_final: 0.8395 (m-40) REVERT: B 541 GLU cc_start: 0.8967 (tt0) cc_final: 0.8623 (tm-30) outliers start: 16 outliers final: 3 residues processed: 138 average time/residue: 1.2410 time to fit residues: 183.4165 Evaluate side-chains 118 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 52 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 0.0970 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9150 Z= 0.205 Angle : 0.541 5.487 12465 Z= 0.282 Chirality : 0.042 0.231 1399 Planarity : 0.003 0.037 1498 Dihedral : 16.999 151.827 1437 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.95 % Allowed : 11.24 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1027 helix: 1.80 (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 TRP 0.004 0.000 TRP B 513 HIS 0.004 0.001 HIS A 176 PHE 0.032 0.001 PHE B 107 TYR 0.010 0.001 TYR A 88 ARG 0.005 0.000 ARG F 295 *********************** 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 147 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8449 (tppt) cc_final: 0.8159 (ttmm) REVERT: A 172 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7934 (tm-30) REVERT: A 332 GLU cc_start: 0.8763 (mp0) cc_final: 0.8307 (pm20) REVERT: A 335 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8481 (mm-30) REVERT: A 341 ASP cc_start: 0.8949 (m-30) cc_final: 0.8679 (m-30) REVERT: B 20 MET cc_start: 0.9001 (mtp) cc_final: 0.8458 (mtt) REVERT: B 53 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7487 (mm-30) REVERT: B 93 ASP cc_start: 0.8905 (m-30) cc_final: 0.8633 (m-30) REVERT: B 157 CYS cc_start: 0.9200 (m) cc_final: 0.8786 (m) REVERT: B 210 MET cc_start: 0.9687 (tmm) cc_final: 0.9382 (tmm) REVERT: B 229 GLU cc_start: 0.8862 (pt0) cc_final: 0.8555 (pt0) REVERT: B 241 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8047 (mt-10) REVERT: B 414 HIS cc_start: 0.8233 (p-80) cc_final: 0.7923 (p-80) REVERT: B 415 ASN cc_start: 0.8710 (m-40) cc_final: 0.8374 (m-40) REVERT: B 541 GLU cc_start: 0.8952 (tt0) cc_final: 0.8608 (tm-30) REVERT: C 184 SER cc_start: 0.8136 (t) cc_final: 0.7855 (t) outliers start: 18 outliers final: 6 residues processed: 138 average time/residue: 1.1432 time to fit residues: 169.5020 Evaluate side-chains 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 165 LEU 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 93 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9150 Z= 0.366 Angle : 0.593 8.979 12465 Z= 0.307 Chirality : 0.044 0.196 1399 Planarity : 0.003 0.035 1498 Dihedral : 17.050 151.002 1437 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.62 % Allowed : 13.19 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1027 helix: 1.78 (0.29), residues: 335 sheet: 0.27 (0.40), residues: 161 loop : -0.23 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 513 HIS 0.005 0.001 HIS A 176 PHE 0.031 0.001 PHE B 107 TYR 0.013 0.001 TYR B 74 ARG 0.005 0.000 ARG F 295 *********************** 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 135 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8436 (tppt) cc_final: 0.8143 (ttmm) REVERT: A 172 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 294 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8264 (mm-30) REVERT: A 332 GLU cc_start: 0.8776 (mp0) cc_final: 0.8334 (pm20) REVERT: A 341 ASP cc_start: 0.9027 (m-30) cc_final: 0.8751 (m-30) REVERT: B 15 ASP cc_start: 0.8855 (t0) cc_final: 0.8549 (t0) REVERT: B 20 MET cc_start: 0.8860 (mtp) cc_final: 0.8637 (mtt) REVERT: B 53 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7497 (mm-30) REVERT: B 93 ASP cc_start: 0.8905 (m-30) cc_final: 0.8620 (m-30) REVERT: B 115 MET cc_start: 0.9537 (mtm) cc_final: 0.9235 (mtm) REVERT: B 157 CYS cc_start: 0.9206 (m) cc_final: 0.8814 (m) REVERT: B 210 MET cc_start: 0.9695 (tmm) cc_final: 0.9385 (tmm) REVERT: B 229 GLU cc_start: 0.8858 (pt0) cc_final: 0.8546 (pt0) REVERT: B 241 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8121 (mt-10) REVERT: B 414 HIS cc_start: 0.8246 (p-80) cc_final: 0.7932 (p-80) REVERT: B 415 ASN cc_start: 0.8739 (m-40) cc_final: 0.8406 (m-40) REVERT: B 541 GLU cc_start: 0.8958 (tt0) cc_final: 0.8620 (tm-30) REVERT: C 184 SER cc_start: 0.8231 (t) cc_final: 0.7956 (t) outliers start: 15 outliers final: 8 residues processed: 127 average time/residue: 1.1780 time to fit residues: 160.4732 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 : 1.024 ------------------------------------------------------------------------------- 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 449 THR 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 515 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9150 Z= 0.269 Angle : 0.561 6.857 12465 Z= 0.291 Chirality : 0.043 0.158 1399 Planarity : 0.003 0.035 1498 Dihedral : 17.050 151.693 1437 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.62 % Allowed : 13.84 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1027 helix: 1.84 (0.29), residues: 335 sheet: 0.22 (0.41), residues: 157 loop : -0.22 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 513 HIS 0.006 0.001 HIS A 176 PHE 0.034 0.001 PHE B 107 TYR 0.010 0.001 TYR B 74 ARG 0.005 0.000 ARG F 295 *********************** 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 138 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8436 (tppt) cc_final: 0.8208 (ttmm) REVERT: A 143 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8492 (tp) REVERT: A 172 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7956 (tm-30) REVERT: A 294 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8269 (mm-30) REVERT: A 341 ASP cc_start: 0.9008 (m-30) cc_final: 0.8751 (m-30) REVERT: B 15 ASP cc_start: 0.8872 (t0) cc_final: 0.8594 (t0) REVERT: B 20 MET cc_start: 0.8908 (mtp) cc_final: 0.8607 (mtt) REVERT: B 53 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7576 (mm-30) REVERT: B 93 ASP cc_start: 0.8892 (m-30) cc_final: 0.8603 (m-30) REVERT: B 115 MET cc_start: 0.9504 (mtm) cc_final: 0.9248 (mtm) REVERT: B 157 CYS cc_start: 0.9224 (m) cc_final: 0.8817 (m) REVERT: B 210 MET cc_start: 0.9699 (tmm) cc_final: 0.9387 (tmm) REVERT: B 229 GLU cc_start: 0.8854 (pt0) cc_final: 0.8542 (pt0) REVERT: B 241 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8111 (mt-10) REVERT: B 414 HIS cc_start: 0.8221 (p-80) cc_final: 0.7899 (p-80) REVERT: B 415 ASN cc_start: 0.8721 (m-40) cc_final: 0.8397 (m-40) REVERT: B 541 GLU cc_start: 0.8957 (tt0) cc_final: 0.8637 (tm-30) REVERT: C 184 SER cc_start: 0.8147 (t) cc_final: 0.7876 (t) outliers start: 15 outliers final: 9 residues processed: 129 average time/residue: 1.1811 time to fit residues: 163.4716 Evaluate side-chains 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 449 THR 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 B residue 515 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 97 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1908 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= 0.185 Angle : 0.561 12.228 12465 Z= 0.287 Chirality : 0.043 0.384 1399 Planarity : 0.003 0.053 1498 Dihedral : 16.981 151.704 1437 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.73 % Allowed : 14.16 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1027 helix: 1.95 (0.29), residues: 334 sheet: 0.25 (0.41), residues: 157 loop : -0.19 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 513 HIS 0.005 0.001 HIS A 176 PHE 0.033 0.001 PHE B 107 TYR 0.019 0.001 TYR B 74 ARG 0.015 0.000 ARG B 502 *********************** 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 144 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8445 (tppt) cc_final: 0.8130 (ttmm) REVERT: A 172 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 294 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8263 (mm-30) REVERT: A 332 GLU cc_start: 0.8758 (mp0) cc_final: 0.8501 (pm20) REVERT: A 341 ASP cc_start: 0.8951 (m-30) cc_final: 0.8654 (m-30) REVERT: B 15 ASP cc_start: 0.8884 (t0) cc_final: 0.8597 (t0) REVERT: B 20 MET cc_start: 0.8910 (mtp) cc_final: 0.8608 (mtt) REVERT: B 53 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 74 TYR cc_start: 0.8220 (m-10) cc_final: 0.7998 (m-10) REVERT: B 93 ASP cc_start: 0.8892 (m-30) cc_final: 0.8595 (m-30) REVERT: B 115 MET cc_start: 0.9508 (mtm) cc_final: 0.9191 (mtm) REVERT: B 157 CYS cc_start: 0.9232 (m) cc_final: 0.8826 (m) REVERT: B 210 MET cc_start: 0.9701 (tmm) cc_final: 0.9398 (tmm) REVERT: B 229 GLU cc_start: 0.8849 (pt0) cc_final: 0.8539 (pt0) REVERT: B 241 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8061 (mt-10) REVERT: B 414 HIS cc_start: 0.8217 (p-80) cc_final: 0.7882 (p-80) REVERT: B 415 ASN cc_start: 0.8707 (m-40) cc_final: 0.8375 (m-40) REVERT: B 541 GLU cc_start: 0.8951 (tt0) cc_final: 0.8631 (tm-30) REVERT: C 184 SER cc_start: 0.8110 (t) cc_final: 0.7836 (t) outliers start: 16 outliers final: 7 residues processed: 133 average time/residue: 1.1747 time to fit residues: 167.9169 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 : 1.054 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9150 Z= 0.324 Angle : 0.594 8.795 12465 Z= 0.307 Chirality : 0.044 0.300 1399 Planarity : 0.004 0.064 1498 Dihedral : 17.035 151.275 1437 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.41 % Allowed : 15.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1027 helix: 1.97 (0.29), residues: 334 sheet: 0.20 (0.40), residues: 157 loop : -0.22 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 513 HIS 0.004 0.001 HIS A 176 PHE 0.037 0.001 PHE B 107 TYR 0.020 0.001 TYR B 74 ARG 0.016 0.001 ARG B 502 *********************** 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 133 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8404 (tppt) cc_final: 0.8165 (ttmm) REVERT: A 172 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7959 (tm-30) REVERT: A 294 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8269 (mm-30) REVERT: A 332 GLU cc_start: 0.8769 (mp0) cc_final: 0.8441 (pm20) REVERT: A 341 ASP cc_start: 0.9007 (m-30) cc_final: 0.8731 (m-30) REVERT: B 15 ASP cc_start: 0.8858 (t0) cc_final: 0.8578 (t0) REVERT: B 20 MET cc_start: 0.8906 (mtp) cc_final: 0.8575 (mtt) REVERT: B 53 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7554 (mm-30) REVERT: B 74 TYR cc_start: 0.8226 (m-10) cc_final: 0.7921 (m-10) REVERT: B 93 ASP cc_start: 0.8887 (m-30) cc_final: 0.8605 (m-30) REVERT: B 157 CYS cc_start: 0.9233 (m) cc_final: 0.8855 (m) REVERT: B 210 MET cc_start: 0.9698 (tmm) cc_final: 0.9387 (tmm) REVERT: B 222 ASP cc_start: 0.8863 (m-30) cc_final: 0.8659 (m-30) REVERT: B 229 GLU cc_start: 0.8850 (pt0) cc_final: 0.8537 (pt0) REVERT: B 241 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8114 (mt-10) REVERT: B 414 HIS cc_start: 0.8233 (p-80) cc_final: 0.7924 (p-80) REVERT: B 415 ASN cc_start: 0.8725 (m-40) cc_final: 0.8426 (m-40) REVERT: B 432 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8651 (mm-40) REVERT: B 541 GLU cc_start: 0.8964 (tt0) cc_final: 0.8650 (tm-30) REVERT: C 184 SER cc_start: 0.8204 (t) cc_final: 0.7936 (t) REVERT: F 295 ARG cc_start: 0.8864 (ptt-90) cc_final: 0.8592 (ptt-90) outliers start: 13 outliers final: 6 residues processed: 125 average time/residue: 1.2607 time to fit residues: 168.5629 Evaluate side-chains 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 63 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 9 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2072 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= 0.186 Angle : 0.567 8.389 12465 Z= 0.292 Chirality : 0.042 0.271 1399 Planarity : 0.004 0.064 1498 Dihedral : 16.964 152.061 1437 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.62 % Allowed : 16.00 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1027 helix: 2.01 (0.29), residues: 334 sheet: 0.24 (0.40), residues: 157 loop : -0.20 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 513 HIS 0.003 0.001 HIS B 246 PHE 0.034 0.001 PHE B 107 TYR 0.013 0.001 TYR B 74 ARG 0.017 0.001 ARG B 502 *********************** 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 141 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8416 (tppt) cc_final: 0.8176 (ttmm) REVERT: A 172 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7896 (tm-30) REVERT: A 332 GLU cc_start: 0.8785 (mp0) cc_final: 0.8449 (pm20) REVERT: A 341 ASP cc_start: 0.8932 (m-30) cc_final: 0.8655 (m-30) REVERT: A 374 LEU cc_start: 0.9109 (mm) cc_final: 0.8857 (mm) REVERT: B 15 ASP cc_start: 0.8777 (t0) cc_final: 0.8556 (t0) REVERT: B 20 MET cc_start: 0.8910 (mtp) cc_final: 0.8576 (mtt) REVERT: B 53 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 93 ASP cc_start: 0.8888 (m-30) cc_final: 0.8579 (m-30) REVERT: B 115 MET cc_start: 0.9552 (mtm) cc_final: 0.9315 (mtm) REVERT: B 157 CYS cc_start: 0.9242 (m) cc_final: 0.8835 (m) REVERT: B 210 MET cc_start: 0.9702 (tmm) cc_final: 0.9397 (tmm) REVERT: B 222 ASP cc_start: 0.8835 (m-30) cc_final: 0.8627 (m-30) REVERT: B 229 GLU cc_start: 0.8845 (pt0) cc_final: 0.8533 (pt0) REVERT: B 241 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8069 (mt-10) REVERT: B 294 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7855 (m) REVERT: B 414 HIS cc_start: 0.8201 (p-80) cc_final: 0.7880 (p-80) REVERT: B 415 ASN cc_start: 0.8717 (m-40) cc_final: 0.8454 (m-40) REVERT: B 541 GLU cc_start: 0.8959 (tt0) cc_final: 0.8640 (tm-30) REVERT: C 184 SER cc_start: 0.8123 (t) cc_final: 0.7859 (t) REVERT: F 295 ARG cc_start: 0.8908 (ptt-90) cc_final: 0.8667 (ptt-90) outliers start: 15 outliers final: 5 residues processed: 135 average time/residue: 1.1914 time to fit residues: 172.7997 Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 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 96 optimal weight: 4.9990 chunk 56 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2147 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= 0.200 Angle : 0.578 8.265 12465 Z= 0.297 Chirality : 0.042 0.253 1399 Planarity : 0.004 0.074 1498 Dihedral : 16.947 151.424 1437 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.08 % Allowed : 17.30 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1027 helix: 2.03 (0.29), residues: 334 sheet: 0.24 (0.40), residues: 157 loop : -0.21 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 513 HIS 0.003 0.001 HIS A 176 PHE 0.039 0.001 PHE B 107 TYR 0.029 0.001 TYR B 74 ARG 0.019 0.001 ARG B 502 *********************** 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 135 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8416 (tppt) cc_final: 0.8173 (ttmm) REVERT: A 107 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7094 (mp0) REVERT: A 172 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 289 TYR cc_start: 0.8216 (t80) cc_final: 0.7913 (t80) REVERT: A 294 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8500 (mp0) REVERT: A 332 GLU cc_start: 0.8782 (mp0) cc_final: 0.8421 (pm20) REVERT: A 341 ASP cc_start: 0.8962 (m-30) cc_final: 0.8686 (m-30) REVERT: A 374 LEU cc_start: 0.9112 (mm) cc_final: 0.8861 (mm) REVERT: B 15 ASP cc_start: 0.8825 (t0) cc_final: 0.8542 (t0) REVERT: B 20 MET cc_start: 0.8911 (mtp) cc_final: 0.8527 (mtt) REVERT: B 53 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 93 ASP cc_start: 0.8881 (m-30) cc_final: 0.8609 (m-30) REVERT: B 115 MET cc_start: 0.9559 (mtm) cc_final: 0.9299 (mtm) REVERT: B 157 CYS cc_start: 0.9249 (m) cc_final: 0.8847 (m) REVERT: B 210 MET cc_start: 0.9702 (tmm) cc_final: 0.9388 (tmm) REVERT: B 222 ASP cc_start: 0.8831 (m-30) cc_final: 0.8623 (m-30) REVERT: B 229 GLU cc_start: 0.8849 (pt0) cc_final: 0.8536 (pt0) REVERT: B 241 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8059 (mt-10) REVERT: B 414 HIS cc_start: 0.8185 (p-80) cc_final: 0.7861 (p-80) REVERT: B 415 ASN cc_start: 0.8703 (m-40) cc_final: 0.8444 (m-40) REVERT: B 541 GLU cc_start: 0.8954 (tt0) cc_final: 0.8637 (tm-30) REVERT: C 184 SER cc_start: 0.8145 (t) cc_final: 0.7884 (t) REVERT: F 295 ARG cc_start: 0.8929 (ptt-90) cc_final: 0.8692 (ptt-90) outliers start: 10 outliers final: 6 residues processed: 132 average time/residue: 1.1718 time to fit residues: 165.8986 Evaluate side-chains 127 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 192 ASP Chi-restraints excluded: chain A residue 294 GLU 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 46 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 0.0470 chunk 50 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9150 Z= 0.241 Angle : 0.603 8.602 12465 Z= 0.311 Chirality : 0.043 0.236 1399 Planarity : 0.004 0.083 1498 Dihedral : 16.955 151.351 1437 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.65 % Allowed : 17.84 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1027 helix: 1.98 (0.29), residues: 334 sheet: 0.23 (0.40), residues: 157 loop : -0.25 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 513 HIS 0.003 0.001 HIS B 246 PHE 0.040 0.001 PHE B 107 TYR 0.026 0.001 TYR B 74 ARG 0.020 0.001 ARG B 502 ********************** 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 126 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8421 (tppt) cc_final: 0.8178 (ttmm) REVERT: A 107 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7119 (mp0) REVERT: A 172 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7857 (tm-30) REVERT: A 289 TYR cc_start: 0.8170 (t80) cc_final: 0.7924 (t80) REVERT: A 294 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8545 (pm20) REVERT: A 332 GLU cc_start: 0.8793 (mp0) cc_final: 0.8429 (pm20) REVERT: A 341 ASP cc_start: 0.8969 (m-30) cc_final: 0.8669 (m-30) REVERT: A 374 LEU cc_start: 0.9113 (mm) cc_final: 0.8866 (mm) REVERT: B 15 ASP cc_start: 0.8817 (t0) cc_final: 0.8507 (t0) REVERT: B 20 MET cc_start: 0.8919 (mtp) cc_final: 0.8541 (mtt) REVERT: B 93 ASP cc_start: 0.8891 (m-30) cc_final: 0.8599 (m-30) REVERT: B 157 CYS cc_start: 0.9244 (m) cc_final: 0.8834 (m) REVERT: B 210 MET cc_start: 0.9704 (tmm) cc_final: 0.9395 (tmm) REVERT: B 222 ASP cc_start: 0.8837 (m-30) cc_final: 0.8625 (m-30) REVERT: B 229 GLU cc_start: 0.8848 (pt0) cc_final: 0.8535 (pt0) REVERT: B 241 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8082 (mt-10) REVERT: B 414 HIS cc_start: 0.8188 (p-80) cc_final: 0.7852 (p-80) REVERT: B 415 ASN cc_start: 0.8696 (m-40) cc_final: 0.8423 (m-40) REVERT: B 541 GLU cc_start: 0.8951 (tt0) cc_final: 0.8635 (tm-30) REVERT: C 184 SER cc_start: 0.8144 (t) cc_final: 0.7871 (t) REVERT: F 295 ARG cc_start: 0.8942 (ptt-90) cc_final: 0.8715 (ptt-90) outliers start: 6 outliers final: 5 residues processed: 124 average time/residue: 1.2285 time to fit residues: 163.0318 Evaluate side-chains 122 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 76 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.105034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.064383 restraints weight = 15398.798| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.59 r_work: 0.2497 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2172 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= 0.362 Angle : 0.631 8.926 12465 Z= 0.326 Chirality : 0.044 0.214 1399 Planarity : 0.004 0.046 1498 Dihedral : 17.088 152.068 1437 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.08 % Allowed : 17.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1027 helix: 1.95 (0.29), residues: 335 sheet: 0.23 (0.41), residues: 157 loop : -0.28 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 513 HIS 0.004 0.001 HIS A 176 PHE 0.040 0.001 PHE B 107 TYR 0.025 0.002 TYR B 74 ARG 0.008 0.000 ARG B 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3585.09 seconds wall clock time: 65 minutes 19.05 seconds (3919.05 seconds total)