Starting phenix.real_space_refine on Thu Feb 13 13:30:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zyg_15022/02_2025/7zyg_15022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyg_15022/02_2025/7zyg_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_15022/02_2025/7zyg_15022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyg_15022/02_2025/7zyg_15022.map" model { file = "/net/cci-nas-00/data/ceres_data/7zyg_15022/02_2025/7zyg_15022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyg_15022/02_2025/7zyg_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-5592/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: 2.25 Conformation dependent library (CDL) restraints added in 964.6 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: 2.79 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: 2.81 Time building geometry restraints manager: 2.58 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: 5.680 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.720 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.030 ------------------------------------------------------------------------------- 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 : 1.014 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: 1.1623 time to fit residues: 205.4773 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 : 0.975 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.066601 restraints weight = 15259.282| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.63 r_work: 0.2548 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 1.007 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8399 (tppt) cc_final: 0.8093 (ttmm) REVERT: A 172 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 294 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8372 (mp0) REVERT: A 332 GLU cc_start: 0.8819 (mp0) cc_final: 0.8464 (pm20) REVERT: A 341 ASP cc_start: 0.8907 (m-30) cc_final: 0.8609 (m-30) REVERT: B 15 ASP cc_start: 0.8744 (t0) cc_final: 0.8497 (t0) REVERT: B 20 MET cc_start: 0.8895 (mtp) cc_final: 0.8352 (mtt) REVERT: B 53 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7419 (mm-30) REVERT: B 83 LEU cc_start: 0.9302 (tp) cc_final: 0.9068 (tm) REVERT: B 93 ASP cc_start: 0.8892 (m-30) cc_final: 0.8608 (m-30) REVERT: B 157 CYS cc_start: 0.9133 (m) cc_final: 0.8754 (m) REVERT: B 210 MET cc_start: 0.9691 (tmm) cc_final: 0.9377 (tmm) REVERT: B 229 GLU cc_start: 0.8886 (pt0) cc_final: 0.8605 (pt0) REVERT: B 241 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8308 (mt-10) REVERT: B 414 HIS cc_start: 0.8403 (p-80) cc_final: 0.8116 (p-80) REVERT: B 415 ASN cc_start: 0.8819 (m-40) cc_final: 0.8510 (m-40) REVERT: B 541 GLU cc_start: 0.9181 (tt0) cc_final: 0.8755 (tm-30) outliers start: 16 outliers final: 3 residues processed: 138 average time/residue: 1.2267 time to fit residues: 181.4051 Evaluate side-chains 118 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 55 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.106135 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 = 15548.571| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 3.62 r_work: 0.2519 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.004 0.041 9150 Z= 0.283 Angle : 0.559 5.587 12465 Z= 0.293 Chirality : 0.043 0.227 1399 Planarity : 0.003 0.036 1498 Dihedral : 17.060 151.662 1437 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.05 % Allowed : 11.35 % Favored : 86.59 % 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: 0.72 (0.26), residues: 1027 helix: 1.70 (0.29), residues: 335 sheet: 0.24 (0.41), residues: 157 loop : -0.18 (0.27), residues: 535 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 0.030 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 145 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8412 (tppt) cc_final: 0.8112 (ttmm) REVERT: A 172 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 265 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.9099 (ptmm) REVERT: A 294 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8359 (mm-30) REVERT: A 332 GLU cc_start: 0.8846 (mp0) cc_final: 0.8399 (pm20) REVERT: A 335 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8675 (mm-30) REVERT: A 341 ASP cc_start: 0.8977 (m-30) cc_final: 0.8701 (m-30) REVERT: B 20 MET cc_start: 0.8926 (mtp) cc_final: 0.8295 (mtt) REVERT: B 52 ASP cc_start: 0.8720 (m-30) cc_final: 0.8486 (m-30) REVERT: B 53 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7425 (mm-30) REVERT: B 83 LEU cc_start: 0.9313 (tp) cc_final: 0.9066 (tm) REVERT: B 93 ASP cc_start: 0.8892 (m-30) cc_final: 0.8601 (m-30) REVERT: B 157 CYS cc_start: 0.9170 (m) cc_final: 0.8796 (m) REVERT: B 210 MET cc_start: 0.9700 (tmm) cc_final: 0.9388 (tmm) REVERT: B 229 GLU cc_start: 0.8880 (pt0) cc_final: 0.8594 (pt0) REVERT: B 241 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8357 (mt-10) REVERT: B 414 HIS cc_start: 0.8411 (p-80) cc_final: 0.8110 (p-80) REVERT: B 415 ASN cc_start: 0.8819 (m-40) cc_final: 0.8514 (m-40) REVERT: B 432 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8653 (mm-40) REVERT: B 541 GLU cc_start: 0.9160 (tt0) cc_final: 0.8746 (tm-30) REVERT: C 184 SER cc_start: 0.8006 (t) cc_final: 0.7698 (t) outliers start: 19 outliers final: 7 residues processed: 135 average time/residue: 1.1672 time to fit residues: 169.5604 Evaluate side-chains 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 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 84 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 56 optimal weight: 0.0030 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.107642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.066824 restraints weight = 15289.974| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.61 r_work: 0.2550 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9150 Z= 0.183 Angle : 0.538 6.802 12465 Z= 0.282 Chirality : 0.042 0.188 1399 Planarity : 0.003 0.036 1498 Dihedral : 16.976 151.787 1437 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.05 % Allowed : 12.54 % Favored : 85.41 % 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: 0.79 (0.26), residues: 1027 helix: 1.80 (0.29), residues: 334 sheet: 0.32 (0.41), residues: 157 loop : -0.18 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 513 HIS 0.005 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 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 147 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8423 (tppt) cc_final: 0.8129 (ttmm) REVERT: A 172 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8004 (tm-30) REVERT: A 265 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9098 (ptmm) REVERT: A 294 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8343 (mm-30) REVERT: A 332 GLU cc_start: 0.8856 (mp0) cc_final: 0.8436 (pm20) REVERT: A 341 ASP cc_start: 0.8952 (m-30) cc_final: 0.8671 (m-30) REVERT: B 15 ASP cc_start: 0.8912 (t0) cc_final: 0.8590 (t0) REVERT: B 20 MET cc_start: 0.8745 (mtp) cc_final: 0.8504 (mtt) REVERT: B 52 ASP cc_start: 0.8706 (m-30) cc_final: 0.8441 (m-30) REVERT: B 53 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7429 (mm-30) REVERT: B 83 LEU cc_start: 0.9310 (tp) cc_final: 0.9060 (tm) REVERT: B 93 ASP cc_start: 0.8872 (m-30) cc_final: 0.8604 (m-30) REVERT: B 115 MET cc_start: 0.9606 (mtm) cc_final: 0.9404 (mtm) REVERT: B 157 CYS cc_start: 0.9186 (m) cc_final: 0.8816 (m) REVERT: B 210 MET cc_start: 0.9710 (tmm) cc_final: 0.9409 (tmm) REVERT: B 229 GLU cc_start: 0.8864 (pt0) cc_final: 0.8581 (pt0) REVERT: B 241 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8303 (mt-10) REVERT: B 414 HIS cc_start: 0.8378 (p-80) cc_final: 0.8067 (p-80) REVERT: B 415 ASN cc_start: 0.8798 (m-40) cc_final: 0.8501 (m-40) REVERT: B 541 GLU cc_start: 0.9172 (tt0) cc_final: 0.8750 (tm-30) REVERT: C 184 SER cc_start: 0.8042 (t) cc_final: 0.7774 (t) outliers start: 19 outliers final: 8 residues processed: 135 average time/residue: 1.1189 time to fit residues: 162.4695 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 : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 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 70 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 27 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 119 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 = 0.106330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.065563 restraints weight = 15337.002| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 3.61 r_work: 0.2522 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1758 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= 0.285 Angle : 0.557 6.222 12465 Z= 0.291 Chirality : 0.042 0.156 1399 Planarity : 0.003 0.035 1498 Dihedral : 17.003 151.109 1437 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.73 % Allowed : 13.08 % 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: 0.83 (0.26), residues: 1027 helix: 1.91 (0.29), residues: 334 sheet: 0.27 (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 0.004 0.001 HIS A 176 PHE 0.034 0.001 PHE B 107 TYR 0.011 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: 16 poor density : 122 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8428 (tppt) cc_final: 0.8132 (ttmm) REVERT: A 172 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 265 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9117 (ptmm) REVERT: A 294 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8368 (mm-30) REVERT: A 341 ASP cc_start: 0.8991 (m-30) cc_final: 0.8709 (m-30) REVERT: B 15 ASP cc_start: 0.8867 (t0) cc_final: 0.8599 (t0) REVERT: B 20 MET cc_start: 0.8819 (mtp) cc_final: 0.8509 (mtt) REVERT: B 52 ASP cc_start: 0.8710 (m-30) cc_final: 0.8498 (m-30) REVERT: B 53 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7540 (mm-30) REVERT: B 83 LEU cc_start: 0.9333 (tp) cc_final: 0.9122 (tm) REVERT: B 93 ASP cc_start: 0.8872 (m-30) cc_final: 0.8588 (m-30) REVERT: B 157 CYS cc_start: 0.9217 (m) cc_final: 0.8801 (m) REVERT: B 210 MET cc_start: 0.9713 (tmm) cc_final: 0.9402 (tmm) REVERT: B 229 GLU cc_start: 0.8877 (pt0) cc_final: 0.8609 (pt0) REVERT: B 241 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8340 (mt-10) REVERT: B 414 HIS cc_start: 0.8408 (p-80) cc_final: 0.8092 (p-80) REVERT: B 415 ASN cc_start: 0.8820 (m-40) cc_final: 0.8510 (m-40) REVERT: B 541 GLU cc_start: 0.9168 (tt0) cc_final: 0.8771 (tm-30) REVERT: C 184 SER cc_start: 0.8155 (t) cc_final: 0.7879 (t) outliers start: 16 outliers final: 7 residues processed: 129 average time/residue: 1.2130 time to fit residues: 167.3897 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 : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 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 85 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.107381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.066617 restraints weight = 15267.695| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.63 r_work: 0.2543 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9150 Z= 0.206 Angle : 0.548 6.741 12465 Z= 0.287 Chirality : 0.042 0.155 1399 Planarity : 0.003 0.051 1498 Dihedral : 16.963 151.622 1437 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.62 % Allowed : 14.05 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.96 (0.29), residues: 334 sheet: 0.27 (0.41), residues: 157 loop : -0.18 (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 0.036 0.001 PHE B 107 TYR 0.013 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 146 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8418 (tppt) cc_final: 0.8110 (ttmm) REVERT: A 172 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8029 (tm-30) REVERT: A 265 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9121 (ptmm) REVERT: A 332 GLU cc_start: 0.8869 (mp0) cc_final: 0.8635 (pm20) REVERT: A 341 ASP cc_start: 0.8933 (m-30) cc_final: 0.8588 (m-30) REVERT: B 15 ASP cc_start: 0.8913 (t0) cc_final: 0.8636 (t0) REVERT: B 20 MET cc_start: 0.8836 (mtp) cc_final: 0.8477 (mtt) REVERT: B 93 ASP cc_start: 0.8864 (m-30) cc_final: 0.8578 (m-30) REVERT: B 157 CYS cc_start: 0.9210 (m) cc_final: 0.8814 (m) REVERT: B 210 MET cc_start: 0.9715 (tmm) cc_final: 0.9413 (tmm) REVERT: B 229 GLU cc_start: 0.8874 (pt0) cc_final: 0.8587 (pt0) REVERT: B 241 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8323 (mt-10) REVERT: B 414 HIS cc_start: 0.8390 (p-80) cc_final: 0.8065 (p-80) REVERT: B 415 ASN cc_start: 0.8810 (m-40) cc_final: 0.8500 (m-40) REVERT: B 541 GLU cc_start: 0.9163 (tt0) cc_final: 0.8767 (tm-30) REVERT: C 184 SER cc_start: 0.8090 (t) cc_final: 0.7839 (t) outliers start: 15 outliers final: 8 residues processed: 137 average time/residue: 1.1333 time to fit residues: 166.7668 Evaluate side-chains 129 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 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 70 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 90 optimal weight: 0.0570 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 0.0470 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.108349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.067788 restraints weight = 15471.242| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.65 r_work: 0.2562 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2052 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= 0.177 Angle : 0.578 8.824 12465 Z= 0.298 Chirality : 0.042 0.268 1399 Planarity : 0.004 0.063 1498 Dihedral : 16.917 151.519 1437 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.62 % Allowed : 15.46 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.26), residues: 1027 helix: 1.98 (0.29), residues: 334 sheet: 0.32 (0.41), residues: 157 loop : -0.17 (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 0.032 0.001 PHE B 107 TYR 0.016 0.001 TYR B 74 ARG 0.016 0.000 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 143 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8409 (tppt) cc_final: 0.8102 (ttmm) REVERT: A 172 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 294 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8592 (mp0) REVERT: A 332 GLU cc_start: 0.8875 (mp0) cc_final: 0.8591 (pm20) REVERT: A 341 ASP cc_start: 0.8910 (m-30) cc_final: 0.8576 (m-30) REVERT: B 15 ASP cc_start: 0.8903 (t0) cc_final: 0.8576 (t0) REVERT: B 20 MET cc_start: 0.8818 (mtp) cc_final: 0.8412 (mtt) REVERT: B 93 ASP cc_start: 0.8867 (m-30) cc_final: 0.8572 (m-30) REVERT: B 157 CYS cc_start: 0.9217 (m) cc_final: 0.8822 (m) REVERT: B 210 MET cc_start: 0.9715 (tmm) cc_final: 0.9412 (tmm) REVERT: B 229 GLU cc_start: 0.8868 (pt0) cc_final: 0.8581 (pt0) REVERT: B 241 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8309 (mt-10) REVERT: B 414 HIS cc_start: 0.8371 (p-80) cc_final: 0.8058 (p-80) REVERT: B 415 ASN cc_start: 0.8783 (m-40) cc_final: 0.8509 (m-40) REVERT: B 541 GLU cc_start: 0.9175 (tt0) cc_final: 0.8783 (tm-30) REVERT: C 184 SER cc_start: 0.8079 (t) cc_final: 0.7804 (t) REVERT: C 185 LEU cc_start: 0.9379 (tp) cc_final: 0.9179 (tp) outliers start: 15 outliers final: 6 residues processed: 136 average time/residue: 1.1607 time to fit residues: 169.6102 Evaluate side-chains 126 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 65 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.108002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.067117 restraints weight = 15591.528| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.67 r_work: 0.2550 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9150 Z= 0.207 Angle : 0.581 7.581 12465 Z= 0.301 Chirality : 0.042 0.173 1399 Planarity : 0.004 0.073 1498 Dihedral : 16.904 151.178 1437 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.41 % Allowed : 16.00 % Favored : 82.59 % 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: 0.83 (0.26), residues: 1027 helix: 1.89 (0.29), residues: 334 sheet: 0.33 (0.41), residues: 157 loop : -0.19 (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 0.038 0.001 PHE B 107 TYR 0.015 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 134 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8399 (tppt) cc_final: 0.8082 (ttmm) REVERT: A 107 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7195 (mp0) REVERT: A 172 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7993 (tm-30) REVERT: A 250 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8898 (tp30) REVERT: A 289 TYR cc_start: 0.8129 (t80) cc_final: 0.7877 (t80) REVERT: A 294 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8622 (pm20) REVERT: A 332 GLU cc_start: 0.8877 (mp0) cc_final: 0.8534 (pm20) REVERT: A 341 ASP cc_start: 0.8930 (m-30) cc_final: 0.8577 (m-30) REVERT: B 15 ASP cc_start: 0.8887 (t0) cc_final: 0.8600 (t0) REVERT: B 20 MET cc_start: 0.8814 (mtp) cc_final: 0.8412 (mtt) REVERT: B 93 ASP cc_start: 0.8869 (m-30) cc_final: 0.8575 (m-30) REVERT: B 157 CYS cc_start: 0.9226 (m) cc_final: 0.8834 (m) REVERT: B 210 MET cc_start: 0.9720 (tmm) cc_final: 0.9415 (tmm) REVERT: B 229 GLU cc_start: 0.8866 (pt0) cc_final: 0.8579 (pt0) REVERT: B 241 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8307 (mt-10) REVERT: B 414 HIS cc_start: 0.8378 (p-80) cc_final: 0.8077 (p-80) REVERT: B 415 ASN cc_start: 0.8784 (m-40) cc_final: 0.8518 (m-40) REVERT: B 541 GLU cc_start: 0.9159 (tt0) cc_final: 0.8771 (tm-30) REVERT: C 184 SER cc_start: 0.8116 (t) cc_final: 0.7846 (t) outliers start: 13 outliers final: 6 residues processed: 128 average time/residue: 1.1926 time to fit residues: 163.5629 Evaluate side-chains 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 357 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.4980 chunk 38 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 0.0470 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 90 optimal weight: 0.0670 chunk 11 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 overall best weight: 0.3016 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.109667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.069116 restraints weight = 15431.258| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.65 r_work: 0.2588 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2240 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= 0.164 Angle : 0.578 9.606 12465 Z= 0.298 Chirality : 0.042 0.153 1399 Planarity : 0.004 0.068 1498 Dihedral : 16.806 151.334 1437 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.08 % Allowed : 16.97 % Favored : 81.95 % 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: 0.90 (0.26), residues: 1027 helix: 1.96 (0.29), residues: 334 sheet: 0.38 (0.41), residues: 157 loop : -0.17 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 513 HIS 0.003 0.000 HIS A 176 PHE 0.033 0.001 PHE B 107 TYR 0.011 0.001 TYR B 74 ARG 0.018 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 140 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8377 (tppt) cc_final: 0.8013 (ttmm) REVERT: A 107 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7173 (mp0) REVERT: A 172 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7963 (tm-30) REVERT: A 289 TYR cc_start: 0.8033 (t80) cc_final: 0.7776 (t80) REVERT: A 294 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8632 (pm20) REVERT: A 332 GLU cc_start: 0.8878 (mp0) cc_final: 0.8523 (pm20) REVERT: A 341 ASP cc_start: 0.8858 (m-30) cc_final: 0.8514 (m-30) REVERT: A 374 LEU cc_start: 0.9120 (mm) cc_final: 0.8858 (mm) REVERT: B 15 ASP cc_start: 0.8860 (t0) cc_final: 0.8560 (t0) REVERT: B 20 MET cc_start: 0.8799 (mtp) cc_final: 0.8397 (mtt) REVERT: B 93 ASP cc_start: 0.8848 (m-30) cc_final: 0.8576 (m-30) REVERT: B 115 MET cc_start: 0.9642 (mtm) cc_final: 0.9441 (pmm) REVERT: B 210 MET cc_start: 0.9710 (tmm) cc_final: 0.9418 (tmm) REVERT: B 229 GLU cc_start: 0.8854 (pt0) cc_final: 0.8558 (pt0) REVERT: B 241 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8293 (mt-10) REVERT: B 414 HIS cc_start: 0.8348 (p-80) cc_final: 0.8039 (p-80) REVERT: B 415 ASN cc_start: 0.8773 (m-40) cc_final: 0.8524 (m-40) REVERT: B 541 GLU cc_start: 0.9167 (tt0) cc_final: 0.8782 (tm-30) REVERT: C 184 SER cc_start: 0.8035 (t) cc_final: 0.7797 (t) outliers start: 10 outliers final: 6 residues processed: 135 average time/residue: 1.1600 time to fit residues: 167.8137 Evaluate side-chains 129 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 294 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 357 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.106802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.065710 restraints weight = 15361.419| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.64 r_work: 0.2519 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2185 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= 0.300 Angle : 0.627 11.582 12465 Z= 0.323 Chirality : 0.043 0.157 1399 Planarity : 0.004 0.083 1498 Dihedral : 16.927 150.760 1437 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.30 % Allowed : 16.97 % Favored : 81.73 % 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 (0.27), residues: 1027 helix: 1.95 (0.29), residues: 334 sheet: 0.29 (0.41), residues: 157 loop : -0.21 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 148 HIS 0.004 0.001 HIS A 176 PHE 0.039 0.001 PHE B 107 TYR 0.014 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 131 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8372 (tppt) cc_final: 0.8144 (ttmm) REVERT: A 107 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7267 (mp0) REVERT: A 172 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7989 (tm-30) REVERT: A 205 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8461 (mm) REVERT: A 250 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8893 (tp30) REVERT: A 294 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8616 (pm20) REVERT: A 332 GLU cc_start: 0.8891 (mp0) cc_final: 0.8534 (pm20) REVERT: A 341 ASP cc_start: 0.8987 (m-30) cc_final: 0.8675 (m-30) REVERT: A 403 ARG cc_start: 0.8721 (ptp90) cc_final: 0.8392 (ptp90) REVERT: B 15 ASP cc_start: 0.8836 (t0) cc_final: 0.8527 (t0) REVERT: B 20 MET cc_start: 0.8794 (mtp) cc_final: 0.8379 (mtt) REVERT: B 93 ASP cc_start: 0.8870 (m-30) cc_final: 0.8577 (m-30) REVERT: B 115 MET cc_start: 0.9652 (mtm) cc_final: 0.9446 (pmm) REVERT: B 210 MET cc_start: 0.9708 (tmm) cc_final: 0.9421 (tmm) REVERT: B 223 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7274 (mp0) REVERT: B 229 GLU cc_start: 0.8867 (pt0) cc_final: 0.8577 (pt0) REVERT: B 241 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8357 (mt-10) REVERT: B 414 HIS cc_start: 0.8354 (p-80) cc_final: 0.8044 (p-80) REVERT: B 415 ASN cc_start: 0.8785 (m-40) cc_final: 0.8521 (m-40) REVERT: B 541 GLU cc_start: 0.9169 (tt0) cc_final: 0.8768 (tm-30) REVERT: C 184 SER cc_start: 0.8180 (t) cc_final: 0.7906 (t) REVERT: C 185 LEU cc_start: 0.9401 (tp) cc_final: 0.9189 (tp) REVERT: C 191 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8853 (pmtt) outliers start: 12 outliers final: 5 residues processed: 125 average time/residue: 1.2260 time to fit residues: 163.8065 Evaluate side-chains 126 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 250 GLU 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 275 THR Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain C residue 191 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.107863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.067016 restraints weight = 15422.130| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.65 r_work: 0.2551 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2232 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= 0.208 Angle : 0.605 11.792 12465 Z= 0.310 Chirality : 0.042 0.155 1399 Planarity : 0.004 0.080 1498 Dihedral : 16.894 151.679 1437 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.19 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: 0.82 (0.26), residues: 1027 helix: 1.90 (0.29), residues: 334 sheet: 0.28 (0.40), residues: 157 loop : -0.20 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 513 HIS 0.004 0.001 HIS A 176 PHE 0.040 0.001 PHE B 107 TYR 0.012 0.001 TYR B 74 ARG 0.020 0.001 ARG B 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6630.27 seconds wall clock time: 117 minutes 46.51 seconds (7066.51 seconds total)