Starting phenix.real_space_refine on Wed Feb 14 08:19:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyg_15022/02_2024/7zyg_15022.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyg_15022/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyg_15022/02_2024/7zyg_15022.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyg_15022/02_2024/7zyg_15022.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyg_15022/02_2024/7zyg_15022.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyg_15022/02_2024/7zyg_15022.pdb" } 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 Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.04, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 3.56 Conformation dependent library (CDL) restraints added in 1.5 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: 2.92 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: 3.75 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: 100.17 - 106.93: 470 106.93 - 113.69: 5021 113.69 - 120.46: 3384 120.46 - 127.22: 3461 127.22 - 133.98: 129 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 2.520 nonbonded pdb=" OH TYR A 369 " pdb=" O SER B 436 " model vdw 2.320 2.440 nonbonded pdb=" OG SER A 270 " pdb=" O GLU A 371 " model vdw 2.328 2.440 nonbonded pdb=" O MET B 20 " pdb=" OG SER B 29 " model vdw 2.333 2.440 nonbonded pdb=" OG SER A 78 " pdb=" OD2 ASP A 81 " model vdw 2.354 2.440 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 14.650 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 28.350 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.220 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.172 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: 1.0569 time to fit residues: 187.3448 Evaluate side-chains 121 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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: 0.8980 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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: 0.8138 moved from start: 0.1256 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= 0.184 Angle : 0.564 9.918 12465 Z= 0.294 Chirality : 0.043 0.347 1399 Planarity : 0.003 0.038 1498 Dihedral : 16.988 152.012 1437 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.84 % Allowed : 10.49 % Favored : 87.68 % 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: 1.71 (0.29), residues: 334 sheet: 0.36 (0.41), residues: 157 loop : -0.14 (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 0.029 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 147 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8425 (tppt) cc_final: 0.8128 (ttmm) REVERT: A 172 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8016 (tm-30) REVERT: A 205 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8137 (mm) REVERT: A 294 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8295 (mp0) REVERT: A 341 ASP cc_start: 0.8840 (m-30) cc_final: 0.8610 (m-30) REVERT: B 15 ASP cc_start: 0.8772 (t0) cc_final: 0.8465 (t0) REVERT: B 20 MET cc_start: 0.8903 (mtp) cc_final: 0.8488 (mtt) REVERT: B 53 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7398 (mm-30) REVERT: B 93 ASP cc_start: 0.8898 (m-30) cc_final: 0.8629 (m-30) REVERT: B 115 MET cc_start: 0.9451 (mtm) cc_final: 0.9235 (mtm) REVERT: B 157 CYS cc_start: 0.9069 (m) cc_final: 0.8655 (m) REVERT: B 210 MET cc_start: 0.9680 (tmm) cc_final: 0.9377 (tmm) REVERT: B 229 GLU cc_start: 0.8889 (pt0) cc_final: 0.8591 (pt0) REVERT: B 241 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8009 (mt-10) REVERT: B 414 HIS cc_start: 0.8254 (p-80) cc_final: 0.7954 (p-80) REVERT: B 415 ASN cc_start: 0.8725 (m-40) cc_final: 0.8392 (m-40) REVERT: B 541 GLU cc_start: 0.8961 (tt0) cc_final: 0.8612 (tm-30) outliers start: 17 outliers final: 4 residues processed: 136 average time/residue: 1.1862 time to fit residues: 172.8322 Evaluate side-chains 119 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 230 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 26 optimal weight: 8.9990 chunk 94 optimal weight: 0.0050 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- 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: 0.8144 moved from start: 0.1467 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= 0.225 Angle : 0.531 6.166 12465 Z= 0.277 Chirality : 0.042 0.217 1399 Planarity : 0.003 0.037 1498 Dihedral : 16.990 151.726 1437 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.84 % Allowed : 11.89 % Favored : 86.27 % 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: 1.84 (0.29), residues: 334 sheet: 0.34 (0.41), residues: 155 loop : -0.15 (0.27), residues: 538 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 0.009 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 141 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8457 (tppt) cc_final: 0.8173 (ttmm) REVERT: A 172 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7948 (tm-30) REVERT: A 205 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8152 (mm) REVERT: A 294 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8311 (mm-30) REVERT: A 332 GLU cc_start: 0.8734 (mp0) cc_final: 0.8364 (pm20) REVERT: A 341 ASP cc_start: 0.8879 (m-30) cc_final: 0.8601 (m-30) REVERT: B 15 ASP cc_start: 0.8720 (t0) cc_final: 0.8468 (t0) REVERT: B 20 MET cc_start: 0.8887 (mtp) cc_final: 0.8432 (mtt) REVERT: B 53 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7516 (mm-30) REVERT: B 93 ASP cc_start: 0.8917 (m-30) cc_final: 0.8643 (m-30) REVERT: B 157 CYS cc_start: 0.9091 (m) cc_final: 0.8684 (m) REVERT: B 210 MET cc_start: 0.9688 (tmm) cc_final: 0.9385 (tmm) REVERT: B 229 GLU cc_start: 0.8883 (pt0) cc_final: 0.8580 (pt0) REVERT: B 241 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8047 (mt-10) REVERT: B 414 HIS cc_start: 0.8251 (p-80) cc_final: 0.7958 (p-80) REVERT: B 415 ASN cc_start: 0.8717 (m-40) cc_final: 0.8392 (m-40) REVERT: B 541 GLU cc_start: 0.8955 (tt0) cc_final: 0.8609 (tm-30) outliers start: 17 outliers final: 7 residues processed: 132 average time/residue: 1.0965 time to fit residues: 155.5594 Evaluate side-chains 119 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.8156 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9150 Z= 0.281 Angle : 0.545 7.268 12465 Z= 0.283 Chirality : 0.042 0.157 1399 Planarity : 0.003 0.036 1498 Dihedral : 16.991 151.330 1437 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.73 % Allowed : 13.19 % Favored : 85.08 % 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: 1.83 (0.29), residues: 334 sheet: 0.33 (0.40), residues: 155 loop : -0.21 (0.27), residues: 538 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 0.030 0.001 PHE B 107 TYR 0.009 0.001 TYR A 88 ARG 0.004 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 137 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8450 (tppt) cc_final: 0.8151 (ttmm) REVERT: A 172 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 332 GLU cc_start: 0.8746 (mp0) cc_final: 0.8362 (pm20) REVERT: A 341 ASP cc_start: 0.8898 (m-30) cc_final: 0.8609 (m-30) REVERT: B 15 ASP cc_start: 0.8712 (t0) cc_final: 0.8466 (t0) REVERT: B 20 MET cc_start: 0.8911 (mtp) cc_final: 0.8458 (mtt) REVERT: B 53 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7495 (mm-30) REVERT: B 68 LEU cc_start: 0.9400 (mt) cc_final: 0.9121 (pp) REVERT: B 93 ASP cc_start: 0.8908 (m-30) cc_final: 0.8629 (m-30) REVERT: B 111 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9035 (tt) REVERT: B 115 MET cc_start: 0.9542 (mtm) cc_final: 0.9217 (mtm) REVERT: B 157 CYS cc_start: 0.9100 (m) cc_final: 0.8715 (m) REVERT: B 210 MET cc_start: 0.9689 (tmm) cc_final: 0.9378 (tmm) REVERT: B 229 GLU cc_start: 0.8873 (pt0) cc_final: 0.8568 (pt0) REVERT: B 241 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8082 (mt-10) REVERT: B 414 HIS cc_start: 0.8239 (p-80) cc_final: 0.7917 (p-80) REVERT: B 415 ASN cc_start: 0.8719 (m-40) cc_final: 0.8390 (m-40) REVERT: B 541 GLU cc_start: 0.8948 (tt0) cc_final: 0.8614 (tm-30) REVERT: C 184 SER cc_start: 0.8024 (t) cc_final: 0.7739 (t) outliers start: 16 outliers final: 9 residues processed: 129 average time/residue: 1.0837 time to fit residues: 150.3689 Evaluate side-chains 126 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 111 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 230 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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: 0.8153 moved from start: 0.1730 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= 0.248 Angle : 0.535 6.252 12465 Z= 0.279 Chirality : 0.042 0.156 1399 Planarity : 0.003 0.035 1498 Dihedral : 16.985 151.631 1437 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.62 % Allowed : 14.16 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.91 (0.29), residues: 334 sheet: 0.33 (0.40), residues: 157 loop : -0.23 (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 0.009 0.001 TYR A 88 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 139 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8442 (tppt) cc_final: 0.8143 (ttmm) REVERT: A 172 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7959 (tm-30) REVERT: A 294 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8275 (mm-30) REVERT: A 341 ASP cc_start: 0.8857 (m-30) cc_final: 0.8540 (m-30) REVERT: B 15 ASP cc_start: 0.8703 (t0) cc_final: 0.8484 (t0) REVERT: B 20 MET cc_start: 0.8905 (mtp) cc_final: 0.8404 (mtt) REVERT: B 68 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9120 (pp) REVERT: B 93 ASP cc_start: 0.8880 (m-30) cc_final: 0.8601 (m-30) REVERT: B 157 CYS cc_start: 0.9098 (m) cc_final: 0.8697 (m) REVERT: B 210 MET cc_start: 0.9691 (tmm) cc_final: 0.9379 (tmm) REVERT: B 229 GLU cc_start: 0.8865 (pt0) cc_final: 0.8557 (pt0) REVERT: B 241 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8076 (mt-10) REVERT: B 414 HIS cc_start: 0.8232 (p-80) cc_final: 0.7899 (p-80) REVERT: B 415 ASN cc_start: 0.8721 (m-40) cc_final: 0.8392 (m-40) REVERT: B 541 GLU cc_start: 0.8954 (tt0) cc_final: 0.8637 (tm-30) REVERT: C 184 SER cc_start: 0.7993 (t) cc_final: 0.7698 (t) outliers start: 15 outliers final: 9 residues processed: 131 average time/residue: 1.1829 time to fit residues: 166.5070 Evaluate side-chains 124 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 230 SER 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: 5.9990 chunk 19 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 100 optimal weight: 0.0770 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- 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: 0.8146 moved from start: 0.1809 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= 0.212 Angle : 0.532 6.263 12465 Z= 0.277 Chirality : 0.041 0.155 1399 Planarity : 0.003 0.036 1498 Dihedral : 16.946 151.636 1437 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.51 % Allowed : 15.14 % Favored : 83.35 % 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: 0.35 (0.41), 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 0.004 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 B 400 *********************** 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 133 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8426 (tppt) cc_final: 0.8111 (ttmm) REVERT: A 172 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7902 (tm-30) REVERT: A 332 GLU cc_start: 0.8748 (mp0) cc_final: 0.8422 (pm20) REVERT: A 341 ASP cc_start: 0.8820 (m-30) cc_final: 0.8505 (m-30) REVERT: B 15 ASP cc_start: 0.8710 (t0) cc_final: 0.8419 (t0) REVERT: B 20 MET cc_start: 0.8917 (mtp) cc_final: 0.8378 (mtt) REVERT: B 68 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9195 (pp) REVERT: B 93 ASP cc_start: 0.8878 (m-30) cc_final: 0.8608 (m-30) REVERT: B 115 MET cc_start: 0.9559 (mtm) cc_final: 0.9263 (mtm) REVERT: B 157 CYS cc_start: 0.9109 (m) cc_final: 0.8722 (m) REVERT: B 210 MET cc_start: 0.9693 (tmm) cc_final: 0.9389 (tmm) REVERT: B 229 GLU cc_start: 0.8854 (pt0) cc_final: 0.8538 (pt0) REVERT: B 241 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8066 (mt-10) REVERT: B 414 HIS cc_start: 0.8218 (p-80) cc_final: 0.7880 (p-80) REVERT: B 415 ASN cc_start: 0.8707 (m-40) cc_final: 0.8381 (m-40) REVERT: B 541 GLU cc_start: 0.8955 (tt0) cc_final: 0.8634 (tm-30) outliers start: 14 outliers final: 7 residues processed: 127 average time/residue: 1.0417 time to fit residues: 142.6658 Evaluate side-chains 119 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 0.0030 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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: 0.8131 moved from start: 0.1888 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= 0.174 Angle : 0.528 7.715 12465 Z= 0.273 Chirality : 0.041 0.228 1399 Planarity : 0.003 0.036 1498 Dihedral : 16.882 151.727 1437 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.51 % Allowed : 16.00 % Favored : 82.49 % 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: 0.91 (0.26), residues: 1027 helix: 2.03 (0.29), residues: 334 sheet: 0.35 (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 0.039 0.001 PHE B 107 TYR 0.011 0.001 TYR A 88 ARG 0.006 0.000 ARG F 295 *********************** 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 137 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8427 (tppt) cc_final: 0.8109 (ttmm) REVERT: A 172 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7864 (tm-30) REVERT: A 332 GLU cc_start: 0.8750 (mp0) cc_final: 0.8391 (pm20) REVERT: A 341 ASP cc_start: 0.8770 (m-30) cc_final: 0.8466 (m-30) REVERT: A 423 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8484 (mp10) REVERT: B 15 ASP cc_start: 0.8674 (t0) cc_final: 0.8407 (t0) REVERT: B 20 MET cc_start: 0.8908 (mtp) cc_final: 0.8328 (mtt) REVERT: B 68 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9155 (pp) REVERT: B 93 ASP cc_start: 0.8879 (m-30) cc_final: 0.8602 (m-30) REVERT: B 111 LEU cc_start: 0.9209 (tt) cc_final: 0.8940 (tm) REVERT: B 157 CYS cc_start: 0.9114 (m) cc_final: 0.8726 (m) REVERT: B 210 MET cc_start: 0.9697 (tmm) cc_final: 0.9396 (tmm) REVERT: B 229 GLU cc_start: 0.8849 (pt0) cc_final: 0.8552 (pt0) REVERT: B 241 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8024 (mt-10) REVERT: B 414 HIS cc_start: 0.8202 (p-80) cc_final: 0.7883 (p-80) REVERT: B 415 ASN cc_start: 0.8694 (m-40) cc_final: 0.8425 (m-40) REVERT: B 541 GLU cc_start: 0.8956 (tt0) cc_final: 0.8643 (tm-30) outliers start: 14 outliers final: 7 residues processed: 129 average time/residue: 1.0862 time to fit residues: 151.0259 Evaluate side-chains 125 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 230 SER 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: 2.9990 chunk 19 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 68 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1933 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 : 0.551 6.855 12465 Z= 0.287 Chirality : 0.042 0.156 1399 Planarity : 0.003 0.036 1498 Dihedral : 16.954 151.289 1437 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.51 % Allowed : 16.32 % Favored : 82.16 % 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: 0.91 (0.26), residues: 1027 helix: 2.05 (0.29), residues: 334 sheet: 0.29 (0.41), residues: 157 loop : -0.19 (0.27), residues: 536 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 0.033 0.001 PHE B 107 TYR 0.011 0.001 TYR A 289 ARG 0.005 0.000 ARG B 400 *********************** 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 130 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8404 (tppt) cc_final: 0.8170 (ttmm) REVERT: A 172 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7867 (tm-30) REVERT: A 332 GLU cc_start: 0.8754 (mp0) cc_final: 0.8402 (pm20) REVERT: A 341 ASP cc_start: 0.8851 (m-30) cc_final: 0.8567 (m-30) REVERT: B 15 ASP cc_start: 0.8676 (t0) cc_final: 0.8418 (t0) REVERT: B 20 MET cc_start: 0.8920 (mtp) cc_final: 0.8358 (mtt) REVERT: B 68 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9216 (pp) REVERT: B 93 ASP cc_start: 0.8884 (m-30) cc_final: 0.8599 (m-30) REVERT: B 210 MET cc_start: 0.9693 (tmm) cc_final: 0.9379 (tmm) REVERT: B 229 GLU cc_start: 0.8846 (pt0) cc_final: 0.8552 (pt0) REVERT: B 241 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8050 (mt-10) REVERT: B 294 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7895 (m) REVERT: B 414 HIS cc_start: 0.8205 (p-80) cc_final: 0.7873 (p-80) REVERT: B 415 ASN cc_start: 0.8683 (m-40) cc_final: 0.8401 (m-40) REVERT: B 541 GLU cc_start: 0.8956 (tt0) cc_final: 0.8651 (tm-30) outliers start: 14 outliers final: 8 residues processed: 125 average time/residue: 1.1128 time to fit residues: 149.5026 Evaluate side-chains 125 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 275 THR 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: 1.9990 chunk 56 optimal weight: 8.9990 chunk 40 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.8150 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9150 Z= 0.244 Angle : 0.550 7.724 12465 Z= 0.285 Chirality : 0.042 0.155 1399 Planarity : 0.003 0.037 1498 Dihedral : 16.954 151.951 1437 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.51 % Allowed : 16.97 % 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: 0.87 (0.26), residues: 1027 helix: 2.00 (0.29), residues: 334 sheet: 0.29 (0.41), residues: 157 loop : -0.20 (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 0.035 0.001 PHE B 107 TYR 0.014 0.001 TYR A 88 ARG 0.006 0.000 ARG B 400 *********************** 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 129 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8383 (tppt) cc_final: 0.8139 (ttmm) REVERT: A 172 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 332 GLU cc_start: 0.8761 (mp0) cc_final: 0.8387 (pm20) REVERT: A 341 ASP cc_start: 0.8822 (m-30) cc_final: 0.8502 (m-30) REVERT: B 15 ASP cc_start: 0.8662 (t0) cc_final: 0.8415 (t0) REVERT: B 20 MET cc_start: 0.8950 (mtp) cc_final: 0.8392 (mtt) REVERT: B 68 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9208 (pp) REVERT: B 93 ASP cc_start: 0.8880 (m-30) cc_final: 0.8598 (m-30) REVERT: B 210 MET cc_start: 0.9695 (tmm) cc_final: 0.9381 (tmm) REVERT: B 216 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7470 (tm-30) REVERT: B 229 GLU cc_start: 0.8842 (pt0) cc_final: 0.8550 (pt0) REVERT: B 241 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8046 (mt-10) REVERT: B 414 HIS cc_start: 0.8217 (p-80) cc_final: 0.7884 (p-80) REVERT: B 415 ASN cc_start: 0.8702 (m-40) cc_final: 0.8425 (m-40) REVERT: B 541 GLU cc_start: 0.8950 (tt0) cc_final: 0.8645 (tm-30) outliers start: 14 outliers final: 9 residues processed: 124 average time/residue: 1.1048 time to fit residues: 147.4030 Evaluate side-chains 122 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 293 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 46 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 25 optimal weight: 0.0060 overall best weight: 0.7600 ------------------------------------------------------------------------------- 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: 0.8136 moved from start: 0.2038 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= 0.192 Angle : 0.539 8.536 12465 Z= 0.281 Chirality : 0.041 0.154 1399 Planarity : 0.003 0.037 1498 Dihedral : 16.914 151.866 1437 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.30 % Allowed : 17.19 % 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: 0.90 (0.26), residues: 1027 helix: 2.02 (0.29), residues: 334 sheet: 0.29 (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 0.003 0.001 HIS A 176 PHE 0.035 0.001 PHE B 107 TYR 0.013 0.001 TYR A 88 ARG 0.007 0.000 ARG B 400 ********************** 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 129 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8430 (tppt) cc_final: 0.8185 (ttmm) REVERT: A 172 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7841 (tm-30) REVERT: A 332 GLU cc_start: 0.8765 (mp0) cc_final: 0.8400 (pm20) REVERT: A 341 ASP cc_start: 0.8777 (m-30) cc_final: 0.8489 (m-30) REVERT: B 15 ASP cc_start: 0.8670 (t0) cc_final: 0.8431 (t0) REVERT: B 20 MET cc_start: 0.8940 (mtp) cc_final: 0.8398 (mtt) REVERT: B 93 ASP cc_start: 0.8876 (m-30) cc_final: 0.8593 (m-30) REVERT: B 115 MET cc_start: 0.9577 (mtm) cc_final: 0.9298 (mtm) REVERT: B 116 ASP cc_start: 0.9124 (t0) cc_final: 0.8870 (t0) REVERT: B 210 MET cc_start: 0.9696 (tmm) cc_final: 0.9384 (tmm) REVERT: B 216 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 229 GLU cc_start: 0.8836 (pt0) cc_final: 0.8541 (pt0) REVERT: B 241 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 414 HIS cc_start: 0.8208 (p-80) cc_final: 0.7866 (p-80) REVERT: B 415 ASN cc_start: 0.8696 (m-40) cc_final: 0.8446 (m-40) REVERT: B 541 GLU cc_start: 0.8948 (tt0) cc_final: 0.8631 (tm-30) outliers start: 12 outliers final: 8 residues processed: 126 average time/residue: 1.0693 time to fit residues: 145.0273 Evaluate side-chains 125 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 230 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 293 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 76 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.106366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.065640 restraints weight = 15399.059| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.62 r_work: 0.2520 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9150 Z= 0.318 Angle : 0.585 8.978 12465 Z= 0.301 Chirality : 0.043 0.157 1399 Planarity : 0.003 0.034 1498 Dihedral : 16.986 151.492 1437 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.19 % Allowed : 17.62 % 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: 0.85 (0.26), residues: 1027 helix: 1.99 (0.29), residues: 334 sheet: 0.25 (0.41), residues: 157 loop : -0.22 (0.27), residues: 536 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 0.033 0.001 PHE B 107 TYR 0.026 0.002 TYR B 74 ARG 0.007 0.000 ARG B 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3497.78 seconds wall clock time: 62 minutes 49.34 seconds (3769.34 seconds total)