Starting phenix.real_space_refine on Sat May 17 17:18:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymt_39407/05_2025/8ymt_39407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymt_39407/05_2025/8ymt_39407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ymt_39407/05_2025/8ymt_39407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymt_39407/05_2025/8ymt_39407.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymt_39407/05_2025/8ymt_39407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymt_39407/05_2025/8ymt_39407.cif" } resolution = 2.93 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= 0.045 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 S 57 5.16 5 C 5652 2.51 5 N 1482 2.21 5 O 1611 1.98 5 H 7173 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15975 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5325 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 17, 'TRANS': 344} Chain: "B" Number of atoms: 5325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5325 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 17, 'TRANS': 344} Chain: "C" Number of atoms: 5325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5325 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 17, 'TRANS': 344} Time building chain proxies: 8.74, per 1000 atoms: 0.55 Number of scatterers: 15975 At special positions: 0 Unit cell: (100.44, 93.93, 121.83, 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 57 16.00 O 1611 8.00 N 1482 7.00 C 5652 6.00 H 7173 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 188 " distance=2.02 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 341 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 188 " distance=2.02 Simple disulfide: pdb=" SG CYS B 273 " - pdb=" SG CYS B 341 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 337 " distance=2.04 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 188 " distance=2.02 Simple disulfide: pdb=" SG CYS C 273 " - pdb=" SG CYS C 341 " distance=2.04 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 299 " - pdb=" SG CYS C 311 " distance=2.03 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: 4.23 Conformation dependent library (CDL) restraints added in 1.3 seconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 37.4% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 53 through 83 removed outlier: 3.702A pdb=" N ILE A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.515A pdb=" N LEU A 133 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 275 through 296 removed outlier: 3.806A pdb=" N ALA A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 330 removed outlier: 3.612A pdb=" N ASN A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 4.162A pdb=" N GLU A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 396 Processing helix chain 'A' and resid 401 through 413 Processing helix chain 'B' and resid 54 through 83 removed outlier: 3.754A pdb=" N ILE B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B 76 " --> pdb=" O HIS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 115 through 122 Processing helix chain 'B' and resid 129 through 136 removed outlier: 3.602A pdb=" N LEU B 133 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 134 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 275 through 293 Processing helix chain 'B' and resid 313 through 330 removed outlier: 3.614A pdb=" N ASN B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 396 Processing helix chain 'B' and resid 401 through 413 Processing helix chain 'C' and resid 54 through 83 removed outlier: 3.781A pdb=" N ILE C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET C 76 " --> pdb=" O HIS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 115 through 122 Processing helix chain 'C' and resid 129 through 136 removed outlier: 3.639A pdb=" N LEU C 133 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE C 134 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 147 Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 275 through 293 Processing helix chain 'C' and resid 313 through 330 removed outlier: 3.628A pdb=" N ASN C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.915A pdb=" N GLU C 334 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 396 Processing helix chain 'C' and resid 401 through 413 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 94 removed outlier: 8.183A pdb=" N TYR A 371 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N PHE A 260 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE A 254 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N TYR A 366 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE A 256 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 161 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR A 170 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94 removed outlier: 8.183A pdb=" N TYR A 371 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N PHE A 260 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 183 removed outlier: 3.730A pdb=" N ILE A 103 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 94 removed outlier: 14.696A pdb=" N TYR B 371 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 10.955A pdb=" N ILE B 258 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 9.734A pdb=" N GLN B 373 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE B 260 " --> pdb=" O GLN B 373 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ALA B 375 " --> pdb=" O PHE B 260 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN B 262 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLU B 377 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN B 264 " --> pdb=" O GLU B 377 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N LEU B 379 " --> pdb=" O ASN B 264 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE B 256 " --> pdb=" O TYR B 366 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 161 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR B 170 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 94 removed outlier: 14.696A pdb=" N TYR B 371 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 10.955A pdb=" N ILE B 258 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 9.734A pdb=" N GLN B 373 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE B 260 " --> pdb=" O GLN B 373 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ALA B 375 " --> pdb=" O PHE B 260 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN B 262 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLU B 377 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN B 264 " --> pdb=" O GLU B 377 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N LEU B 379 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 183 removed outlier: 3.625A pdb=" N ILE B 103 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 94 removed outlier: 14.605A pdb=" N TYR C 371 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 10.956A pdb=" N ILE C 258 " --> pdb=" O TYR C 371 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N GLN C 373 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N PHE C 260 " --> pdb=" O GLN C 373 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ALA C 375 " --> pdb=" O PHE C 260 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLN C 262 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLU C 377 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN C 264 " --> pdb=" O GLU C 377 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N LEU C 379 " --> pdb=" O ASN C 264 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE C 256 " --> pdb=" O TYR C 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 86 through 94 removed outlier: 14.605A pdb=" N TYR C 371 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 10.956A pdb=" N ILE C 258 " --> pdb=" O TYR C 371 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N GLN C 373 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N PHE C 260 " --> pdb=" O GLN C 373 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ALA C 375 " --> pdb=" O PHE C 260 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLN C 262 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLU C 377 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN C 264 " --> pdb=" O GLU C 377 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N LEU C 379 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB3, first strand: chain 'C' and resid 179 through 183 removed outlier: 3.679A pdb=" N ILE C 103 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 223 through 226 438 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 7170 1.04 - 1.23: 241 1.23 - 1.43: 3659 1.43 - 1.63: 5040 1.63 - 1.82: 81 Bond restraints: 16191 Sorted by residual: bond pdb=" CA ILE C 347 " pdb=" CB ILE C 347 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.06e+00 bond pdb=" CG1 ILE A 258 " pdb=" CD1 ILE A 258 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.32e-01 bond pdb=" CB CYS B 188 " pdb=" SG CYS B 188 " ideal model delta sigma weight residual 1.808 1.777 0.031 3.30e-02 9.18e+02 8.56e-01 bond pdb=" CA GLU C 97 " pdb=" C GLU C 97 " ideal model delta sigma weight residual 1.530 1.520 0.010 1.08e-02 8.57e+03 8.41e-01 bond pdb=" CG1 ILE B 166 " pdb=" CD1 ILE B 166 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 8.16e-01 ... (remaining 16186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.93: 28337 10.93 - 21.86: 22 21.86 - 32.79: 114 32.79 - 43.72: 33 43.72 - 54.65: 24 Bond angle restraints: 28530 Sorted by residual: angle pdb=" C ASP C 316 " pdb=" N ALA C 317 " pdb=" H ALA C 317 " ideal model delta sigma weight residual 125.01 70.36 54.65 3.00e+00 1.11e-01 3.32e+02 angle pdb=" C ASP A 316 " pdb=" N ALA A 317 " pdb=" H ALA A 317 " ideal model delta sigma weight residual 125.01 70.41 54.60 3.00e+00 1.11e-01 3.31e+02 angle pdb=" C ASP B 316 " pdb=" N ALA B 317 " pdb=" H ALA B 317 " ideal model delta sigma weight residual 125.01 70.42 54.59 3.00e+00 1.11e-01 3.31e+02 angle pdb=" CA ALA C 317 " pdb=" N ALA C 317 " pdb=" H ALA C 317 " ideal model delta sigma weight residual 114.71 60.19 54.52 3.00e+00 1.11e-01 3.30e+02 angle pdb=" CA ALA B 317 " pdb=" N ALA B 317 " pdb=" H ALA B 317 " ideal model delta sigma weight residual 114.71 60.34 54.37 3.00e+00 1.11e-01 3.28e+02 ... (remaining 28525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 7079 17.29 - 34.57: 573 34.57 - 51.86: 147 51.86 - 69.15: 47 69.15 - 86.43: 14 Dihedral angle restraints: 7860 sinusoidal: 4116 harmonic: 3744 Sorted by residual: dihedral pdb=" CB CYS C 273 " pdb=" SG CYS C 273 " pdb=" SG CYS C 341 " pdb=" CB CYS C 341 " ideal model delta sinusoidal sigma weight residual 93.00 37.79 55.21 1 1.00e+01 1.00e-02 4.12e+01 dihedral pdb=" CB CYS B 299 " pdb=" SG CYS B 299 " pdb=" SG CYS B 311 " pdb=" CB CYS B 311 " ideal model delta sinusoidal sigma weight residual 93.00 41.74 51.26 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CA CYS C 341 " pdb=" C CYS C 341 " pdb=" N GLU C 342 " pdb=" CA GLU C 342 " ideal model delta harmonic sigma weight residual 180.00 151.97 28.03 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 7857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.346: 1350 0.346 - 0.692: 12 0.692 - 1.038: 0 1.038 - 1.384: 0 1.384 - 1.730: 3 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CG LEU B 394 " pdb=" CB LEU B 394 " pdb=" CD1 LEU B 394 " pdb=" CD2 LEU B 394 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.48e+01 chirality pdb=" CG LEU A 394 " pdb=" CB LEU A 394 " pdb=" CD1 LEU A 394 " pdb=" CD2 LEU A 394 " both_signs ideal model delta sigma weight residual False -2.59 -0.92 -1.67 2.00e-01 2.50e+01 6.98e+01 chirality pdb=" CG LEU C 394 " pdb=" CB LEU C 394 " pdb=" CD1 LEU C 394 " pdb=" CD2 LEU C 394 " both_signs ideal model delta sigma weight residual False -2.59 -0.92 -1.67 2.00e-01 2.50e+01 6.95e+01 ... (remaining 1362 not shown) Planarity restraints: 2436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 321 " 0.026 2.00e-02 2.50e+03 1.35e-02 5.50e+00 pdb=" CG PHE C 321 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE C 321 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 321 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 321 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 321 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 321 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE C 321 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE C 321 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE C 321 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE C 321 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE C 321 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 321 " 0.024 2.00e-02 2.50e+03 1.27e-02 4.86e+00 pdb=" CG PHE A 321 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 321 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 321 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 321 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 321 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 321 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 321 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 321 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 321 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 321 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 321 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 305 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO C 306 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 306 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 306 " 0.028 5.00e-02 4.00e+02 ... (remaining 2433 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 350 2.05 - 2.69: 22910 2.69 - 3.33: 44082 3.33 - 3.96: 59271 3.96 - 4.60: 90825 Nonbonded interactions: 217438 Sorted by model distance: nonbonded pdb=" H HIS C 235 " pdb=" HA HIS C 235 " model vdw 1.413 1.816 nonbonded pdb=" H HIS A 235 " pdb=" HA HIS A 235 " model vdw 1.415 1.816 nonbonded pdb=" H HIS B 235 " pdb=" HA HIS B 235 " model vdw 1.416 1.816 nonbonded pdb=" H ILE B 115 " pdb=" HA ILE B 115 " model vdw 1.459 1.816 nonbonded pdb=" H ILE C 115 " pdb=" HA ILE C 115 " model vdw 1.460 1.816 ... (remaining 217433 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=1.00 max=1.00 mean=1.00 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: 1.120 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: 0.300 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.800 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 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 : 0.004 0.038 9030 Z= 0.175 Angle : 0.935 18.865 12276 Z= 0.574 Chirality : 0.099 1.730 1365 Planarity : 0.005 0.050 1581 Dihedral : 13.437 86.431 3306 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 1.20 % Allowed : 6.39 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -2.25 (0.25), residues: 1080 helix: 0.38 (0.27), residues: 393 sheet: -2.16 (0.30), residues: 267 loop : -2.82 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 145 HIS 0.005 0.001 HIS B 160 PHE 0.038 0.002 PHE C 321 TYR 0.007 0.001 TYR B 279 ARG 0.006 0.001 ARG C 207 Details of bonding type rmsd hydrogen bonds : bond 0.14395 ( 409) hydrogen bonds : angle 7.19762 ( 1215) SS BOND : bond 0.00613 ( 12) SS BOND : angle 1.04924 ( 24) covalent geometry : bond 0.00361 ( 9018) covalent geometry : angle 0.93495 (12252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.6783 (mmt) cc_final: 0.6511 (mmt) REVERT: A 128 MET cc_start: 0.7061 (mmm) cc_final: 0.6720 (mmt) REVERT: A 145 TRP cc_start: 0.7118 (m-10) cc_final: 0.6526 (m-10) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 2.0435 time to fit residues: 274.6638 Evaluate side-chains 89 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** 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 = 0.4377 r_free = 0.4377 target = 0.214237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.176506 restraints weight = 23387.584| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.76 r_work: 0.3812 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9030 Z= 0.158 Angle : 0.838 18.798 12276 Z= 0.457 Chirality : 0.099 1.720 1365 Planarity : 0.005 0.047 1581 Dihedral : 5.448 20.595 1206 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 1.11 % Allowed : 6.85 % Favored : 92.04 % Rotamer: Outliers : 1.83 % Allowed : 7.14 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.95 (0.25), residues: 1080 helix: 0.66 (0.27), residues: 402 sheet: -2.03 (0.30), residues: 267 loop : -2.74 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 145 HIS 0.005 0.001 HIS A 160 PHE 0.013 0.002 PHE C 367 TYR 0.009 0.001 TYR C 246 ARG 0.004 0.000 ARG B 220 Details of bonding type rmsd hydrogen bonds : bond 0.03103 ( 409) hydrogen bonds : angle 5.24793 ( 1215) SS BOND : bond 0.00435 ( 12) SS BOND : angle 0.94273 ( 24) covalent geometry : bond 0.00375 ( 9018) covalent geometry : angle 0.83822 (12252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8101 (mmt) cc_final: 0.7819 (mmt) REVERT: A 145 TRP cc_start: 0.7358 (m100) cc_final: 0.6549 (m-10) REVERT: A 278 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: A 326 ASP cc_start: 0.8018 (t70) cc_final: 0.7522 (m-30) REVERT: B 119 MET cc_start: 0.8086 (mmt) cc_final: 0.7823 (mmt) REVERT: B 220 ARG cc_start: 0.7645 (pmm150) cc_final: 0.7053 (mmt-90) REVERT: C 278 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7248 (mp0) outliers start: 18 outliers final: 6 residues processed: 106 average time/residue: 2.0232 time to fit residues: 231.0360 Evaluate side-chains 98 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 278 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0970 chunk 94 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** 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 = 0.4384 r_free = 0.4384 target = 0.215108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.177988 restraints weight = 23098.419| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.75 r_work: 0.3844 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9030 Z= 0.123 Angle : 0.811 19.225 12276 Z= 0.441 Chirality : 0.098 1.721 1365 Planarity : 0.004 0.043 1581 Dihedral : 5.154 20.399 1206 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 1.20 % Allowed : 6.67 % Favored : 92.13 % Rotamer: Outliers : 1.94 % Allowed : 8.87 % Favored : 89.19 % 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: -1.71 (0.26), residues: 1080 helix: 0.94 (0.27), residues: 402 sheet: -1.96 (0.30), residues: 267 loop : -2.65 (0.26), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 145 HIS 0.004 0.001 HIS B 160 PHE 0.010 0.001 PHE A 367 TYR 0.007 0.001 TYR C 279 ARG 0.003 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.02691 ( 409) hydrogen bonds : angle 4.80433 ( 1215) SS BOND : bond 0.00541 ( 12) SS BOND : angle 0.83674 ( 24) covalent geometry : bond 0.00293 ( 9018) covalent geometry : angle 0.81122 (12252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8038 (mmt) cc_final: 0.7797 (mmt) REVERT: A 145 TRP cc_start: 0.7476 (m100) cc_final: 0.6494 (m-10) REVERT: A 278 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: A 292 TYR cc_start: 0.7621 (m-10) cc_final: 0.7387 (m-10) REVERT: A 326 ASP cc_start: 0.8092 (t70) cc_final: 0.7581 (m-30) REVERT: B 76 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.5933 (mpp) REVERT: B 100 ILE cc_start: 0.7726 (mm) cc_final: 0.7234 (pt) REVERT: B 119 MET cc_start: 0.7997 (mmt) cc_final: 0.7672 (mmt) REVERT: B 129 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7857 (mtpp) REVERT: B 166 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.5522 (pt) REVERT: B 220 ARG cc_start: 0.7608 (pmm150) cc_final: 0.7107 (mmt-90) outliers start: 19 outliers final: 6 residues processed: 110 average time/residue: 1.8984 time to fit residues: 226.1421 Evaluate side-chains 100 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 258 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 0.0270 chunk 107 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.214993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.177537 restraints weight = 23173.477| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.77 r_work: 0.3860 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9030 Z= 0.119 Angle : 0.802 19.375 12276 Z= 0.435 Chirality : 0.098 1.718 1365 Planarity : 0.004 0.039 1581 Dihedral : 5.097 35.590 1206 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 1.20 % Allowed : 6.85 % Favored : 91.94 % Rotamer: Outliers : 1.94 % Allowed : 11.01 % Favored : 87.05 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.51 (0.26), residues: 1080 helix: 1.17 (0.28), residues: 402 sheet: -1.83 (0.31), residues: 264 loop : -2.63 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.004 0.001 HIS A 160 PHE 0.010 0.001 PHE A 367 TYR 0.006 0.001 TYR C 246 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.02480 ( 409) hydrogen bonds : angle 4.56089 ( 1215) SS BOND : bond 0.00596 ( 12) SS BOND : angle 0.85742 ( 24) covalent geometry : bond 0.00283 ( 9018) covalent geometry : angle 0.80201 (12252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.6873 (mmt) cc_final: 0.6606 (mmt) REVERT: A 119 MET cc_start: 0.7988 (mmt) cc_final: 0.7767 (mmt) REVERT: A 326 ASP cc_start: 0.8067 (t70) cc_final: 0.7567 (m-30) REVERT: B 76 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.5810 (mpp) REVERT: B 100 ILE cc_start: 0.7804 (mm) cc_final: 0.7354 (pt) REVERT: B 111 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6918 (mm110) REVERT: B 128 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.6390 (mpm) REVERT: B 129 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7819 (mtpp) REVERT: B 166 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.5757 (pt) REVERT: B 220 ARG cc_start: 0.7638 (pmm150) cc_final: 0.7185 (mmt-90) outliers start: 19 outliers final: 7 residues processed: 106 average time/residue: 1.8857 time to fit residues: 216.8965 Evaluate side-chains 102 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 341 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** B 55 GLN ** 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 = 0.4355 r_free = 0.4355 target = 0.211732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.173461 restraints weight = 23257.118| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.77 r_work: 0.3815 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9030 Z= 0.164 Angle : 0.823 18.895 12276 Z= 0.447 Chirality : 0.098 1.724 1365 Planarity : 0.004 0.036 1581 Dihedral : 5.175 29.411 1206 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 1.20 % Allowed : 7.31 % Favored : 91.48 % Rotamer: Outliers : 2.04 % Allowed : 11.62 % Favored : 86.34 % 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: -1.51 (0.26), residues: 1080 helix: 1.15 (0.27), residues: 402 sheet: -1.81 (0.32), residues: 264 loop : -2.63 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 145 HIS 0.007 0.001 HIS A 160 PHE 0.013 0.001 PHE A 367 TYR 0.006 0.001 TYR A 279 ARG 0.003 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.02572 ( 409) hydrogen bonds : angle 4.57042 ( 1215) SS BOND : bond 0.00490 ( 12) SS BOND : angle 1.40989 ( 24) covalent geometry : bond 0.00393 ( 9018) covalent geometry : angle 0.82118 (12252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: A 274 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8247 (m) REVERT: A 326 ASP cc_start: 0.8153 (t70) cc_final: 0.7577 (m-30) REVERT: B 76 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.5883 (mpp) REVERT: B 100 ILE cc_start: 0.7940 (mm) cc_final: 0.7553 (pt) REVERT: B 111 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7066 (mm110) REVERT: B 166 ILE cc_start: 0.7086 (OUTLIER) cc_final: 0.6167 (pt) REVERT: B 220 ARG cc_start: 0.7664 (pmm150) cc_final: 0.7175 (mmt-90) REVERT: C 100 ILE cc_start: 0.8096 (mm) cc_final: 0.7714 (pt) REVERT: C 111 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7064 (mm-40) outliers start: 20 outliers final: 8 residues processed: 105 average time/residue: 1.9316 time to fit residues: 220.1652 Evaluate side-chains 101 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 341 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** 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 = 0.4353 r_free = 0.4353 target = 0.211736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.174470 restraints weight = 23124.600| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.75 r_work: 0.3826 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9030 Z= 0.135 Angle : 0.806 19.243 12276 Z= 0.436 Chirality : 0.098 1.723 1365 Planarity : 0.004 0.033 1581 Dihedral : 5.039 27.162 1206 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 1.20 % Allowed : 6.94 % Favored : 91.85 % Rotamer: Outliers : 2.24 % Allowed : 12.13 % Favored : 85.63 % 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: -1.36 (0.26), residues: 1080 helix: 1.35 (0.28), residues: 402 sheet: -1.78 (0.32), residues: 264 loop : -2.59 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 145 HIS 0.005 0.001 HIS A 160 PHE 0.013 0.001 PHE A 367 TYR 0.005 0.001 TYR C 246 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.02436 ( 409) hydrogen bonds : angle 4.41140 ( 1215) SS BOND : bond 0.00471 ( 12) SS BOND : angle 1.13674 ( 24) covalent geometry : bond 0.00324 ( 9018) covalent geometry : angle 0.80520 (12252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8109 (m) REVERT: A 326 ASP cc_start: 0.8093 (t70) cc_final: 0.7563 (m-30) REVERT: A 398 LEU cc_start: 0.4544 (OUTLIER) cc_final: 0.4075 (tp) REVERT: B 76 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.5990 (mpp) REVERT: B 100 ILE cc_start: 0.7868 (mm) cc_final: 0.7535 (pt) REVERT: B 111 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7097 (mm110) REVERT: B 166 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6484 (pt) REVERT: C 100 ILE cc_start: 0.8073 (mm) cc_final: 0.7765 (pt) REVERT: C 111 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7131 (mm-40) REVERT: C 340 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7451 (mtpt) outliers start: 22 outliers final: 7 residues processed: 106 average time/residue: 1.8727 time to fit residues: 215.1497 Evaluate side-chains 102 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 341 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 76 optimal weight: 0.0980 chunk 99 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.212713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.174977 restraints weight = 23159.331| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.78 r_work: 0.3835 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9030 Z= 0.121 Angle : 0.796 19.419 12276 Z= 0.431 Chirality : 0.097 1.719 1365 Planarity : 0.004 0.034 1581 Dihedral : 4.959 24.663 1206 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 1.11 % Allowed : 7.13 % Favored : 91.76 % Rotamer: Outliers : 2.04 % Allowed : 12.95 % Favored : 85.02 % Cbeta Deviations : 0.19 % 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: -1.31 (0.26), residues: 1080 helix: 1.43 (0.28), residues: 402 sheet: -1.77 (0.32), residues: 264 loop : -2.59 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.004 0.001 HIS A 160 PHE 0.013 0.001 PHE A 367 TYR 0.006 0.001 TYR C 246 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.02340 ( 409) hydrogen bonds : angle 4.32000 ( 1215) SS BOND : bond 0.00451 ( 12) SS BOND : angle 1.08694 ( 24) covalent geometry : bond 0.00292 ( 9018) covalent geometry : angle 0.79556 (12252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.5043 (OUTLIER) cc_final: 0.4276 (mp10) REVERT: A 274 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8057 (m) REVERT: A 398 LEU cc_start: 0.4933 (OUTLIER) cc_final: 0.4499 (tp) REVERT: B 73 GLN cc_start: 0.4984 (OUTLIER) cc_final: 0.3362 (mp10) REVERT: B 76 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.5944 (mpp) REVERT: B 100 ILE cc_start: 0.7845 (mm) cc_final: 0.7513 (pt) REVERT: B 111 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7083 (mm110) REVERT: B 166 ILE cc_start: 0.6848 (OUTLIER) cc_final: 0.6435 (pt) REVERT: C 100 ILE cc_start: 0.8047 (mm) cc_final: 0.7723 (pt) REVERT: C 340 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7429 (mtpt) outliers start: 20 outliers final: 9 residues processed: 103 average time/residue: 1.9133 time to fit residues: 213.5834 Evaluate side-chains 103 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 233 HIS Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 341 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** 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 = 0.4333 r_free = 0.4333 target = 0.209407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.170925 restraints weight = 23060.261| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.77 r_work: 0.3775 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9030 Z= 0.194 Angle : 0.828 18.628 12276 Z= 0.450 Chirality : 0.099 1.728 1365 Planarity : 0.004 0.042 1581 Dihedral : 5.194 25.850 1206 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 1.11 % Allowed : 8.33 % Favored : 90.56 % Rotamer: Outliers : 2.55 % Allowed : 12.54 % Favored : 84.91 % 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: -1.43 (0.26), residues: 1080 helix: 1.31 (0.27), residues: 402 sheet: -1.85 (0.32), residues: 264 loop : -2.64 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 145 HIS 0.007 0.002 HIS A 160 PHE 0.017 0.002 PHE A 367 TYR 0.007 0.001 TYR A 279 ARG 0.002 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.02611 ( 409) hydrogen bonds : angle 4.50340 ( 1215) SS BOND : bond 0.00536 ( 12) SS BOND : angle 1.34848 ( 24) covalent geometry : bond 0.00467 ( 9018) covalent geometry : angle 0.82702 (12252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.4925 (OUTLIER) cc_final: 0.4172 (mp10) REVERT: A 274 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8013 (m) REVERT: B 100 ILE cc_start: 0.7981 (mm) cc_final: 0.7669 (pt) REVERT: B 128 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6629 (mpm) REVERT: B 166 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6632 (pt) REVERT: C 100 ILE cc_start: 0.8112 (mm) cc_final: 0.7842 (pt) REVERT: C 340 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7587 (mtpt) outliers start: 25 outliers final: 9 residues processed: 104 average time/residue: 1.8820 time to fit residues: 211.7929 Evaluate side-chains 101 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 233 HIS Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 341 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 0.0870 chunk 77 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 0.0060 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** 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 = 0.4361 r_free = 0.4361 target = 0.212590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.175152 restraints weight = 22935.795| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.75 r_work: 0.3837 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9030 Z= 0.114 Angle : 0.801 19.635 12276 Z= 0.433 Chirality : 0.097 1.719 1365 Planarity : 0.004 0.033 1581 Dihedral : 5.007 24.651 1206 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 1.11 % Allowed : 6.30 % Favored : 92.59 % Rotamer: Outliers : 1.33 % Allowed : 14.48 % Favored : 84.20 % Cbeta Deviations : 0.10 % 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: -1.17 (0.26), residues: 1080 helix: 1.55 (0.28), residues: 399 sheet: -1.59 (0.32), residues: 252 loop : -2.57 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.004 0.001 HIS B 160 PHE 0.009 0.001 PHE A 367 TYR 0.006 0.001 TYR C 246 ARG 0.002 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.02330 ( 409) hydrogen bonds : angle 4.31327 ( 1215) SS BOND : bond 0.00469 ( 12) SS BOND : angle 1.33496 ( 24) covalent geometry : bond 0.00275 ( 9018) covalent geometry : angle 0.79927 (12252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.7928 (m) REVERT: B 100 ILE cc_start: 0.7882 (mm) cc_final: 0.7586 (pt) REVERT: B 166 ILE cc_start: 0.7022 (OUTLIER) cc_final: 0.6773 (pt) REVERT: B 349 GLU cc_start: 0.8556 (pm20) cc_final: 0.8266 (mm-30) REVERT: C 100 ILE cc_start: 0.8040 (mm) cc_final: 0.7757 (pt) REVERT: C 340 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7500 (mtpt) outliers start: 13 outliers final: 8 residues processed: 99 average time/residue: 1.9290 time to fit residues: 207.1470 Evaluate side-chains 101 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 233 HIS Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 341 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 0.0270 chunk 68 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 264 ASN C 113 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.211962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.174161 restraints weight = 23117.359| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.76 r_work: 0.3824 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9030 Z= 0.137 Angle : 0.815 19.281 12276 Z= 0.440 Chirality : 0.098 1.718 1365 Planarity : 0.004 0.034 1581 Dihedral : 5.120 35.235 1206 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 1.11 % Allowed : 7.41 % Favored : 91.48 % Rotamer: Outliers : 1.22 % Allowed : 14.88 % Favored : 83.89 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.23 (0.26), residues: 1080 helix: 1.55 (0.27), residues: 399 sheet: -1.64 (0.32), residues: 252 loop : -2.65 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.005 0.001 HIS B 160 PHE 0.016 0.001 PHE A 367 TYR 0.012 0.001 TYR C 292 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.02351 ( 409) hydrogen bonds : angle 4.31003 ( 1215) SS BOND : bond 0.00514 ( 12) SS BOND : angle 1.45925 ( 24) covalent geometry : bond 0.00333 ( 9018) covalent geometry : angle 0.81283 (12252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.7884 (m) REVERT: B 100 ILE cc_start: 0.7869 (mm) cc_final: 0.7571 (pt) REVERT: C 100 ILE cc_start: 0.8063 (mm) cc_final: 0.7772 (pt) REVERT: C 340 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7495 (mtpt) outliers start: 12 outliers final: 8 residues processed: 99 average time/residue: 1.9234 time to fit residues: 206.2916 Evaluate side-chains 98 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 233 HIS Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 341 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN ** C 177 GLN ** 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 = 0.4378 r_free = 0.4378 target = 0.214341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.176697 restraints weight = 22988.408| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.78 r_work: 0.3809 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9030 Z= 0.111 Angle : 0.796 19.668 12276 Z= 0.430 Chirality : 0.097 1.717 1365 Planarity : 0.004 0.034 1581 Dihedral : 4.919 28.553 1206 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 1.11 % Allowed : 6.48 % Favored : 92.41 % Rotamer: Outliers : 1.22 % Allowed : 14.88 % Favored : 83.89 % Cbeta Deviations : 0.29 % 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: -1.14 (0.26), residues: 1080 helix: 1.66 (0.28), residues: 399 sheet: -1.64 (0.32), residues: 252 loop : -2.59 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.004 0.001 HIS B 160 PHE 0.010 0.001 PHE A 367 TYR 0.011 0.001 TYR B 265 ARG 0.002 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.02243 ( 409) hydrogen bonds : angle 4.19551 ( 1215) SS BOND : bond 0.00426 ( 12) SS BOND : angle 1.35690 ( 24) covalent geometry : bond 0.00272 ( 9018) covalent geometry : angle 0.79425 (12252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10358.24 seconds wall clock time: 177 minutes 48.43 seconds (10668.43 seconds total)