Starting phenix.real_space_refine on Sat May 17 17:05:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymu_39408/05_2025/8ymu_39408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymu_39408/05_2025/8ymu_39408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ymu_39408/05_2025/8ymu_39408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymu_39408/05_2025/8ymu_39408.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymu_39408/05_2025/8ymu_39408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymu_39408/05_2025/8ymu_39408.cif" } resolution = 2.89 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= 0.052 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 18 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: 8.19, per 1000 atoms: 0.51 Number of scatterers: 15975 At special positions: 0 Unit cell: (99.51, 94.86, 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=2.05 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=2.03 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=2.03 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: 4.43 Conformation dependent library (CDL) restraints added in 1.4 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: 31 helices and 12 sheets defined 37.8% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 53 through 83 removed outlier: 3.737A pdb=" N CYS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 129 through 135 removed outlier: 3.692A pdb=" N LEU A 133 " --> pdb=" O PHE A 130 " (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 Processing helix chain 'A' and resid 313 through 329 removed outlier: 3.535A pdb=" N LYS A 319 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 402 through 414 Processing helix chain 'B' and resid 54 through 83 removed outlier: 3.713A pdb=" N CYS B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 129 through 135 removed outlier: 3.668A pdb=" N LEU B 133 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.838A pdb=" N SER B 148 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 239 removed outlier: 4.146A pdb=" N SER B 237 " --> pdb=" O HIS B 233 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 275 through 296 Processing helix chain 'B' and resid 313 through 329 removed outlier: 3.587A pdb=" N LYS B 319 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 398 removed outlier: 3.572A pdb=" N PHE B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 414 Processing helix chain 'C' and resid 54 through 83 removed outlier: 3.656A pdb=" N CYS C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 129 through 135 removed outlier: 3.542A pdb=" N LEU C 133 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 134 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 135 " --> pdb=" O ASP C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 147 Processing helix chain 'C' and resid 233 through 239 removed outlier: 4.105A pdb=" N SER C 237 " --> pdb=" O HIS C 233 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 275 through 296 Processing helix chain 'C' and resid 313 through 329 removed outlier: 3.585A pdb=" N LYS C 319 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 396 Processing helix chain 'C' and resid 402 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 94 removed outlier: 14.486A pdb=" N TYR A 371 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N ILE A 258 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N GLN A 373 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE A 260 " --> pdb=" O GLN A 373 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA A 375 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN A 262 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLU A 377 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN A 264 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N LEU A 379 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE A 254 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N TYR A 366 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE A 256 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 361 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 5.242A 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: 14.486A pdb=" N TYR A 371 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N ILE A 258 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N GLN A 373 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE A 260 " --> pdb=" O GLN A 373 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA A 375 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN A 262 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLU A 377 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN A 264 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N LEU A 379 " --> pdb=" O ASN A 264 " (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: 7.177A pdb=" N GLN A 187 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 94 removed outlier: 14.434A pdb=" N TYR B 371 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N ILE B 258 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N GLN B 373 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE B 260 " --> pdb=" O GLN B 373 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ALA B 375 " --> pdb=" O PHE B 260 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN B 262 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLU B 377 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN B 264 " --> pdb=" O GLU B 377 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N LEU B 379 " --> pdb=" O ASN B 264 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE B 254 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR B 366 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE B 256 " --> pdb=" O TYR B 366 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 361 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 5.253A 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: 14.434A pdb=" N TYR B 371 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N ILE B 258 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N GLN B 373 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE B 260 " --> pdb=" O GLN B 373 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ALA B 375 " --> pdb=" O PHE B 260 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN B 262 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLU B 377 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN B 264 " --> pdb=" O GLU B 377 " (cutoff:3.500A) removed outlier: 8.720A 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: 7.220A pdb=" N GLN B 187 " --> pdb=" O PRO B 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 94 removed outlier: 14.396A pdb=" N TYR C 371 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ILE C 258 " --> pdb=" O TYR C 371 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N GLN C 373 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE C 260 " --> pdb=" O GLN C 373 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA C 375 " --> pdb=" O PHE C 260 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN C 262 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLU C 377 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN C 264 " --> pdb=" O GLU C 377 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N LEU C 379 " --> pdb=" O ASN C 264 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE C 254 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TYR C 366 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE C 256 " --> pdb=" O TYR C 366 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR C 170 " --> pdb=" O GLU C 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 86 through 94 removed outlier: 14.396A pdb=" N TYR C 371 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ILE C 258 " --> pdb=" O TYR C 371 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N GLN C 373 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE C 260 " --> pdb=" O GLN C 373 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA C 375 " --> pdb=" O PHE C 260 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN C 262 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLU C 377 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN C 264 " --> pdb=" O GLU C 377 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N LEU C 379 " --> pdb=" O ASN C 264 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 255 " --> pdb=" O MET C 351 " (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: 7.251A pdb=" N GLN C 187 " --> pdb=" O PRO C 107 " (cutoff:3.500A) 433 hydrogen bonds defined for protein. 1218 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: 6.10 Time building geometry restraints manager: 5.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7170 1.03 - 1.23: 22 1.23 - 1.42: 3880 1.42 - 1.62: 5038 1.62 - 1.81: 81 Bond restraints: 16191 Sorted by residual: bond pdb=" CA ARG A 99 " pdb=" CB ARG A 99 " ideal model delta sigma weight residual 1.525 1.545 -0.019 1.29e-02 6.01e+03 2.25e+00 bond pdb=" CA ARG C 99 " pdb=" CB ARG C 99 " ideal model delta sigma weight residual 1.525 1.541 -0.016 1.25e-02 6.40e+03 1.62e+00 bond pdb=" N ASP C 275 " pdb=" CA ASP C 275 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.14e+00 bond pdb=" CA GLY A 162 " pdb=" C GLY A 162 " ideal model delta sigma weight residual 1.516 1.506 0.010 1.05e-02 9.07e+03 9.42e-01 bond pdb=" CA GLU A 355 " pdb=" CB GLU A 355 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.35e-02 5.49e+03 7.73e-01 ... (remaining 16186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.10: 28461 11.10 - 22.19: 7 22.19 - 33.29: 35 33.29 - 44.39: 21 44.39 - 55.49: 6 Bond angle restraints: 28530 Sorted by residual: angle pdb=" C THR C 114 " pdb=" N ILE C 115 " pdb=" H ILE C 115 " ideal model delta sigma weight residual 124.33 68.84 55.49 3.00e+00 1.11e-01 3.42e+02 angle pdb=" C THR A 114 " pdb=" N ILE A 115 " pdb=" H ILE A 115 " ideal model delta sigma weight residual 123.83 68.79 55.05 3.00e+00 1.11e-01 3.37e+02 angle pdb=" C THR B 114 " pdb=" N ILE B 115 " pdb=" H ILE B 115 " ideal model delta sigma weight residual 123.83 68.84 55.00 3.00e+00 1.11e-01 3.36e+02 angle pdb=" CA ILE C 115 " pdb=" N ILE C 115 " pdb=" H ILE C 115 " ideal model delta sigma weight residual 114.03 59.49 54.54 3.00e+00 1.11e-01 3.30e+02 angle pdb=" CA ILE A 115 " pdb=" N ILE A 115 " pdb=" H ILE A 115 " ideal model delta sigma weight residual 113.53 59.68 53.86 3.00e+00 1.11e-01 3.22e+02 ... (remaining 28525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 7013 16.85 - 33.70: 631 33.70 - 50.55: 142 50.55 - 67.40: 52 67.40 - 84.25: 22 Dihedral angle restraints: 7860 sinusoidal: 4116 harmonic: 3744 Sorted by residual: dihedral pdb=" CA CYS A 337 " pdb=" C CYS A 337 " pdb=" N LYS A 338 " pdb=" CA LYS A 338 " ideal model delta harmonic sigma weight residual -180.00 -144.55 -35.45 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA CYS C 337 " pdb=" C CYS C 337 " pdb=" N LYS C 338 " pdb=" CA LYS C 338 " ideal model delta harmonic sigma weight residual 180.00 -146.48 -33.52 0 5.00e+00 4.00e-02 4.49e+01 dihedral pdb=" CA CYS B 337 " pdb=" C CYS B 337 " pdb=" N LYS B 338 " pdb=" CA LYS B 338 " ideal model delta harmonic sigma weight residual -180.00 -146.49 -33.51 0 5.00e+00 4.00e-02 4.49e+01 ... (remaining 7857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1230 0.078 - 0.157: 126 0.157 - 0.235: 0 0.235 - 0.313: 0 0.313 - 0.391: 9 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CA PRO A 249 " pdb=" N PRO A 249 " pdb=" C PRO A 249 " pdb=" CB PRO A 249 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA PRO B 249 " pdb=" N PRO B 249 " pdb=" C PRO B 249 " pdb=" CB PRO B 249 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CA PRO C 249 " pdb=" N PRO C 249 " pdb=" C PRO C 249 " pdb=" CB PRO C 249 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 1362 not shown) Planarity restraints: 2436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 274 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C VAL C 274 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL C 274 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP C 275 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 252 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 253 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 127 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.01e+00 pdb=" C LYS B 127 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS B 127 " -0.013 2.00e-02 2.50e+03 pdb=" N MET B 128 " -0.012 2.00e-02 2.50e+03 ... (remaining 2433 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 197 2.04 - 2.68: 22421 2.68 - 3.32: 44095 3.32 - 3.96: 60095 3.96 - 4.60: 92045 Nonbonded interactions: 218853 Sorted by model distance: nonbonded pdb=" H ILE B 115 " pdb=" HA ILE B 115 " model vdw 1.397 1.816 nonbonded pdb=" H ILE A 115 " pdb=" HA ILE A 115 " model vdw 1.397 1.816 nonbonded pdb=" H ILE C 115 " pdb=" HA ILE C 115 " model vdw 1.418 1.816 nonbonded pdb=" H PHE A 354 " pdb=" HA PHE A 354 " model vdw 1.574 1.816 nonbonded pdb=" H PHE C 354 " pdb=" HA PHE C 354 " model vdw 1.576 1.816 ... (remaining 218848 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: 0.04 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: 1.200 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: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.730 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 : 0.003 0.029 9030 Z= 0.166 Angle : 0.720 8.899 12276 Z= 0.440 Chirality : 0.053 0.391 1365 Planarity : 0.004 0.052 1581 Dihedral : 13.504 84.254 3306 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.57 % Favored : 92.87 % Rotamer: Outliers : 0.20 % Allowed : 0.41 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.91 (0.26), residues: 1080 helix: 0.09 (0.29), residues: 357 sheet: -0.88 (0.32), residues: 276 loop : -2.65 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 145 HIS 0.009 0.001 HIS B 229 PHE 0.011 0.001 PHE B 256 TYR 0.011 0.001 TYR A 292 ARG 0.005 0.001 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.15644 ( 409) hydrogen bonds : angle 6.79308 ( 1218) SS BOND : bond 0.00740 ( 12) SS BOND : angle 1.88804 ( 24) covalent geometry : bond 0.00324 ( 9018) covalent geometry : angle 0.71557 (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 140 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6464 (mpp) cc_final: 0.6186 (mpt) REVERT: C 119 MET cc_start: 0.6742 (mpp) cc_final: 0.6415 (mpt) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 2.0592 time to fit residues: 309.6565 Evaluate side-chains 107 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 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: 0.8980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 177 GLN C 296 GLN C 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.164060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.128763 restraints weight = 24865.751| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.66 r_work: 0.3278 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9030 Z= 0.147 Angle : 0.648 13.184 12276 Z= 0.361 Chirality : 0.055 0.417 1365 Planarity : 0.004 0.046 1581 Dihedral : 5.592 30.659 1206 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.74 % Favored : 93.70 % Rotamer: Outliers : 1.43 % Allowed : 9.38 % Favored : 89.19 % Cbeta Deviations : 0.00 % 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: -1.58 (0.26), residues: 1080 helix: 0.52 (0.29), residues: 369 sheet: -0.78 (0.34), residues: 255 loop : -2.57 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 145 HIS 0.006 0.001 HIS B 231 PHE 0.011 0.001 PHE B 256 TYR 0.008 0.001 TYR C 170 ARG 0.006 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 409) hydrogen bonds : angle 4.93814 ( 1218) SS BOND : bond 0.00599 ( 12) SS BOND : angle 1.69601 ( 24) covalent geometry : bond 0.00338 ( 9018) covalent geometry : angle 0.64460 (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 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6844 (mpp) cc_final: 0.6564 (mmm) REVERT: B 80 ASP cc_start: 0.7580 (t0) cc_final: 0.7283 (t0) REVERT: B 118 ASP cc_start: 0.7327 (m-30) cc_final: 0.6403 (m-30) REVERT: C 119 MET cc_start: 0.6978 (mpp) cc_final: 0.6522 (mpt) REVERT: C 129 LYS cc_start: 0.8152 (mmtp) cc_final: 0.7345 (mmmt) REVERT: C 140 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7532 (p0) outliers start: 14 outliers final: 3 residues processed: 119 average time/residue: 1.8921 time to fit residues: 243.8803 Evaluate side-chains 101 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 140 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 77 HIS A 177 GLN A 330 ASN B 95 GLN B 330 ASN C 95 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.162746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.127694 restraints weight = 24656.379| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.64 r_work: 0.3266 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 0.026 9030 Z= 0.147 Angle : 0.619 12.761 12276 Z= 0.343 Chirality : 0.054 0.418 1365 Planarity : 0.004 0.040 1581 Dihedral : 5.457 26.942 1206 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.02 % Favored : 93.70 % Rotamer: Outliers : 1.83 % Allowed : 10.09 % Favored : 88.07 % 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: 0.81 (0.29), residues: 369 sheet: -0.83 (0.31), residues: 279 loop : -2.50 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 145 HIS 0.003 0.001 HIS B 231 PHE 0.010 0.001 PHE B 205 TYR 0.005 0.001 TYR C 279 ARG 0.003 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02886 ( 409) hydrogen bonds : angle 4.62950 ( 1218) SS BOND : bond 0.00556 ( 12) SS BOND : angle 1.60492 ( 24) covalent geometry : bond 0.00341 ( 9018) covalent geometry : angle 0.61507 (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 124 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.7990 (t0) cc_final: 0.7604 (t0) REVERT: A 293 GLU cc_start: 0.7841 (tt0) cc_final: 0.7549 (tt0) REVERT: B 99 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6812 (mmt90) REVERT: B 118 ASP cc_start: 0.7400 (m-30) cc_final: 0.6541 (m-30) REVERT: B 119 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6308 (mpt) REVERT: B 289 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: C 119 MET cc_start: 0.6838 (mpp) cc_final: 0.6474 (mpt) REVERT: C 140 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7539 (p0) outliers start: 18 outliers final: 6 residues processed: 114 average time/residue: 1.7713 time to fit residues: 220.5975 Evaluate side-chains 109 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 140 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 177 GLN A 330 ASN B 77 HIS B 111 GLN B 177 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.163008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127882 restraints weight = 24813.512| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.66 r_work: 0.3267 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9030 Z= 0.128 Angle : 0.598 12.765 12276 Z= 0.332 Chirality : 0.054 0.418 1365 Planarity : 0.004 0.038 1581 Dihedral : 5.260 23.894 1206 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.11 % Favored : 93.61 % Rotamer: Outliers : 1.83 % Allowed : 10.91 % Favored : 87.26 % 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: -1.15 (0.26), residues: 1080 helix: 1.05 (0.29), residues: 369 sheet: -0.71 (0.31), residues: 273 loop : -2.43 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 145 HIS 0.008 0.001 HIS B 231 PHE 0.009 0.001 PHE C 367 TYR 0.005 0.001 TYR A 239 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02527 ( 409) hydrogen bonds : angle 4.43132 ( 1218) SS BOND : bond 0.00500 ( 12) SS BOND : angle 1.41490 ( 24) covalent geometry : bond 0.00299 ( 9018) covalent geometry : angle 0.59508 (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 122 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7776 (tt0) cc_final: 0.7494 (tt0) REVERT: B 99 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6801 (mmt90) REVERT: B 102 GLU cc_start: 0.7643 (pp20) cc_final: 0.7332 (pt0) REVERT: B 118 ASP cc_start: 0.7446 (m-30) cc_final: 0.6626 (m-30) REVERT: B 119 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.6162 (mpt) REVERT: B 129 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7814 (mptt) REVERT: B 289 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: C 119 MET cc_start: 0.6828 (mpp) cc_final: 0.6400 (mpt) REVERT: C 140 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7477 (p0) REVERT: C 293 GLU cc_start: 0.7998 (tt0) cc_final: 0.7486 (pt0) outliers start: 18 outliers final: 6 residues processed: 114 average time/residue: 1.6973 time to fit residues: 211.3935 Evaluate side-chains 109 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 140 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 0.0040 chunk 77 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 177 GLN A 330 ASN B 177 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.155825 restraints weight = 24097.601| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.72 r_work: 0.3534 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9030 Z= 0.150 Angle : 0.605 12.697 12276 Z= 0.335 Chirality : 0.054 0.421 1365 Planarity : 0.004 0.039 1581 Dihedral : 5.235 22.296 1206 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.83 % Favored : 93.89 % Rotamer: Outliers : 2.65 % Allowed : 10.09 % Favored : 87.26 % 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: -0.97 (0.26), residues: 1080 helix: 1.31 (0.29), residues: 366 sheet: -0.69 (0.31), residues: 273 loop : -2.35 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 145 HIS 0.010 0.002 HIS B 231 PHE 0.010 0.001 PHE B 205 TYR 0.010 0.001 TYR C 292 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02545 ( 409) hydrogen bonds : angle 4.35938 ( 1218) SS BOND : bond 0.00566 ( 12) SS BOND : angle 1.60898 ( 24) covalent geometry : bond 0.00353 ( 9018) covalent geometry : angle 0.60185 (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 128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.7725 (m-30) cc_final: 0.6970 (m-30) REVERT: B 99 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6851 (mmt90) REVERT: B 102 GLU cc_start: 0.7696 (pp20) cc_final: 0.7380 (pt0) REVERT: B 118 ASP cc_start: 0.7727 (m-30) cc_final: 0.6882 (m-30) REVERT: B 154 ASN cc_start: 0.8026 (t0) cc_final: 0.7698 (t160) REVERT: B 289 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: B 342 GLU cc_start: 0.8277 (tt0) cc_final: 0.7988 (tt0) REVERT: C 140 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7653 (p0) outliers start: 26 outliers final: 9 residues processed: 119 average time/residue: 1.6763 time to fit residues: 218.3602 Evaluate side-chains 110 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 337 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 113 ASN A 177 GLN A 289 GLN A 330 ASN B 113 ASN B 177 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.190128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.155218 restraints weight = 23812.233| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.69 r_work: 0.3385 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9030 Z= 0.166 Angle : 0.622 12.551 12276 Z= 0.344 Chirality : 0.054 0.421 1365 Planarity : 0.004 0.039 1581 Dihedral : 5.303 21.922 1206 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.30 % Favored : 93.43 % Rotamer: Outliers : 2.55 % Allowed : 11.01 % Favored : 86.44 % 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: 1080 helix: 1.44 (0.29), residues: 366 sheet: -0.63 (0.31), residues: 273 loop : -2.31 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 145 HIS 0.008 0.002 HIS B 231 PHE 0.010 0.001 PHE B 205 TYR 0.006 0.001 TYR C 239 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02584 ( 409) hydrogen bonds : angle 4.36734 ( 1218) SS BOND : bond 0.00645 ( 12) SS BOND : angle 2.03492 ( 24) covalent geometry : bond 0.00391 ( 9018) covalent geometry : angle 0.61614 (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 128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.7789 (m-30) cc_final: 0.7033 (m-30) REVERT: B 99 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6854 (mmt90) REVERT: B 102 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7448 (pt0) REVERT: B 119 MET cc_start: 0.7042 (mmm) cc_final: 0.6455 (mpt) REVERT: B 129 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8100 (mptt) REVERT: B 289 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: B 290 ARG cc_start: 0.8200 (tpp-160) cc_final: 0.7840 (tpt90) REVERT: B 342 GLU cc_start: 0.8351 (tt0) cc_final: 0.8144 (tt0) REVERT: B 349 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: C 129 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7806 (mmtp) REVERT: C 140 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7641 (p0) outliers start: 25 outliers final: 11 residues processed: 116 average time/residue: 1.8279 time to fit residues: 231.6992 Evaluate side-chains 117 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 337 CYS 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: 1.9990 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 113 ASN A 177 GLN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN B 96 ASN B 113 ASN B 177 GLN C 177 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.179854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.143336 restraints weight = 24654.608| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.81 r_work: 0.3469 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9030 Z= 0.213 Angle : 0.660 12.642 12276 Z= 0.364 Chirality : 0.056 0.427 1365 Planarity : 0.004 0.042 1581 Dihedral : 5.539 24.101 1206 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.48 % Favored : 93.24 % Rotamer: Outliers : 2.96 % Allowed : 11.62 % Favored : 85.42 % 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: 1080 helix: 1.39 (0.29), residues: 366 sheet: -0.63 (0.31), residues: 273 loop : -2.25 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 145 HIS 0.015 0.002 HIS A 233 PHE 0.013 0.002 PHE C 116 TYR 0.009 0.001 TYR C 292 ARG 0.002 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.02860 ( 409) hydrogen bonds : angle 4.51729 ( 1218) SS BOND : bond 0.00658 ( 12) SS BOND : angle 2.42367 ( 24) covalent geometry : bond 0.00507 ( 9018) covalent geometry : angle 0.65164 (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 137 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: B 99 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6851 (mmt90) REVERT: B 102 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7676 (pt0) REVERT: B 154 ASN cc_start: 0.7979 (t0) cc_final: 0.7285 (t0) REVERT: B 289 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: B 290 ARG cc_start: 0.8334 (tpp-160) cc_final: 0.7914 (tpt90) REVERT: B 349 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: C 140 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7701 (p0) outliers start: 29 outliers final: 10 residues processed: 127 average time/residue: 1.8623 time to fit residues: 257.2110 Evaluate side-chains 114 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 337 CYS 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: 1.9990 chunk 91 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 40.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 113 ASN A 177 GLN A 330 ASN B 113 ASN B 177 GLN C 177 GLN C 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.181297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144762 restraints weight = 24564.201| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.81 r_work: 0.3489 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9030 Z= 0.177 Angle : 0.654 12.619 12276 Z= 0.360 Chirality : 0.055 0.437 1365 Planarity : 0.004 0.041 1581 Dihedral : 5.586 24.487 1206 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.48 % Favored : 93.24 % Rotamer: Outliers : 2.85 % Allowed : 12.54 % Favored : 84.61 % 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: 1080 helix: 1.50 (0.29), residues: 366 sheet: -0.66 (0.31), residues: 273 loop : -2.23 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 145 HIS 0.007 0.002 HIS A 233 PHE 0.011 0.001 PHE C 116 TYR 0.006 0.001 TYR C 239 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02638 ( 409) hydrogen bonds : angle 4.45526 ( 1218) SS BOND : bond 0.00586 ( 12) SS BOND : angle 3.21790 ( 24) covalent geometry : bond 0.00418 ( 9018) covalent geometry : angle 0.63933 (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 132 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: B 99 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6808 (mmt90) REVERT: B 102 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7610 (pt0) REVERT: B 129 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8091 (mptt) REVERT: B 154 ASN cc_start: 0.7982 (t0) cc_final: 0.7272 (t0) REVERT: B 289 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: B 290 ARG cc_start: 0.8306 (tpp-160) cc_final: 0.7882 (tpt90) REVERT: B 349 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: C 128 MET cc_start: 0.6787 (mtm) cc_final: 0.6304 (mmt) REVERT: C 140 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7666 (p0) outliers start: 28 outliers final: 12 residues processed: 121 average time/residue: 1.9892 time to fit residues: 260.2165 Evaluate side-chains 116 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 341 CYS Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 337 CYS 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: 1.9990 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 113 ASN A 177 GLN A 330 ASN B 96 ASN B 113 ASN B 177 GLN C 177 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.181690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144879 restraints weight = 24474.885| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.84 r_work: 0.3491 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2655 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= 0.165 Angle : 0.646 12.600 12276 Z= 0.355 Chirality : 0.055 0.437 1365 Planarity : 0.004 0.041 1581 Dihedral : 5.528 22.941 1206 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.67 % Favored : 93.06 % Rotamer: Outliers : 2.85 % Allowed : 12.54 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.26), residues: 1080 helix: 1.57 (0.29), residues: 366 sheet: -0.69 (0.31), residues: 273 loop : -2.22 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 145 HIS 0.007 0.002 HIS A 231 PHE 0.010 0.001 PHE C 116 TYR 0.006 0.001 TYR C 239 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02575 ( 409) hydrogen bonds : angle 4.43297 ( 1218) SS BOND : bond 0.00581 ( 12) SS BOND : angle 2.84512 ( 24) covalent geometry : bond 0.00389 ( 9018) covalent geometry : angle 0.63386 (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 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7826 (pt0) REVERT: B 99 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6799 (mmt90) REVERT: B 102 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7603 (pt0) REVERT: B 154 ASN cc_start: 0.7939 (t0) cc_final: 0.7224 (t0) REVERT: B 289 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: B 290 ARG cc_start: 0.8313 (tpp-160) cc_final: 0.7883 (tpt90) REVERT: B 349 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: C 128 MET cc_start: 0.6766 (mtm) cc_final: 0.6275 (mmt) REVERT: C 129 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7853 (mmtp) REVERT: C 140 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7633 (p0) outliers start: 28 outliers final: 14 residues processed: 116 average time/residue: 1.8499 time to fit residues: 233.2213 Evaluate side-chains 118 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 341 CYS Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 337 CYS 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: 1.9990 chunk 68 optimal weight: 1.9990 chunk 97 optimal weight: 0.0370 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 4 optimal weight: 0.6980 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 113 ASN A 177 GLN A 330 ASN B 113 ASN B 177 GLN C 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.184995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148964 restraints weight = 24469.467| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.84 r_work: 0.3541 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9030 Z= 0.108 Angle : 0.603 12.522 12276 Z= 0.332 Chirality : 0.054 0.424 1365 Planarity : 0.003 0.039 1581 Dihedral : 5.215 22.957 1206 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.83 % Favored : 93.89 % Rotamer: Outliers : 1.94 % Allowed : 13.56 % Favored : 84.51 % 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: -0.55 (0.26), residues: 1080 helix: 1.85 (0.29), residues: 366 sheet: -0.74 (0.32), residues: 270 loop : -2.07 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.007 0.001 HIS A 231 PHE 0.009 0.001 PHE B 256 TYR 0.006 0.001 TYR C 239 ARG 0.002 0.000 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.02173 ( 409) hydrogen bonds : angle 4.23948 ( 1218) SS BOND : bond 0.00422 ( 12) SS BOND : angle 2.08838 ( 24) covalent geometry : bond 0.00251 ( 9018) covalent geometry : angle 0.59619 (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 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: A 341 CYS cc_start: 0.6960 (OUTLIER) cc_final: 0.5614 (m) REVERT: A 342 GLU cc_start: 0.7670 (tt0) cc_final: 0.7434 (tt0) REVERT: B 99 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6833 (mmt90) REVERT: B 102 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7264 (pt0) REVERT: B 129 LYS cc_start: 0.8477 (mmtp) cc_final: 0.8085 (mptt) REVERT: B 154 ASN cc_start: 0.7957 (t0) cc_final: 0.7229 (t0) REVERT: B 289 GLN cc_start: 0.7716 (tt0) cc_final: 0.7448 (tm-30) REVERT: B 341 CYS cc_start: 0.6741 (OUTLIER) cc_final: 0.5424 (m) REVERT: C 128 MET cc_start: 0.6693 (mtm) cc_final: 0.6205 (mmt) REVERT: C 140 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7543 (p0) outliers start: 19 outliers final: 7 residues processed: 117 average time/residue: 1.7142 time to fit residues: 219.0572 Evaluate side-chains 112 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 341 CYS Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 337 CYS 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: 2.9990 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 94 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 113 ASN A 177 GLN A 330 ASN B 113 ASN B 177 GLN C 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.184360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.147748 restraints weight = 24429.029| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.86 r_work: 0.3527 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9030 Z= 0.123 Angle : 0.610 12.517 12276 Z= 0.335 Chirality : 0.054 0.429 1365 Planarity : 0.004 0.040 1581 Dihedral : 5.173 23.154 1206 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.74 % Favored : 93.98 % Rotamer: Outliers : 2.14 % Allowed : 13.46 % Favored : 84.40 % 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: -0.50 (0.26), residues: 1080 helix: 1.92 (0.29), residues: 366 sheet: -0.65 (0.32), residues: 273 loop : -2.13 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.006 0.001 HIS A 231 PHE 0.009 0.001 PHE B 256 TYR 0.007 0.001 TYR A 369 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02206 ( 409) hydrogen bonds : angle 4.19450 ( 1218) SS BOND : bond 0.00483 ( 12) SS BOND : angle 2.14946 ( 24) covalent geometry : bond 0.00290 ( 9018) covalent geometry : angle 0.60322 (12252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10147.82 seconds wall clock time: 174 minutes 11.18 seconds (10451.18 seconds total)