Starting phenix.real_space_refine on Sun Aug 24 01:12:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymu_39408/08_2025/8ymu_39408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymu_39408/08_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_39408/08_2025/8ymu_39408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymu_39408/08_2025/8ymu_39408.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymu_39408/08_2025/8ymu_39408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymu_39408/08_2025/8ymu_39408.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.83, per 1000 atoms: 0.18 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: 1.30 Conformation dependent library (CDL) restraints added in 384.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.48 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: 3.11 Time building geometry restraints manager: 1.85 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: 0.01 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: 1.080 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: 0.070 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.370 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.110 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG A 99 TYR 0.011 0.001 TYR A 292 PHE 0.011 0.001 PHE B 256 TRP 0.007 0.001 TRP B 145 HIS 0.009 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9018) covalent geometry : angle 0.71557 (12252) SS BOND : bond 0.00740 ( 12) SS BOND : angle 1.88804 ( 24) hydrogen bonds : bond 0.15644 ( 409) hydrogen bonds : angle 6.79308 ( 1218) *********************** 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 : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6464 (mpp) cc_final: 0.6187 (mpt) REVERT: C 119 MET cc_start: 0.6742 (mpp) cc_final: 0.6416 (mpt) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 0.9132 time to fit residues: 136.9366 Evaluate side-chains 108 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 330 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 95 GLN C 111 GLN C 177 GLN C 229 HIS C 296 GLN C 330 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.162231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.126747 restraints weight = 24719.916| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.65 r_work: 0.3249 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9030 Z= 0.178 Angle : 0.670 13.283 12276 Z= 0.372 Chirality : 0.055 0.420 1365 Planarity : 0.004 0.044 1581 Dihedral : 5.686 30.952 1206 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.65 % Favored : 93.80 % Rotamer: Outliers : 1.83 % Allowed : 8.87 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.26), residues: 1080 helix: 0.51 (0.29), residues: 366 sheet: -0.77 (0.32), residues: 276 loop : -2.68 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.008 0.001 TYR C 170 PHE 0.012 0.002 PHE C 367 TRP 0.012 0.002 TRP C 145 HIS 0.006 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9018) covalent geometry : angle 0.66486 (12252) SS BOND : bond 0.00692 ( 12) SS BOND : angle 1.94160 ( 24) hydrogen bonds : bond 0.03234 ( 409) hydrogen bonds : angle 4.97101 ( 1218) *********************** 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 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6891 (mpp) cc_final: 0.6600 (mmm) REVERT: A 154 ASN cc_start: 0.8065 (t0) cc_final: 0.7663 (t0) REVERT: B 99 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6779 (mmt90) REVERT: B 118 ASP cc_start: 0.7416 (m-30) cc_final: 0.6464 (m-30) REVERT: B 128 MET cc_start: 0.7227 (mmt) cc_final: 0.6949 (mmt) REVERT: C 119 MET cc_start: 0.6958 (mpp) cc_final: 0.6503 (mpt) REVERT: C 129 LYS cc_start: 0.8179 (mmtp) cc_final: 0.7369 (mmmt) REVERT: C 140 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7586 (p0) outliers start: 18 outliers final: 3 residues processed: 119 average time/residue: 1.0218 time to fit residues: 130.5280 Evaluate side-chains 103 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 99 ARG 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 13 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 330 ASN B 95 GLN B 330 ASN C 177 GLN C 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.162788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.127603 restraints weight = 24917.216| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.65 r_work: 0.3261 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9030 Z= 0.137 Angle : 0.612 12.725 12276 Z= 0.340 Chirality : 0.054 0.417 1365 Planarity : 0.004 0.040 1581 Dihedral : 5.472 26.555 1206 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.93 % Favored : 93.80 % Rotamer: Outliers : 1.63 % Allowed : 10.60 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.26), residues: 1080 helix: 0.84 (0.29), residues: 369 sheet: -0.86 (0.31), residues: 279 loop : -2.51 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.006 0.001 TYR A 292 PHE 0.010 0.001 PHE C 367 TRP 0.009 0.001 TRP C 145 HIS 0.005 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9018) covalent geometry : angle 0.60881 (12252) SS BOND : bond 0.00529 ( 12) SS BOND : angle 1.55242 ( 24) hydrogen bonds : bond 0.02810 ( 409) hydrogen bonds : angle 4.60017 ( 1218) *********************** 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 121 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.7943 (t0) cc_final: 0.7427 (t0) REVERT: A 293 GLU cc_start: 0.7907 (tt0) cc_final: 0.7642 (tt0) REVERT: B 99 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6809 (mmt90) REVERT: B 118 ASP cc_start: 0.7467 (m-30) cc_final: 0.6598 (m-30) REVERT: B 119 MET cc_start: 0.6427 (OUTLIER) cc_final: 0.6180 (mpt) REVERT: B 128 MET cc_start: 0.6948 (mmt) cc_final: 0.6548 (mmt) REVERT: B 289 GLN cc_start: 0.7486 (tt0) cc_final: 0.7230 (tm-30) REVERT: C 119 MET cc_start: 0.6837 (mpp) cc_final: 0.6425 (mpt) REVERT: C 140 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7505 (p0) REVERT: C 293 GLU cc_start: 0.7876 (tt0) cc_final: 0.7521 (tt0) outliers start: 16 outliers final: 6 residues processed: 114 average time/residue: 0.8069 time to fit residues: 100.4345 Evaluate side-chains 107 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 94 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 330 ASN B 77 HIS ** 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 = 0.4119 r_free = 0.4119 target = 0.187404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.152356 restraints weight = 23878.150| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.69 r_work: 0.3439 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9030 Z= 0.215 Angle : 0.661 12.716 12276 Z= 0.365 Chirality : 0.056 0.430 1365 Planarity : 0.005 0.042 1581 Dihedral : 5.610 24.686 1206 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.93 % Favored : 93.80 % Rotamer: Outliers : 3.26 % Allowed : 10.09 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.25), residues: 1080 helix: 0.80 (0.29), residues: 369 sheet: -0.87 (0.30), residues: 279 loop : -2.41 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 99 TYR 0.006 0.001 TYR A 346 PHE 0.013 0.002 PHE C 367 TRP 0.012 0.002 TRP C 145 HIS 0.012 0.002 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 9018) covalent geometry : angle 0.65543 (12252) SS BOND : bond 0.00721 ( 12) SS BOND : angle 2.08213 ( 24) hydrogen bonds : bond 0.03030 ( 409) hydrogen bonds : angle 4.65544 ( 1218) *********************** 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 135 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6940 (mmt90) REVERT: B 102 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7642 (pt0) REVERT: B 128 MET cc_start: 0.7259 (mmt) cc_final: 0.6983 (mmt) REVERT: B 129 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8193 (mptt) REVERT: B 154 ASN cc_start: 0.8051 (t0) cc_final: 0.7677 (t160) REVERT: B 289 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: B 290 ARG cc_start: 0.8272 (tpp-160) cc_final: 0.7912 (tpt90) REVERT: B 349 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: C 140 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7710 (p0) REVERT: C 154 ASN cc_start: 0.8133 (t0) cc_final: 0.7088 (t0) REVERT: C 293 GLU cc_start: 0.8175 (tt0) cc_final: 0.7747 (tt0) outliers start: 32 outliers final: 10 residues processed: 122 average time/residue: 0.7853 time to fit residues: 104.1032 Evaluate side-chains 112 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 189 ILE Chi-restraints excluded: chain A residue 211 SER 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 165 ILE 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 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 337 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 26 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 330 ASN B 113 ASN B 177 GLN C 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.187884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.152901 restraints weight = 23832.793| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.70 r_work: 0.3399 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9030 Z= 0.188 Angle : 0.639 12.601 12276 Z= 0.354 Chirality : 0.055 0.423 1365 Planarity : 0.004 0.041 1581 Dihedral : 5.610 23.999 1206 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.30 % Favored : 93.43 % Rotamer: Outliers : 2.65 % Allowed : 11.52 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.25), residues: 1080 helix: 1.02 (0.29), residues: 366 sheet: -0.80 (0.30), residues: 273 loop : -2.35 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 99 TYR 0.006 0.001 TYR C 239 PHE 0.011 0.001 PHE C 367 TRP 0.010 0.001 TRP A 145 HIS 0.009 0.002 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 9018) covalent geometry : angle 0.63404 (12252) SS BOND : bond 0.00646 ( 12) SS BOND : angle 1.96787 ( 24) hydrogen bonds : bond 0.02812 ( 409) hydrogen bonds : angle 4.56715 ( 1218) *********************** 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 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.385 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: 0.8138 (OUTLIER) cc_final: 0.7833 (pt0) REVERT: B 99 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6826 (mmt90) REVERT: B 102 GLU cc_start: 0.7888 (pp20) cc_final: 0.7598 (pt0) REVERT: B 119 MET cc_start: 0.7044 (mmm) cc_final: 0.6511 (mpt) REVERT: B 128 MET cc_start: 0.7253 (mmt) cc_final: 0.7000 (mmt) REVERT: B 289 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: B 290 ARG cc_start: 0.8295 (tpp-160) cc_final: 0.7908 (tpt90) REVERT: B 349 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: C 140 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7656 (p0) REVERT: C 293 GLU cc_start: 0.8249 (tt0) cc_final: 0.7823 (tt0) outliers start: 26 outliers final: 10 residues processed: 115 average time/residue: 0.7603 time to fit residues: 95.0239 Evaluate side-chains 107 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 B residue 99 ARG Chi-restraints excluded: chain B residue 114 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 330 ASN B 113 ASN B 177 GLN C 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.189384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.155656 restraints weight = 24533.766| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.66 r_work: 0.3612 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9030 Z= 0.140 Angle : 0.614 12.593 12276 Z= 0.340 Chirality : 0.054 0.430 1365 Planarity : 0.004 0.039 1581 Dihedral : 5.458 23.854 1206 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.20 % Favored : 93.52 % Rotamer: Outliers : 2.65 % Allowed : 12.03 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.26), residues: 1080 helix: 1.35 (0.29), residues: 366 sheet: -0.77 (0.31), residues: 273 loop : -2.25 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 268 TYR 0.006 0.001 TYR C 239 PHE 0.009 0.001 PHE C 367 TRP 0.009 0.001 TRP A 145 HIS 0.005 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9018) covalent geometry : angle 0.60745 (12252) SS BOND : bond 0.00642 ( 12) SS BOND : angle 2.17014 ( 24) hydrogen bonds : bond 0.02499 ( 409) hydrogen bonds : angle 4.43140 ( 1218) *********************** 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: 26 poor density : 102 time to evaluate : 0.293 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: A 102 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: B 99 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6897 (mmt90) REVERT: B 102 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7454 (pt0) REVERT: B 128 MET cc_start: 0.7144 (mmt) cc_final: 0.6916 (mmt) REVERT: B 289 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: B 290 ARG cc_start: 0.8282 (tpp-160) cc_final: 0.7923 (tpt90) REVERT: C 140 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7640 (p0) REVERT: C 293 GLU cc_start: 0.8211 (tt0) cc_final: 0.7784 (tt0) outliers start: 26 outliers final: 9 residues processed: 118 average time/residue: 0.7661 time to fit residues: 98.0362 Evaluate side-chains 110 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 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 341 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 97 optimal weight: 0.1980 chunk 96 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.190135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155771 restraints weight = 24030.978| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.72 r_work: 0.3544 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2562 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= 0.116 Angle : 0.602 12.523 12276 Z= 0.333 Chirality : 0.054 0.427 1365 Planarity : 0.003 0.037 1581 Dihedral : 5.310 24.552 1206 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.02 % Favored : 93.70 % Rotamer: Outliers : 2.65 % Allowed : 12.54 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.26), residues: 1080 helix: 1.63 (0.29), residues: 366 sheet: -0.70 (0.31), residues: 273 loop : -2.19 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 268 TYR 0.006 0.001 TYR C 239 PHE 0.009 0.001 PHE B 256 TRP 0.008 0.001 TRP A 145 HIS 0.005 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9018) covalent geometry : angle 0.59436 (12252) SS BOND : bond 0.00501 ( 12) SS BOND : angle 2.27148 ( 24) hydrogen bonds : bond 0.02270 ( 409) hydrogen bonds : angle 4.28640 ( 1218) *********************** 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 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.416 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: 0.7987 (OUTLIER) cc_final: 0.7652 (pt0) REVERT: B 102 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7333 (pt0) REVERT: B 128 MET cc_start: 0.7127 (mmt) cc_final: 0.6903 (mmt) REVERT: B 129 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8173 (mptt) REVERT: B 289 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: C 140 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7651 (p0) REVERT: C 293 GLU cc_start: 0.8268 (tt0) cc_final: 0.7925 (tt0) outliers start: 26 outliers final: 11 residues processed: 119 average time/residue: 0.7373 time to fit residues: 95.9402 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 : 0.259 ------------------------------------------------------------------------------- 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 341 CYS Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 126 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.187908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.152989 restraints weight = 24136.721| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.75 r_work: 0.3586 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2623 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= 0.169 Angle : 0.632 12.559 12276 Z= 0.349 Chirality : 0.055 0.438 1365 Planarity : 0.004 0.039 1581 Dihedral : 5.365 22.732 1206 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.20 % Favored : 93.52 % Rotamer: Outliers : 2.75 % Allowed : 12.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.26), residues: 1080 helix: 1.62 (0.29), residues: 366 sheet: -0.68 (0.31), residues: 273 loop : -2.16 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 99 TYR 0.007 0.001 TYR A 369 PHE 0.010 0.001 PHE B 205 TRP 0.009 0.001 TRP A 145 HIS 0.007 0.002 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9018) covalent geometry : angle 0.62241 (12252) SS BOND : bond 0.00583 ( 12) SS BOND : angle 2.56490 ( 24) hydrogen bonds : bond 0.02489 ( 409) hydrogen bonds : angle 4.34475 ( 1218) *********************** 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: 27 poor density : 105 time to evaluate : 0.522 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: symmetry clash REVERT: A 102 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7819 (pt0) REVERT: A 342 GLU cc_start: 0.7673 (tt0) cc_final: 0.7445 (tt0) REVERT: B 102 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7504 (pt0) REVERT: B 126 ASP cc_start: 0.7246 (p0) cc_final: 0.6887 (p0) REVERT: B 128 MET cc_start: 0.7195 (mmt) cc_final: 0.6928 (mmt) REVERT: B 129 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8043 (mptt) REVERT: B 289 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: B 290 ARG cc_start: 0.8378 (tpp-160) cc_final: 0.7936 (tpt90) REVERT: C 128 MET cc_start: 0.6719 (mtm) cc_final: 0.6282 (mmt) REVERT: C 140 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7707 (p0) REVERT: C 293 GLU cc_start: 0.8255 (tt0) cc_final: 0.7773 (tt0) outliers start: 27 outliers final: 12 residues processed: 123 average time/residue: 0.9462 time to fit residues: 125.5729 Evaluate side-chains 118 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 337 CYS 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 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 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 98 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.0040 chunk 0 optimal weight: 40.0000 chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 0.0570 chunk 106 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6312 ------------------------------------------------------------------------------- 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 C 233 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.189914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.155182 restraints weight = 23947.327| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.74 r_work: 0.3506 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 0.028 9030 Z= 0.120 Angle : 0.606 12.525 12276 Z= 0.334 Chirality : 0.054 0.426 1365 Planarity : 0.004 0.046 1581 Dihedral : 5.221 22.354 1206 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.48 % Favored : 93.24 % Rotamer: Outliers : 2.34 % Allowed : 13.46 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.26), residues: 1080 helix: 1.80 (0.29), residues: 366 sheet: -0.67 (0.32), residues: 273 loop : -2.16 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 339 TYR 0.007 0.001 TYR C 239 PHE 0.009 0.001 PHE B 256 TRP 0.009 0.001 TRP A 145 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9018) covalent geometry : angle 0.59946 (12252) SS BOND : bond 0.00470 ( 12) SS BOND : angle 2.08236 ( 24) hydrogen bonds : bond 0.02234 ( 409) hydrogen bonds : angle 4.23344 ( 1218) *********************** 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 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.452 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: 0.8029 (OUTLIER) cc_final: 0.7711 (pt0) REVERT: B 102 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7389 (pt0) REVERT: B 126 ASP cc_start: 0.7268 (p0) cc_final: 0.7024 (p0) REVERT: B 128 MET cc_start: 0.7139 (mmt) cc_final: 0.6913 (mmt) REVERT: B 154 ASN cc_start: 0.7973 (t0) cc_final: 0.7236 (t0) REVERT: B 289 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: C 128 MET cc_start: 0.6639 (mtm) cc_final: 0.6192 (mmt) REVERT: C 140 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7588 (p0) REVERT: C 293 GLU cc_start: 0.8224 (tt0) cc_final: 0.7743 (tt0) outliers start: 23 outliers final: 13 residues processed: 118 average time/residue: 0.8455 time to fit residues: 108.4631 Evaluate side-chains 117 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 337 CYS 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 289 GLN Chi-restraints excluded: chain B residue 341 CYS 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 233 HIS 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 46 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 233 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.190254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.155795 restraints weight = 23932.598| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.72 r_work: 0.3583 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9030 Z= 0.122 Angle : 0.606 12.525 12276 Z= 0.334 Chirality : 0.054 0.425 1365 Planarity : 0.004 0.038 1581 Dihedral : 5.168 22.097 1206 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.02 % Favored : 93.70 % Rotamer: Outliers : 2.45 % Allowed : 13.35 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.26), residues: 1080 helix: 1.86 (0.29), residues: 366 sheet: -0.67 (0.32), residues: 273 loop : -2.14 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 339 TYR 0.008 0.001 TYR C 279 PHE 0.009 0.001 PHE B 256 TRP 0.008 0.001 TRP A 145 HIS 0.008 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9018) covalent geometry : angle 0.59986 (12252) SS BOND : bond 0.00467 ( 12) SS BOND : angle 2.05201 ( 24) hydrogen bonds : bond 0.02226 ( 409) hydrogen bonds : angle 4.21593 ( 1218) ********************** 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 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.345 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: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7698 (pt0) REVERT: B 102 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7324 (pt0) REVERT: B 154 ASN cc_start: 0.8019 (t0) cc_final: 0.7265 (t0) REVERT: B 289 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: C 128 MET cc_start: 0.6685 (mtm) cc_final: 0.6247 (mmt) REVERT: C 140 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7675 (p0) REVERT: C 293 GLU cc_start: 0.8278 (tt0) cc_final: 0.7906 (tt0) outliers start: 24 outliers final: 13 residues processed: 120 average time/residue: 0.7830 time to fit residues: 102.5170 Evaluate side-chains 117 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 337 CYS 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 289 GLN 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 275 ASP 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 101 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.189806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.155023 restraints weight = 24119.190| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.74 r_work: 0.3462 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2795 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= 0.132 Angle : 0.609 12.516 12276 Z= 0.335 Chirality : 0.054 0.425 1365 Planarity : 0.004 0.038 1581 Dihedral : 5.161 22.127 1206 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.93 % Favored : 93.80 % Rotamer: Outliers : 2.65 % Allowed : 13.56 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.26), residues: 1080 helix: 1.90 (0.29), residues: 366 sheet: -0.66 (0.32), residues: 273 loop : -2.14 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 339 TYR 0.007 0.001 TYR C 239 PHE 0.009 0.001 PHE C 116 TRP 0.009 0.001 TRP A 145 HIS 0.007 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9018) covalent geometry : angle 0.60208 (12252) SS BOND : bond 0.00487 ( 12) SS BOND : angle 2.10941 ( 24) hydrogen bonds : bond 0.02244 ( 409) hydrogen bonds : angle 4.21016 ( 1218) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4817.45 seconds wall clock time: 82 minutes 19.57 seconds (4939.57 seconds total)