Starting phenix.real_space_refine
on Wed Feb 12 05:40:27 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8qey_18379/02_2025/8qey_18379.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qey_18379/02_2025/8qey_18379.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qey_18379/02_2025/8qey_18379.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qey_18379/02_2025/8qey_18379.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qey_18379/02_2025/8qey_18379.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qey_18379/02_2025/8qey_18379.cif"
  }
  resolution = 4.0
  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=   0.001
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: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    4754      2.51       5
     N    1185      2.21       5
     O    1336      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7306
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3462
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3462
          Classifications: {'peptide': 449}
          Link IDs: {'PTRANS': 22, 'TRANS': 426}
    Chain: "B"
      Number of atoms: 3650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3650
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 22, 'TRANS': 446}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 85
          Unusual residues: {'AJP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.65, per 1000 atoms: 0.77
  Number of scatterers: 7306
  At special positions: 0
  Unit cell: (94.734, 83.931, 131.298, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1336      8.00
     N    1185      7.00
     C    4754      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 154 " - pdb=" SG  CYS B 109 " 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
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG B 601 " - " ASN B 264 "
      " NAG C   1 " - " ASN B 323 "
      " NAG D   1 " - " ASN B 280 "
      " NAG E   1 " - " ASN B 405 "
  Time building additional restraints: 2.24
  Conformation dependent library (CDL) restraints added in 882.3 milliseconds
  

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1674

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      58.3% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 54
      removed outlier: 3.616A  pdb=" N   ALA A  45 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 69
      removed outlier: 4.019A  pdb=" N   ILE A  60 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   SER A  61 " --> pdb=" O   GLY A  57 " (cutoff:3.500A)
      Proline residue:  A  62  - end of helix
    Processing helix  chain 'A' and resid 74 through 99
      removed outlier: 3.638A  pdb=" N   GLY A  83 " --> pdb=" O   TRP A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 113
      removed outlier: 4.332A  pdb=" N   VAL A 110 " --> pdb=" O   ASP A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 130
      removed outlier: 4.434A  pdb=" N   ALA A 118 " --> pdb=" O   PHE A 114 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLY A 119 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 148
    Processing helix  chain 'A' and resid 157 through 177
      removed outlier: 3.570A  pdb=" N   SER A 161 " --> pdb=" O   PRO A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 210
      removed outlier: 4.048A  pdb=" N   PHE A 210 " --> pdb=" O   LEU A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 222
    Processing helix  chain 'A' and resid 230 through 245
      removed outlier: 3.713A  pdb=" N   GLN A 240 " --> pdb=" O   LEU A 236 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY A 241 " --> pdb=" O   ALA A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 257
      removed outlier: 3.652A  pdb=" N   THR A 255 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   GLU A 256 " --> pdb=" O   ASN A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 271
    Processing helix  chain 'A' and resid 272 through 290
      removed outlier: 3.670A  pdb=" N   ALA A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 298
      removed outlier: 3.817A  pdb=" N   LEU A 296 " --> pdb=" O   SER A 292 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   LEU A 297 " --> pdb=" O   PRO A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 310
      removed outlier: 3.868A  pdb=" N   LEU A 310 " --> pdb=" O   PHE A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 348
      Proline residue:  A 319  - end of helix
      removed outlier: 3.535A  pdb=" N   GLU A 347 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLY A 348 " --> pdb=" O   GLY A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 381
      removed outlier: 3.637A  pdb=" N   LEU A 368 " --> pdb=" O   PRO A 364 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU A 369 " --> pdb=" O   ILE A 365 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   VAL A 370 " --> pdb=" O   PRO A 366 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA A 374 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR A 375 " --> pdb=" O   CYS A 371 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ILE A 378 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 413
    Processing helix  chain 'A' and resid 425 through 442
    Processing helix  chain 'A' and resid 445 through 458
      removed outlier: 3.806A  pdb=" N   CYS A 449 " --> pdb=" O   GLU A 445 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL A 451 " --> pdb=" O   MET A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 469
      removed outlier: 4.156A  pdb=" N   ILE A 462 " --> pdb=" O   THR A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
    Processing helix  chain 'A' and resid 482 through 487
      removed outlier: 4.287A  pdb=" N   TRP A 486 " --> pdb=" O   SER A 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 73
    Processing helix  chain 'B' and resid 74 through 105
    Processing helix  chain 'B' and resid 128 through 134
    Processing helix  chain 'B' and resid 139 through 145
      removed outlier: 4.105A  pdb=" N   LYS B 144 " --> pdb=" O   ALA B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 153
    Processing helix  chain 'B' and resid 185 through 199
    Processing helix  chain 'B' and resid 221 through 240
      removed outlier: 4.169A  pdb=" N   VAL B 225 " --> pdb=" O   GLN B 221 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LYS B 228 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   VAL B 229 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLU B 234 " --> pdb=" O   LYS B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 270
    Processing helix  chain 'B' and resid 283 through 291
    Processing helix  chain 'B' and resid 310 through 326
    Processing helix  chain 'B' and resid 348 through 357
      removed outlier: 4.472A  pdb=" N   LEU B 354 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 414
      removed outlier: 3.565A  pdb=" N   ASP B 414 " --> pdb=" O   GLY B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 432
      removed outlier: 3.598A  pdb=" N   SER B 430 " --> pdb=" O   SER B 426 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LYS B 431 " --> pdb=" O   ASP B 427 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU B 432 " --> pdb=" O   GLN B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 438
    Processing sheet with id=AA1, first strand: chain 'B' and resid 123 through 125
      removed outlier: 6.662A  pdb=" N   TRP B 332 " --> pdb=" O   VAL B 364 " (cutoff:3.500A)
      removed outlier: 8.668A  pdb=" N   SER B 366 " --> pdb=" O   TRP B 332 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 164 through 165
      removed outlier: 4.218A  pdb=" N   LYS B 165 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASP B 175 " --> pdb=" O   LYS B 165 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 205 through 206
      removed outlier: 7.050A  pdb=" N   LEU B 205 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   PHE B 244 " --> pdb=" O   ILE B 276 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   GLY B 278 " --> pdb=" O   PHE B 244 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   VAL B 246 " --> pdb=" O   GLY B 278 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   ALA B 277 " --> pdb=" O   THR B 300 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 441 through 442
      removed outlier: 3.593A  pdb=" N   HIS B 441 " --> pdb=" O   ILE B 453 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ARG B 524 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   LEU B 494 " --> pdb=" O   ARG B 524 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ALA B 492 " --> pdb=" O   LEU B 508 " (cutoff:3.500A)

    363 hydrogen bonds defined for protein.
    1068 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: 2.71

  Time building geometry restraints manager: 2.46 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 1339
        1.33 -     1.45: 1942
        1.45 -     1.57: 4168
        1.57 -     1.69: 2
        1.69 -     1.82: 49
  Bond restraints: 7500
  Sorted by residual:
  bond pdb=" CB  PRO B 526 "
       pdb=" CG  PRO B 526 "
    ideal  model  delta    sigma   weight residual
    1.492  1.608 -0.116 5.00e-02 4.00e+02 5.35e+00
  bond pdb=" C65 AJP A 601 "
       pdb=" O64 AJP A 601 "
    ideal  model  delta    sigma   weight residual
    1.373  1.407 -0.034 2.00e-02 2.50e+03 2.95e+00
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.553 -0.034 2.00e-02 2.50e+03 2.81e+00
  bond pdb=" CB  PRO A 149 "
       pdb=" CG  PRO A 149 "
    ideal  model  delta    sigma   weight residual
    1.492  1.575 -0.083 5.00e-02 4.00e+02 2.75e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.50e+00
  ... (remaining 7495 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.64: 10103
        3.64 -     7.28: 105
        7.28 -    10.92: 16
       10.92 -    14.56: 3
       14.56 -    18.20: 1
  Bond angle restraints: 10228
  Sorted by residual:
  angle pdb=" CA  PRO B 526 "
        pdb=" N   PRO B 526 "
        pdb=" CD  PRO B 526 "
      ideal   model   delta    sigma   weight residual
     112.00  102.58    9.42 1.40e+00 5.10e-01 4.53e+01
  angle pdb=" CA  PRO A 149 "
        pdb=" N   PRO A 149 "
        pdb=" CD  PRO A 149 "
      ideal   model   delta    sigma   weight residual
     112.00  103.38    8.62 1.40e+00 5.10e-01 3.79e+01
  angle pdb=" CA  LEU A 310 "
        pdb=" CB  LEU A 310 "
        pdb=" CG  LEU A 310 "
      ideal   model   delta    sigma   weight residual
     116.30  134.50  -18.20 3.50e+00 8.16e-02 2.70e+01
  angle pdb=" C   ILE A 129 "
        pdb=" N   MET A 130 "
        pdb=" CA  MET A 130 "
      ideal   model   delta    sigma   weight residual
     122.58  113.49    9.09 2.07e+00 2.33e-01 1.93e+01
  angle pdb=" CA  TYR A 337 "
        pdb=" CB  TYR A 337 "
        pdb=" CG  TYR A 337 "
      ideal   model   delta    sigma   weight residual
     113.90  120.98   -7.08 1.80e+00 3.09e-01 1.55e+01
  ... (remaining 10223 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.22: 4035
       22.22 -    44.43: 472
       44.43 -    66.65: 89
       66.65 -    88.86: 28
       88.86 -   111.08: 12
  Dihedral angle restraints: 4636
    sinusoidal: 2021
      harmonic: 2615
  Sorted by residual:
  dihedral pdb=" CA  LEU A 350 "
           pdb=" C   LEU A 350 "
           pdb=" N   PRO A 351 "
           pdb=" CA  PRO A 351 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.44  -37.56     0      5.00e+00 4.00e-02 5.64e+01
  dihedral pdb=" CB  CYS A 154 "
           pdb=" SG  CYS A 154 "
           pdb=" SG  CYS B 109 "
           pdb=" CB  CYS B 109 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -149.89   63.89     1      1.00e+01 1.00e-02 5.37e+01
  dihedral pdb=" CA  ILE A 100 "
           pdb=" C   ILE A 100 "
           pdb=" N   PRO A 101 "
           pdb=" CA  PRO A 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.05  -27.95     0      5.00e+00 4.00e-02 3.13e+01
  ... (remaining 4633 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1018
       0.065 -    0.130: 166
       0.130 -    0.196: 22
       0.196 -    0.261: 5
       0.261 -    0.326: 2
  Chirality restraints: 1213
  Sorted by residual:
  chirality pdb=" CG  LEU B 233 "
            pdb=" CB  LEU B 233 "
            pdb=" CD1 LEU B 233 "
            pdb=" CD2 LEU B 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.26   -0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" C08 AJP A 601 "
            pdb=" C07 AJP A 601 "
            pdb=" C10 AJP A 601 "
            pdb=" O09 AJP A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.56    2.82   -0.26 2.00e-01 2.50e+01 1.70e+00
  ... (remaining 1210 not shown)

  Planarity restraints: 1254
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 525 "    0.104 5.00e-02 4.00e+02   1.50e-01 3.60e+01
        pdb=" N   PRO B 526 "   -0.259 5.00e-02 4.00e+02
        pdb=" CA  PRO B 526 "    0.080 5.00e-02 4.00e+02
        pdb=" CD  PRO B 526 "    0.076 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 148 "    0.077 5.00e-02 4.00e+02   1.12e-01 2.01e+01
        pdb=" N   PRO A 149 "   -0.194 5.00e-02 4.00e+02
        pdb=" CA  PRO A 149 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO A 149 "    0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 399 "    0.020 2.00e-02 2.50e+03   2.08e-02 8.68e+00
        pdb=" CG  TYR A 399 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 399 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 399 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 399 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 399 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 399 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 399 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1251 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1790
        2.79 -     3.31: 7031
        3.31 -     3.84: 12106
        3.84 -     4.37: 12654
        4.37 -     4.90: 21712
  Nonbonded interactions: 55293
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 367 "
            pdb=" O   PRO B 386 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OH  TYR B 149 "
            pdb=" OE2 GLU B 370 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   LYS B 315 "
            pdb=" OG1 THR B 319 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   GLY A  57 "
            pdb=" OG  SER A  61 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   VAL A 279 "
            pdb=" OG1 THR A 283 "
     model   vdw
     2.291 3.040
  ... (remaining 55288 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.300
  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:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.720
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
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      :  0.005   0.116   7500  Z= 0.308
  Angle     :  0.959  18.202  10228  Z= 0.452
  Chirality :  0.052   0.326   1213
  Planarity :  0.007   0.150   1250
  Dihedral  : 19.802 111.079   2959
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 41.20 %
    Favored  : 57.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -1.09 (0.27), residues: 914
  helix:  0.30 (0.23), residues: 483
  sheet: -0.51 (0.67), residues: 59
  loop : -2.15 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 316 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.045   0.002   PHE A 440 
 TYR   0.052   0.002   TYR A 399 
 ARG   0.003   0.000   ARG A 346 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 155
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 GLU cc_start: 0.7980 (tp30) cc_final: 0.7032 (tm-30)
REVERT: A  140 MET cc_start: 0.8817 (ttm) cc_final: 0.8589 (ttp)
REVERT: A  215 GLU cc_start: 0.7309 (mp0) cc_final: 0.6593 (pm20)
REVERT: A  221 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7492 (p0)
  outliers start: 7
  outliers final: 2
  residues processed: 162
  average time/residue: 0.1491
  time to fit residues: 35.0213
Evaluate side-chains
  154 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 151
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain B residue  357 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0470
   chunk 27 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 81 optimal weight:    4.9990
   overall best weight:    0.6478

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 428 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.177030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.144488 restraints weight = 13011.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.144271 restraints weight = 9769.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.145682 restraints weight = 8752.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.0839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7500  Z= 0.192
  Angle     :  0.669  10.398  10228  Z= 0.318
  Chirality :  0.041   0.203   1213
  Planarity :  0.005   0.091   1250
  Dihedral  : 11.745  96.324   1371
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.13 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 34.55 %
    Favored  : 60.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -0.31 (0.28), residues: 914
  helix:  1.01 (0.24), residues: 480
  sheet: -0.57 (0.64), residues: 55
  loop : -1.78 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 316 
 HIS   0.003   0.001   HIS B 441 
 PHE   0.014   0.001   PHE A 393 
 TYR   0.036   0.002   TYR A 399 
 ARG   0.007   0.000   ARG A 470 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 162
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7223 (mmm)
REVERT: A  215 GLU cc_start: 0.7360 (mp0) cc_final: 0.6784 (pm20)
REVERT: A  356 MET cc_start: 0.6419 (mpp) cc_final: 0.6058 (mpp)
REVERT: B  302 SER cc_start: 0.9417 (OUTLIER) cc_final: 0.9089 (t)
  outliers start: 41
  outliers final: 25
  residues processed: 187
  average time/residue: 0.1466
  time to fit residues: 40.1348
Evaluate side-chains
  179 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0010
   chunk 35 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0570
   chunk 17 optimal weight:    7.9990
   chunk 59 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   overall best weight:    0.3704

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.177894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.140877 restraints weight = 13131.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.143970 restraints weight = 9042.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.146139 restraints weight = 7190.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.1150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7500  Z= 0.160
  Angle     :  0.657  10.987  10228  Z= 0.305
  Chirality :  0.041   0.311   1213
  Planarity :  0.004   0.071   1250
  Dihedral  : 10.306  86.005   1369
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  6.26 %
    Allowed  : 34.55 %
    Favored  : 59.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.04 (0.28), residues: 914
  helix:  1.33 (0.24), residues: 479
  sheet: -0.39 (0.67), residues: 55
  loop : -1.67 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 316 
 HIS   0.003   0.000   HIS B 313 
 PHE   0.009   0.001   PHE B 525 
 TYR   0.032   0.001   TYR A 399 
 ARG   0.001   0.000   ARG B 423 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 169
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7175 (mmm)
REVERT: A  215 GLU cc_start: 0.7380 (mp0) cc_final: 0.6853 (pm20)
REVERT: A  221 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7309 (p0)
REVERT: A  356 MET cc_start: 0.6606 (mpp) cc_final: 0.6256 (mpp)
REVERT: B  237 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7859 (mm)
REVERT: B  302 SER cc_start: 0.9388 (OUTLIER) cc_final: 0.9004 (t)
REVERT: B  336 GLN cc_start: 0.8520 (tp40) cc_final: 0.8141 (tp-100)
  outliers start: 48
  outliers final: 25
  residues processed: 201
  average time/residue: 0.1462
  time to fit residues: 42.4662
Evaluate side-chains
  193 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 164
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 38 optimal weight:    0.8980
   chunk 43 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0030
   chunk 87 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.6790

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 221 GLN
** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.175736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.141402 restraints weight = 13118.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.143607 restraints weight = 9598.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.144842 restraints weight = 7211.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7500  Z= 0.185
  Angle     :  0.656   8.335  10228  Z= 0.307
  Chirality :  0.041   0.273   1213
  Planarity :  0.004   0.061   1250
  Dihedral  :  9.489  75.842   1369
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  6.91 %
    Allowed  : 35.33 %
    Favored  : 57.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.26 (0.29), residues: 914
  helix:  1.50 (0.24), residues: 480
  sheet: -0.34 (0.67), residues: 56
  loop : -1.54 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 316 
 HIS   0.003   0.001   HIS A  68 
 PHE   0.016   0.001   PHE A 463 
 TYR   0.025   0.002   TYR A 399 
 ARG   0.001   0.000   ARG B 424 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 167
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 GLU cc_start: 0.7917 (tp30) cc_final: 0.6956 (tm-30)
REVERT: A  215 GLU cc_start: 0.7370 (mp0) cc_final: 0.6944 (pm20)
REVERT: A  221 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7384 (p0)
REVERT: B  237 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7748 (mm)
REVERT: B  302 SER cc_start: 0.9404 (OUTLIER) cc_final: 0.9032 (t)
REVERT: B  336 GLN cc_start: 0.8627 (tp40) cc_final: 0.8167 (tp-100)
  outliers start: 53
  outliers final: 35
  residues processed: 198
  average time/residue: 0.1402
  time to fit residues: 40.6372
Evaluate side-chains
  198 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 160
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  221 GLN
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  325 THR
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  453 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 65 optimal weight:    0.4980
   chunk 11 optimal weight:    0.0980
   chunk 75 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 81 optimal weight:    0.2980
   chunk 59 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 221 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.179582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.143019 restraints weight = 13821.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.144354 restraints weight = 9708.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.145244 restraints weight = 7663.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7500  Z= 0.177
  Angle     :  0.659   9.652  10228  Z= 0.307
  Chirality :  0.041   0.232   1213
  Planarity :  0.004   0.056   1250
  Dihedral  :  8.901  66.651   1367
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  7.17 %
    Allowed  : 34.55 %
    Favored  : 58.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.38 (0.29), residues: 914
  helix:  1.64 (0.24), residues: 479
  sheet: -0.20 (0.68), residues: 56
  loop : -1.55 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 316 
 HIS   0.002   0.000   HIS B 313 
 PHE   0.015   0.001   PHE A 393 
 TYR   0.013   0.001   TYR A 396 
 ARG   0.001   0.000   ARG B 108 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 170
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.8791 (ttm) cc_final: 0.8529 (ttp)
REVERT: A  215 GLU cc_start: 0.7295 (mp0) cc_final: 0.6834 (pm20)
REVERT: A  221 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7354 (p0)
REVERT: A  354 LEU cc_start: 0.8091 (tp) cc_final: 0.7850 (tp)
REVERT: A  356 MET cc_start: 0.6384 (mpp) cc_final: 0.5935 (mpp)
REVERT: B  237 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7711 (mm)
REVERT: B  302 SER cc_start: 0.9354 (OUTLIER) cc_final: 0.8987 (t)
REVERT: B  336 GLN cc_start: 0.8602 (tp40) cc_final: 0.8207 (tp40)
REVERT: B  426 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.8044 (t)
  outliers start: 55
  outliers final: 37
  residues processed: 205
  average time/residue: 0.1331
  time to fit residues: 40.1822
Evaluate side-chains
  202 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 161
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  168 CYS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  398 CYS
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  230 LYS
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  325 THR
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  426 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 89 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   chunk 78 optimal weight:    0.0070
   chunk 7 optimal weight:    0.0980
   chunk 31 optimal weight:   10.0000
   overall best weight:    0.4598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.179759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.142901 restraints weight = 13887.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.144307 restraints weight = 9830.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.145206 restraints weight = 7665.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7500  Z= 0.169
  Angle     :  0.665  13.165  10228  Z= 0.309
  Chirality :  0.042   0.306   1213
  Planarity :  0.004   0.054   1250
  Dihedral  :  8.234  57.322   1367
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 33.90 %
    Favored  : 59.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.52 (0.29), residues: 914
  helix:  1.80 (0.24), residues: 473
  sheet: -0.06 (0.70), residues: 55
  loop : -1.52 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 316 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.013   0.001   PHE A 393 
 TYR   0.030   0.001   TYR A 399 
 ARG   0.002   0.000   ARG B 108 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 172
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7632 (mmm)
REVERT: A  215 GLU cc_start: 0.7248 (mp0) cc_final: 0.6837 (pm20)
REVERT: A  221 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7330 (p0)
REVERT: A  354 LEU cc_start: 0.8034 (tp) cc_final: 0.7801 (tp)
REVERT: A  356 MET cc_start: 0.6379 (mpp) cc_final: 0.5964 (mpp)
REVERT: B  234 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8047 (pm20)
REVERT: B  237 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7762 (mm)
REVERT: B  302 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.9011 (t)
REVERT: B  426 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8080 (t)
  outliers start: 52
  outliers final: 37
  residues processed: 206
  average time/residue: 0.1396
  time to fit residues: 41.8294
Evaluate side-chains
  203 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 160
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  168 CYS
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  398 CYS
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  234 GLU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  426 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 1 optimal weight:    0.4980
   chunk 27 optimal weight:    0.2980
   chunk 41 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.178887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.142353 restraints weight = 13780.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.142993 restraints weight = 9759.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.144301 restraints weight = 7722.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7500  Z= 0.186
  Angle     :  0.678  11.187  10228  Z= 0.319
  Chirality :  0.042   0.338   1213
  Planarity :  0.004   0.052   1250
  Dihedral  :  7.896  57.308   1367
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 34.42 %
    Favored  : 58.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.29), residues: 914
  helix:  1.84 (0.24), residues: 473
  sheet: -0.13 (0.64), residues: 62
  loop : -1.50 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 316 
 HIS   0.009   0.001   HIS A 213 
 PHE   0.020   0.001   PHE A 463 
 TYR   0.026   0.002   TYR A 399 
 ARG   0.001   0.000   ARG B 108 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 168
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8626 (t)
REVERT: A  215 GLU cc_start: 0.7371 (mp0) cc_final: 0.7035 (mp0)
REVERT: A  221 ASN cc_start: 0.7764 (OUTLIER) cc_final: 0.7359 (p0)
REVERT: A  354 LEU cc_start: 0.7984 (tp) cc_final: 0.7743 (tp)
REVERT: A  356 MET cc_start: 0.6416 (mpp) cc_final: 0.5991 (mpp)
REVERT: B  237 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7728 (mm)
REVERT: B  302 SER cc_start: 0.9366 (OUTLIER) cc_final: 0.9010 (t)
REVERT: B  426 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8181 (t)
  outliers start: 54
  outliers final: 38
  residues processed: 203
  average time/residue: 0.1364
  time to fit residues: 41.0438
Evaluate side-chains
  205 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 162
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  168 CYS
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  325 THR
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  426 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  470 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0030
   chunk 57 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 63 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 71 optimal weight:    0.4980
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.6190

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.178658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.142756 restraints weight = 13870.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.144020 restraints weight = 10098.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.145025 restraints weight = 7657.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7500  Z= 0.189
  Angle     :  0.698  10.714  10228  Z= 0.326
  Chirality :  0.043   0.318   1213
  Planarity :  0.004   0.051   1250
  Dihedral  :  7.710  57.396   1367
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 35.20 %
    Favored  : 58.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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 (0.29), residues: 914
  helix:  1.76 (0.24), residues: 479
  sheet: -0.06 (0.66), residues: 61
  loop : -1.48 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 316 
 HIS   0.006   0.001   HIS B 313 
 PHE   0.017   0.001   PHE A 463 
 TYR   0.024   0.002   TYR A 399 
 ARG   0.001   0.000   ARG B  81 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 166
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8627 (t)
REVERT: A  215 GLU cc_start: 0.7380 (mp0) cc_final: 0.6636 (pm20)
REVERT: A  221 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7408 (p0)
REVERT: A  354 LEU cc_start: 0.7959 (tp) cc_final: 0.7724 (tp)
REVERT: A  356 MET cc_start: 0.6518 (mpp) cc_final: 0.6105 (mpp)
REVERT: B  234 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7982 (pm20)
REVERT: B  237 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7756 (mm)
REVERT: B  302 SER cc_start: 0.9358 (OUTLIER) cc_final: 0.8999 (t)
REVERT: B  426 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8227 (t)
  outliers start: 50
  outliers final: 38
  residues processed: 201
  average time/residue: 0.1456
  time to fit residues: 43.1867
Evaluate side-chains
  208 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 164
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  168 CYS
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  230 LYS
Chi-restraints excluded: chain B residue  234 GLU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  325 THR
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  426 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  470 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 53 optimal weight:    0.0170
   chunk 45 optimal weight:    6.9990
   chunk 23 optimal weight:    0.5980
   chunk 79 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.6220

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.178991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.141352 restraints weight = 14019.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.142361 restraints weight = 10072.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.144375 restraints weight = 7793.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7500  Z= 0.194
  Angle     :  0.700  10.166  10228  Z= 0.327
  Chirality :  0.044   0.315   1213
  Planarity :  0.004   0.050   1250
  Dihedral  :  7.592  57.422   1367
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 34.68 %
    Favored  : 58.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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 (0.29), residues: 914
  helix:  1.75 (0.24), residues: 479
  sheet: -0.03 (0.65), residues: 62
  loop : -1.48 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 316 
 HIS   0.008   0.001   HIS B 313 
 PHE   0.016   0.001   PHE A 463 
 TYR   0.024   0.002   TYR A 399 
 ARG   0.003   0.000   ARG B 424 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 166
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8603 (t)
REVERT: A  221 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7422 (p0)
REVERT: A  354 LEU cc_start: 0.7958 (tp) cc_final: 0.7717 (tp)
REVERT: A  356 MET cc_start: 0.6444 (mpp) cc_final: 0.6002 (mpp)
REVERT: B  234 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7982 (pm20)
REVERT: B  237 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7758 (mm)
REVERT: B  302 SER cc_start: 0.9294 (OUTLIER) cc_final: 0.8850 (t)
REVERT: B  426 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8061 (t)
  outliers start: 52
  outliers final: 41
  residues processed: 204
  average time/residue: 0.1360
  time to fit residues: 40.7926
Evaluate side-chains
  211 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 164
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  168 CYS
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  398 CYS
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  234 GLU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  325 THR
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  426 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  470 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 82 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 10 optimal weight:    0.4980
   chunk 44 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.177755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.140438 restraints weight = 14145.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.142478 restraints weight = 9534.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.143605 restraints weight = 7412.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7500  Z= 0.213
  Angle     :  0.721  10.030  10228  Z= 0.336
  Chirality :  0.044   0.315   1213
  Planarity :  0.004   0.050   1250
  Dihedral  :  7.588  57.351   1367
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  6.26 %
    Allowed  : 35.33 %
    Favored  : 58.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.54 (0.29), residues: 914
  helix:  1.75 (0.24), residues: 479
  sheet: -0.04 (0.65), residues: 62
  loop : -1.49 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 316 
 HIS   0.008   0.001   HIS B 313 
 PHE   0.025   0.001   PHE A 393 
 TYR   0.022   0.002   TYR A 399 
 ARG   0.001   0.000   ARG A 418 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 168
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 GLU cc_start: 0.7580 (pm20) cc_final: 0.7361 (pm20)
REVERT: A  221 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7441 (p0)
REVERT: A  354 LEU cc_start: 0.7993 (tp) cc_final: 0.7751 (tp)
REVERT: A  356 MET cc_start: 0.6472 (mpp) cc_final: 0.6068 (mpp)
REVERT: B  234 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7955 (pm20)
REVERT: B  237 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7759 (mm)
REVERT: B  287 ILE cc_start: 0.9033 (mm) cc_final: 0.8805 (tp)
REVERT: B  426 SER cc_start: 0.8391 (OUTLIER) cc_final: 0.8079 (t)
  outliers start: 48
  outliers final: 41
  residues processed: 200
  average time/residue: 0.1368
  time to fit residues: 40.5649
Evaluate side-chains
  209 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 164
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  168 CYS
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  230 LYS
Chi-restraints excluded: chain B residue  234 GLU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  325 THR
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  426 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  470 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0270
   chunk 42 optimal weight:    0.0030
   chunk 26 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.4448

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.179340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.142819 restraints weight = 13874.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.144932 restraints weight = 9178.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.146696 restraints weight = 7123.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7500  Z= 0.184
  Angle     :  0.721  10.192  10228  Z= 0.334
  Chirality :  0.043   0.310   1213
  Planarity :  0.004   0.049   1250
  Dihedral  :  7.500  57.610   1367
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 36.64 %
    Favored  : 58.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.29), residues: 914
  helix:  1.78 (0.24), residues: 479
  sheet:  0.00 (0.66), residues: 61
  loop : -1.48 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 316 
 HIS   0.008   0.001   HIS B 313 
 PHE   0.023   0.001   PHE A 393 
 TYR   0.023   0.002   TYR A 399 
 ARG   0.001   0.000   ARG B 524 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2417.72 seconds
wall clock time: 44 minutes 33.34 seconds (2673.34 seconds total)