Starting phenix.real_space_refine
on Sat Jun  7 17:47:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fv6_50790/06_2025/9fv6_50790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fv6_50790/06_2025/9fv6_50790.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fv6_50790/06_2025/9fv6_50790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fv6_50790/06_2025/9fv6_50790.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fv6_50790/06_2025/9fv6_50790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fv6_50790/06_2025/9fv6_50790.cif"
  }
  resolution = 3.8
  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=   0.001 sd=   0.006
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      54      5.16       5
     C    5590      2.51       5
     N    1536      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
    Chain: "B"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
  Time building chain proxies: 6.96, per 1000 atoms: 0.79
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (116.96, 106.08, 134.64, 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      54     16.00
     O    1642      8.00
     N    1536      7.00
     C    5590      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.61
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 4 sheets defined
      69.0% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 21
    Processing helix  chain 'A' and resid 23 through 47
    Processing helix  chain 'A' and resid 47 through 54
      removed outlier: 3.607A  pdb=" N   LEU A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 111
      removed outlier: 3.871A  pdb=" N   TRP A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
      Proline residue:  A  68  - end of helix
      removed outlier: 3.902A  pdb=" N   GLY A 110 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 4.447A  pdb=" N   PHE A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 129
      removed outlier: 4.004A  pdb=" N   LEU A 125 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   SER A 126 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 164
    Processing helix  chain 'A' and resid 164 through 213
      removed outlier: 3.590A  pdb=" N   SER A 168 " --> pdb=" O   SER A 164 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ILE A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ILE A 170 " --> pdb=" O   GLN A 166 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
      removed outlier: 3.918A  pdb=" N   THR A 199 " --> pdb=" O   ASN A 195 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   GLY A 213 " --> pdb=" O   GLN A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 220
    Processing helix  chain 'A' and resid 223 through 250
    Processing helix  chain 'A' and resid 250 through 271
    Processing helix  chain 'A' and resid 282 through 324
      removed outlier: 4.394A  pdb=" N   VAL A 286 " --> pdb=" O   GLY A 282 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 3.650A  pdb=" N   ASN A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL A 304 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   ASN A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   ALA A 306 " --> pdb=" O   THR A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 389
      removed outlier: 3.615A  pdb=" N   SER A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 432 through 438
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 466
    Processing helix  chain 'A' and resid 468 through 472
      removed outlier: 3.579A  pdb=" N   ASP A 471 " --> pdb=" O   ASN A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 498
    Processing helix  chain 'A' and resid 515 through 527
    Processing helix  chain 'A' and resid 538 through 545
    Processing helix  chain 'A' and resid 561 through 568
    Processing helix  chain 'A' and resid 571 through 580
    Processing helix  chain 'B' and resid 16 through 21
      removed outlier: 3.935A  pdb=" N   ILE B  20 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 47
    Processing helix  chain 'B' and resid 47 through 53
    Processing helix  chain 'B' and resid 61 through 111
      removed outlier: 3.592A  pdb=" N   MET B  67 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 120 through 129
      removed outlier: 3.748A  pdb=" N   LEU B 125 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 164
      removed outlier: 3.553A  pdb=" N   ALA B 136 " --> pdb=" O   SER B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 213
      Proline residue:  B 176  - end of helix
      removed outlier: 3.678A  pdb=" N   ASN B 198 " --> pdb=" O   LYS B 194 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   THR B 199 " --> pdb=" O   ASN B 195 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   SER B 206 " --> pdb=" O   GLN B 202 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ALA B 207 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 220
      removed outlier: 4.103A  pdb=" N   ILE B 219 " --> pdb=" O   LYS B 215 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   PHE B 220 " --> pdb=" O   GLU B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 272
      removed outlier: 3.549A  pdb=" N   ARG B 229 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   MET B 237 " --> pdb=" O   VAL B 233 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG B 238 " --> pdb=" O   SER B 234 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ALA B 247 " --> pdb=" O   LYS B 243 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   SER B 248 " --> pdb=" O   MET B 244 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
      removed outlier: 3.554A  pdb=" N   SER B 271 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 303
      removed outlier: 4.155A  pdb=" N   ARG B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
      removed outlier: 3.823A  pdb=" N   ASN B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 324
    Processing helix  chain 'B' and resid 381 through 390
      removed outlier: 3.793A  pdb=" N   ILE B 385 " --> pdb=" O   GLY B 381 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ALA B 386 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER B 387 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   THR B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 418
      removed outlier: 3.540A  pdb=" N   ASN B 417 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLN B 418 " --> pdb=" O   SER B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 438
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 459 through 465
      removed outlier: 3.854A  pdb=" N   ILE B 463 " --> pdb=" O   ALA B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 472
      removed outlier: 3.845A  pdb=" N   ASP B 471 " --> pdb=" O   ASN B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 514 through 527
      removed outlier: 3.943A  pdb=" N   ALA B 518 " --> pdb=" O   GLU B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 545
    Processing helix  chain 'B' and resid 561 through 568
    Processing helix  chain 'B' and resid 571 through 579
      removed outlier: 3.834A  pdb=" N   MET B 578 " --> pdb=" O   GLN B 574 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.517A  pdb=" N   GLU A 399 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   VAL A 347 " --> pdb=" O   GLU A 397 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   GLU A 397 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422
      removed outlier: 6.677A  pdb=" N   LEU A 502 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   THR A 371 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   VAL A 549 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL A 550 " --> pdb=" O   GLU A 558 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLU A 558 " --> pdb=" O   VAL A 550 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 365 through 366
      removed outlier: 3.853A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 366 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   PHE B 344 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   LEU B 401 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   ASN B 346 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   GLU B 399 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 422
      removed outlier: 6.346A  pdb=" N   ALA B 420 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   VAL B 372 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   THR B 371 " --> pdb=" O   GLU B 547 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   VAL B 549 " --> pdb=" O   THR B 371 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   VAL B 551 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   VAL B 375 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   ILE B 548 " --> pdb=" O   ARG B 559 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   ARG B 559 " --> pdb=" O   ILE B 548 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   VAL B 550 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)

    560 hydrogen bonds defined for protein.
    1662 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: 2.66

  Time building geometry restraints manager: 3.05 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2928
        1.35 -     1.47: 1943
        1.47 -     1.59: 3975
        1.59 -     1.71: 0
        1.71 -     1.83: 104
  Bond restraints: 8950
  Sorted by residual:
  bond pdb=" N   ARG A 148 "
       pdb=" CA  ARG A 148 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.034 1.28e-02 6.10e+03 6.89e+00
  bond pdb=" N   PHE A 115 "
       pdb=" CA  PHE A 115 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.23e-02 6.61e+03 6.76e+00
  bond pdb=" N   ASN A 303 "
       pdb=" CA  ASN A 303 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.31e-02 5.83e+03 6.63e+00
  bond pdb=" N   MET A 159 "
       pdb=" CA  MET A 159 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.19e-02 7.06e+03 5.80e+00
  bond pdb=" C   MET A 111 "
       pdb=" N   PRO A 112 "
    ideal  model  delta    sigma   weight residual
    1.331  1.360 -0.029 1.21e-02 6.83e+03 5.55e+00
  ... (remaining 8945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 11754
        2.33 -     4.66: 272
        4.66 -     6.99: 51
        6.99 -     9.32: 12
        9.32 -    11.65: 3
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" CB  MET B 456 "
        pdb=" CG  MET B 456 "
        pdb=" SD  MET B 456 "
      ideal   model   delta    sigma   weight residual
     112.70  124.35  -11.65 3.00e+00 1.11e-01 1.51e+01
  angle pdb=" CA  MET B 196 "
        pdb=" CB  MET B 196 "
        pdb=" CG  MET B 196 "
      ideal   model   delta    sigma   weight residual
     114.10  121.65   -7.55 2.00e+00 2.50e-01 1.43e+01
  angle pdb=" CA  MET B 460 "
        pdb=" CB  MET B 460 "
        pdb=" CG  MET B 460 "
      ideal   model   delta    sigma   weight residual
     114.10  121.63   -7.53 2.00e+00 2.50e-01 1.42e+01
  angle pdb=" CB  MET A 244 "
        pdb=" CG  MET A 244 "
        pdb=" SD  MET A 244 "
      ideal   model   delta    sigma   weight residual
     112.70  123.05  -10.35 3.00e+00 1.11e-01 1.19e+01
  angle pdb=" CA  PRO A 273 "
        pdb=" N   PRO A 273 "
        pdb=" CD  PRO A 273 "
      ideal   model   delta    sigma   weight residual
     112.00  107.52    4.48 1.40e+00 5.10e-01 1.02e+01
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 4808
       17.91 -    35.82: 499
       35.82 -    53.72: 119
       53.72 -    71.63: 18
       71.63 -    89.54: 10
  Dihedral angle restraints: 5454
    sinusoidal: 2164
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  MET B 276 "
           pdb=" C   MET B 276 "
           pdb=" N   ASP B 277 "
           pdb=" CA  ASP B 277 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.25   27.75     0      5.00e+00 4.00e-02 3.08e+01
  dihedral pdb=" CA  GLN A 119 "
           pdb=" C   GLN A 119 "
           pdb=" N   SER A 120 "
           pdb=" CA  SER A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.88   22.12     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  VAL B 534 "
           pdb=" C   VAL B 534 "
           pdb=" N   ILE B 535 "
           pdb=" CA  ILE B 535 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.06   21.94     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 5451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1100
       0.044 -    0.089: 262
       0.089 -    0.133: 68
       0.133 -    0.177: 8
       0.177 -    0.221: 2
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CB  ILE B 144 "
            pdb=" CA  ILE B 144 "
            pdb=" CG1 ILE B 144 "
            pdb=" CG2 ILE B 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  MET A 159 "
            pdb=" N   MET A 159 "
            pdb=" C   MET A 159 "
            pdb=" CB  MET A 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CB  ILE B 170 "
            pdb=" CA  ILE B 170 "
            pdb=" CG1 ILE B 170 "
            pdb=" CG2 ILE B 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.03e-01
  ... (remaining 1437 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 272 "   -0.061 5.00e-02 4.00e+02   9.11e-02 1.33e+01
        pdb=" N   PRO A 273 "    0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO A 273 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 273 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B  17 "    0.036 5.00e-02 4.00e+02   5.39e-02 4.65e+00
        pdb=" N   PRO B  18 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B  18 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B  18 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 287 "    0.011 2.00e-02 2.50e+03   2.11e-02 4.44e+00
        pdb=" C   VAL A 287 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   VAL A 287 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE A 288 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 947
        2.74 -     3.28: 9908
        3.28 -     3.82: 15438
        3.82 -     4.36: 17373
        4.36 -     4.90: 28694
  Nonbonded interactions: 72360
  Sorted by model distance:
  nonbonded pdb=" O   MET B 196 "
            pdb=" OG1 THR B 199 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   ASP B 231 "
            pdb=" OG  SER B 234 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   MET A 196 "
            pdb=" OG1 THR A 199 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   VAL A 286 "
            pdb=" OG  SER A 289 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" NZ  LYS A 212 "
            pdb=" OG1 THR B 121 "
     model   vdw
     2.236 3.120
  ... (remaining 72355 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             85.280
  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:             0.000
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     25.530
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  114.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
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   0.094   8950  Z= 0.220
  Angle     :  0.891  11.645  12092  Z= 0.465
  Chirality :  0.042   0.221   1440
  Planarity :  0.006   0.091   1532
  Dihedral  : 15.830  89.538   3326
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.11 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 18.08 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.25), residues: 1134
  helix:  1.11 (0.19), residues: 716
  sheet:  0.21 (0.83), residues: 32
  loop : -0.99 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  17 
 HIS   0.007   0.001   HIS A 427 
 PHE   0.015   0.002   PHE A 429 
 TYR   0.017   0.001   TYR A 439 
 ARG   0.005   0.001   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15212 (  560)
  hydrogen bonds       : angle       6.09752 ( 1662)
  covalent geometry    : bond        0.00469 ( 8950)
  covalent geometry    : angle       0.89057 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9171 (tmm) cc_final: 0.8666 (tmm)
REVERT: A   64 LEU cc_start: 0.9506 (tp) cc_final: 0.9291 (tp)
REVERT: A  200 MET cc_start: 0.9338 (tpp) cc_final: 0.8863 (mmm)
REVERT: A  244 MET cc_start: 0.8915 (tpp) cc_final: 0.8652 (tpp)
REVERT: A  402 MET cc_start: 0.8535 (tmm) cc_final: 0.7866 (tmm)
REVERT: A  460 MET cc_start: 0.8593 (tpp) cc_final: 0.8198 (mmm)
REVERT: B  295 MET cc_start: 0.9353 (mmp) cc_final: 0.9123 (mmm)
REVERT: B  402 MET cc_start: 0.8956 (tmm) cc_final: 0.7362 (tmm)
  outliers start: 3
  outliers final: 0
  residues processed: 82
  average time/residue: 0.2231
  time to fit residues: 25.4858
Evaluate side-chains
  73 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    7.9990
   chunk 84 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0040
   chunk 45 optimal weight:    4.9990
   chunk 87 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 65 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   overall best weight:    0.7596

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 579 GLN
** B 326 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 = 0.3293 r_free = 0.3293 target = 0.044037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.035280 restraints weight = 68202.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.036305 restraints weight = 39157.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.037015 restraints weight = 26911.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.1295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088   8950  Z= 0.129
  Angle     :  0.596  10.104  12092  Z= 0.307
  Chirality :  0.040   0.142   1440
  Planarity :  0.005   0.087   1532
  Dihedral  :  4.257  22.033   1238
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.23 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 19.21 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.25), residues: 1134
  helix:  1.62 (0.19), residues: 734
  sheet:  0.68 (0.89), residues: 32
  loop : -0.99 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  91 
 HIS   0.005   0.001   HIS B 427 
 PHE   0.017   0.001   PHE B 429 
 TYR   0.011   0.001   TYR A 351 
 ARG   0.006   0.000   ARG B 569 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04713 (  560)
  hydrogen bonds       : angle       4.59727 ( 1662)
  covalent geometry    : bond        0.00268 ( 8950)
  covalent geometry    : angle       0.59628 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9060 (tmm) cc_final: 0.8585 (tmm)
REVERT: A   45 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9067 (tp)
REVERT: A   64 LEU cc_start: 0.9504 (tp) cc_final: 0.9195 (tp)
REVERT: A   98 MET cc_start: 0.8846 (tpp) cc_final: 0.8292 (tpp)
REVERT: A  196 MET cc_start: 0.9161 (tmm) cc_final: 0.7814 (tmm)
REVERT: A  200 MET cc_start: 0.9288 (tpp) cc_final: 0.8948 (mmm)
REVERT: A  210 MET cc_start: 0.8564 (tpp) cc_final: 0.8001 (tpp)
REVERT: A  252 ASP cc_start: 0.9486 (m-30) cc_final: 0.9231 (t0)
REVERT: A  402 MET cc_start: 0.8413 (tmm) cc_final: 0.7928 (tmm)
REVERT: A  460 MET cc_start: 0.8630 (tpp) cc_final: 0.8413 (mmm)
REVERT: B  210 MET cc_start: 0.8876 (mmm) cc_final: 0.8628 (tpp)
REVERT: B  295 MET cc_start: 0.9276 (mmp) cc_final: 0.9008 (mmm)
REVERT: B  402 MET cc_start: 0.9016 (tmm) cc_final: 0.7770 (tmm)
REVERT: B  456 MET cc_start: 0.9276 (ttp) cc_final: 0.8553 (tpp)
  outliers start: 13
  outliers final: 5
  residues processed: 82
  average time/residue: 0.2065
  time to fit residues: 24.4576
Evaluate side-chains
  75 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  534 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 4 optimal weight:    6.9990
   chunk 46 optimal weight:    0.0870
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 52 optimal weight:   10.0000
   chunk 16 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    1.1360

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 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 = 0.3288 r_free = 0.3288 target = 0.043933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.035040 restraints weight = 69604.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.036085 restraints weight = 39591.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.036822 restraints weight = 27114.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   8950  Z= 0.125
  Angle     :  0.556   9.994  12092  Z= 0.288
  Chirality :  0.039   0.138   1440
  Planarity :  0.004   0.085   1532
  Dihedral  :  4.132  20.668   1238
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.88 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 19.52 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.25), residues: 1134
  helix:  1.75 (0.19), residues: 734
  sheet:  1.05 (0.95), residues: 32
  loop : -1.00 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  17 
 HIS   0.006   0.001   HIS A 568 
 PHE   0.015   0.001   PHE B 230 
 TYR   0.008   0.001   TYR B 268 
 ARG   0.003   0.000   ARG B  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04259 (  560)
  hydrogen bonds       : angle       4.32850 ( 1662)
  covalent geometry    : bond        0.00263 ( 8950)
  covalent geometry    : angle       0.55612 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9055 (tmm) cc_final: 0.8568 (tmm)
REVERT: A   98 MET cc_start: 0.8881 (tpp) cc_final: 0.8250 (tpp)
REVERT: A  196 MET cc_start: 0.8899 (tmm) cc_final: 0.8026 (tmm)
REVERT: A  200 MET cc_start: 0.9310 (tpp) cc_final: 0.8989 (mmm)
REVERT: A  210 MET cc_start: 0.8505 (tpp) cc_final: 0.8232 (tpp)
REVERT: A  252 ASP cc_start: 0.9464 (m-30) cc_final: 0.9206 (t0)
REVERT: A  402 MET cc_start: 0.8374 (tmm) cc_final: 0.7888 (tmm)
REVERT: B   44 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8559 (tmm)
REVERT: B  402 MET cc_start: 0.9080 (tmm) cc_final: 0.8820 (tmm)
REVERT: B  456 MET cc_start: 0.9310 (ttp) cc_final: 0.8418 (tpp)
REVERT: B  491 ILE cc_start: 0.9548 (OUTLIER) cc_final: 0.9317 (tt)
  outliers start: 20
  outliers final: 8
  residues processed: 91
  average time/residue: 0.2058
  time to fit residues: 27.1003
Evaluate side-chains
  80 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  534 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 92 optimal weight:   10.0000
   chunk 99 optimal weight:    0.9980
   chunk 107 optimal weight:    0.1980
   chunk 2 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0670
   overall best weight:    0.8520

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 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 = 0.3296 r_free = 0.3296 target = 0.044188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.035281 restraints weight = 69563.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.036319 restraints weight = 40156.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.037047 restraints weight = 27683.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084   8950  Z= 0.117
  Angle     :  0.567   8.523  12092  Z= 0.287
  Chirality :  0.039   0.165   1440
  Planarity :  0.004   0.083   1532
  Dihedral  :  4.058  20.320   1238
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.53 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.01 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.25), residues: 1134
  helix:  1.81 (0.19), residues: 730
  sheet:  1.16 (0.95), residues: 32
  loop : -0.96 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  17 
 HIS   0.006   0.001   HIS A 568 
 PHE   0.014   0.001   PHE B 230 
 TYR   0.008   0.001   TYR B 268 
 ARG   0.008   0.000   ARG B  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04040 (  560)
  hydrogen bonds       : angle       4.22777 ( 1662)
  covalent geometry    : bond        0.00251 ( 8950)
  covalent geometry    : angle       0.56719 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 75
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9044 (tmm) cc_final: 0.8568 (tmm)
REVERT: A   88 CYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8718 (t)
REVERT: A   98 MET cc_start: 0.8889 (tpp) cc_final: 0.8229 (tpp)
REVERT: A  252 ASP cc_start: 0.9461 (m-30) cc_final: 0.9185 (t0)
REVERT: A  359 LEU cc_start: 0.9611 (tp) cc_final: 0.9234 (tt)
REVERT: A  402 MET cc_start: 0.8354 (tmm) cc_final: 0.7863 (tmm)
REVERT: A  460 MET cc_start: 0.8649 (mmm) cc_final: 0.8374 (mmm)
REVERT: B   44 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8551 (tmm)
REVERT: B   88 CYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8748 (t)
REVERT: B  402 MET cc_start: 0.9097 (tmm) cc_final: 0.7580 (tmm)
REVERT: B  456 MET cc_start: 0.9341 (ttp) cc_final: 0.8643 (tpp)
REVERT: B  491 ILE cc_start: 0.9539 (OUTLIER) cc_final: 0.9304 (tt)
  outliers start: 28
  outliers final: 12
  residues processed: 100
  average time/residue: 0.1968
  time to fit residues: 28.1917
Evaluate side-chains
  89 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  534 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 89 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 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 = 0.3258 r_free = 0.3258 target = 0.043073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.034076 restraints weight = 70031.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.035079 restraints weight = 40983.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.035778 restraints weight = 28610.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   8950  Z= 0.166
  Angle     :  0.626  12.839  12092  Z= 0.313
  Chirality :  0.040   0.152   1440
  Planarity :  0.004   0.080   1532
  Dihedral  :  4.141  20.969   1238
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.32 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 20.87 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.25), residues: 1134
  helix:  1.81 (0.19), residues: 730
  sheet:  1.20 (0.95), residues: 32
  loop : -0.88 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  17 
 HIS   0.005   0.001   HIS A 568 
 PHE   0.016   0.002   PHE B 230 
 TYR   0.012   0.001   TYR B 268 
 ARG   0.003   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04080 (  560)
  hydrogen bonds       : angle       4.20890 ( 1662)
  covalent geometry    : bond        0.00352 ( 8950)
  covalent geometry    : angle       0.62556 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 74
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9068 (tmm) cc_final: 0.8553 (tmm)
REVERT: A   88 CYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8727 (t)
REVERT: A   98 MET cc_start: 0.8841 (tpp) cc_final: 0.8188 (tpp)
REVERT: A  210 MET cc_start: 0.8531 (tpp) cc_final: 0.8095 (tpp)
REVERT: A  359 LEU cc_start: 0.9618 (tp) cc_final: 0.9245 (tt)
REVERT: A  402 MET cc_start: 0.8442 (tmm) cc_final: 0.7951 (tmm)
REVERT: A  460 MET cc_start: 0.8745 (mmm) cc_final: 0.8449 (mmm)
REVERT: B   44 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8597 (tmm)
REVERT: B  402 MET cc_start: 0.9101 (tmm) cc_final: 0.8565 (tmm)
  outliers start: 29
  outliers final: 18
  residues processed: 101
  average time/residue: 0.2139
  time to fit residues: 30.8201
Evaluate side-chains
  90 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  441 ARG
Chi-restraints excluded: chain B residue  534 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 86 optimal weight:    8.9990
   chunk 51 optimal weight:    0.4980
   chunk 55 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 106 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 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 = 0.3277 r_free = 0.3277 target = 0.043679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.034936 restraints weight = 69309.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.035949 restraints weight = 39501.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.036670 restraints weight = 27087.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.083   8950  Z= 0.115
  Angle     :  0.614  11.922  12092  Z= 0.299
  Chirality :  0.039   0.144   1440
  Planarity :  0.004   0.080   1532
  Dihedral  :  4.055  20.981   1238
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.53 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 21.49 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.25), residues: 1134
  helix:  1.82 (0.19), residues: 730
  sheet:  1.47 (1.00), residues: 32
  loop : -0.96 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  66 
 HIS   0.005   0.001   HIS A 568 
 PHE   0.014   0.001   PHE B 230 
 TYR   0.008   0.001   TYR A 351 
 ARG   0.005   0.000   ARG B 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03904 (  560)
  hydrogen bonds       : angle       4.10930 ( 1662)
  covalent geometry    : bond        0.00247 ( 8950)
  covalent geometry    : angle       0.61410 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9124 (tmm) cc_final: 0.8620 (tmm)
REVERT: A   88 CYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8724 (t)
REVERT: A   98 MET cc_start: 0.8920 (tpp) cc_final: 0.8291 (tpp)
REVERT: A  210 MET cc_start: 0.8601 (tpp) cc_final: 0.8144 (tpp)
REVERT: A  252 ASP cc_start: 0.9479 (m-30) cc_final: 0.9237 (t0)
REVERT: A  295 MET cc_start: 0.8468 (ttt) cc_final: 0.8103 (tpp)
REVERT: A  359 LEU cc_start: 0.9610 (tp) cc_final: 0.9256 (tt)
REVERT: A  402 MET cc_start: 0.8306 (tmm) cc_final: 0.7816 (tmm)
REVERT: A  460 MET cc_start: 0.8782 (mmm) cc_final: 0.8471 (mmm)
REVERT: B   44 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8708 (tmm)
REVERT: B   88 CYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8776 (t)
REVERT: B  402 MET cc_start: 0.9121 (tmm) cc_final: 0.8680 (tmm)
REVERT: B  456 MET cc_start: 0.9324 (ttp) cc_final: 0.8886 (tmm)
  outliers start: 28
  outliers final: 14
  residues processed: 104
  average time/residue: 0.2384
  time to fit residues: 35.0938
Evaluate side-chains
  90 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue  101 ARG
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  534 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 104 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 70 optimal weight:    0.6980
   chunk 74 optimal weight:   10.0000
   chunk 71 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 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 = 0.3286 r_free = 0.3286 target = 0.043988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.035156 restraints weight = 70231.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.036207 restraints weight = 40207.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.036921 restraints weight = 27517.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   8950  Z= 0.118
  Angle     :  0.638  12.367  12092  Z= 0.310
  Chirality :  0.040   0.177   1440
  Planarity :  0.004   0.078   1532
  Dihedral  :  4.037  20.927   1238
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.97 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.31 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.26), residues: 1134
  helix:  1.87 (0.19), residues: 730
  sheet:  1.64 (1.02), residues: 32
  loop : -0.95 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  17 
 HIS   0.005   0.001   HIS A 568 
 PHE   0.014   0.001   PHE B 230 
 TYR   0.008   0.001   TYR B 268 
 ARG   0.005   0.000   ARG B 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03882 (  560)
  hydrogen bonds       : angle       4.09048 ( 1662)
  covalent geometry    : bond        0.00259 ( 8950)
  covalent geometry    : angle       0.63847 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9148 (tmm) cc_final: 0.8652 (tmm)
REVERT: A   45 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8986 (tp)
REVERT: A   88 CYS cc_start: 0.9351 (OUTLIER) cc_final: 0.8739 (t)
REVERT: A   98 MET cc_start: 0.8901 (tpp) cc_final: 0.8263 (tpp)
REVERT: A  210 MET cc_start: 0.8584 (tpp) cc_final: 0.8127 (tpp)
REVERT: A  252 ASP cc_start: 0.9485 (m-30) cc_final: 0.9227 (t0)
REVERT: A  295 MET cc_start: 0.8461 (ttt) cc_final: 0.8096 (tpp)
REVERT: A  359 LEU cc_start: 0.9602 (tp) cc_final: 0.9258 (tt)
REVERT: A  402 MET cc_start: 0.8317 (tmm) cc_final: 0.7835 (tmm)
REVERT: A  460 MET cc_start: 0.8829 (mmm) cc_final: 0.8495 (mmm)
REVERT: B   44 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8732 (tmm)
REVERT: B   88 CYS cc_start: 0.9375 (OUTLIER) cc_final: 0.8821 (t)
REVERT: B  295 MET cc_start: 0.9233 (tpp) cc_final: 0.8729 (ttt)
REVERT: B  402 MET cc_start: 0.9103 (tmm) cc_final: 0.8701 (tmm)
REVERT: B  456 MET cc_start: 0.9371 (ttp) cc_final: 0.8943 (tmm)
  outliers start: 22
  outliers final: 14
  residues processed: 96
  average time/residue: 0.1783
  time to fit residues: 25.8058
Evaluate side-chains
  94 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  534 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 96 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 102 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 49 optimal weight:    0.4980
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 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 = 0.3262 r_free = 0.3262 target = 0.043297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.034435 restraints weight = 71243.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.035454 restraints weight = 40923.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.036186 restraints weight = 28213.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   8950  Z= 0.145
  Angle     :  0.654  11.553  12092  Z= 0.320
  Chirality :  0.041   0.198   1440
  Planarity :  0.004   0.076   1532
  Dihedral  :  4.070  20.691   1238
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.97 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.62 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.26), residues: 1134
  helix:  1.89 (0.19), residues: 730
  sheet:  1.63 (1.03), residues: 32
  loop : -0.94 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  17 
 HIS   0.005   0.001   HIS A 107 
 PHE   0.014   0.001   PHE B 429 
 TYR   0.010   0.001   TYR B 268 
 ARG   0.006   0.000   ARG B 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03940 (  560)
  hydrogen bonds       : angle       4.12127 ( 1662)
  covalent geometry    : bond        0.00315 ( 8950)
  covalent geometry    : angle       0.65352 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9114 (tmm) cc_final: 0.8608 (tmm)
REVERT: A   88 CYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8739 (t)
REVERT: A   98 MET cc_start: 0.8886 (tpp) cc_final: 0.8248 (tpp)
REVERT: A  210 MET cc_start: 0.8480 (tpp) cc_final: 0.8031 (tpp)
REVERT: A  252 ASP cc_start: 0.9466 (m-30) cc_final: 0.9206 (t0)
REVERT: A  295 MET cc_start: 0.8455 (ttt) cc_final: 0.8121 (tpp)
REVERT: A  359 LEU cc_start: 0.9592 (tp) cc_final: 0.9249 (tt)
REVERT: A  402 MET cc_start: 0.8364 (tmm) cc_final: 0.7876 (tmm)
REVERT: A  460 MET cc_start: 0.8794 (mmm) cc_final: 0.8458 (mmm)
REVERT: B   44 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8709 (tmm)
REVERT: B   88 CYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8802 (t)
REVERT: B  295 MET cc_start: 0.9225 (tpp) cc_final: 0.8758 (ttt)
REVERT: B  402 MET cc_start: 0.9100 (tmm) cc_final: 0.8707 (tmm)
  outliers start: 22
  outliers final: 17
  residues processed: 95
  average time/residue: 0.1859
  time to fit residues: 26.2209
Evaluate side-chains
  93 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  534 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
** B 326 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 = 0.3275 r_free = 0.3275 target = 0.043633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.034871 restraints weight = 69493.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.035894 restraints weight = 39657.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.036613 restraints weight = 27243.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   8950  Z= 0.122
  Angle     :  0.672  13.008  12092  Z= 0.320
  Chirality :  0.040   0.202   1440
  Planarity :  0.005   0.119   1532
  Dihedral  :  4.126  20.735   1238
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.79 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 22.52 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.26), residues: 1134
  helix:  1.87 (0.19), residues: 730
  sheet:  1.70 (1.04), residues: 32
  loop : -0.99 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  17 
 HIS   0.005   0.001   HIS A 568 
 PHE   0.012   0.001   PHE B 230 
 TYR   0.008   0.001   TYR B 268 
 ARG   0.006   0.000   ARG B 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03868 (  560)
  hydrogen bonds       : angle       4.09857 ( 1662)
  covalent geometry    : bond        0.00268 ( 8950)
  covalent geometry    : angle       0.67178 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9150 (tmm) cc_final: 0.8848 (tmm)
REVERT: A   64 LEU cc_start: 0.9537 (tp) cc_final: 0.9280 (tp)
REVERT: A   88 CYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8741 (t)
REVERT: A   98 MET cc_start: 0.8911 (tpp) cc_final: 0.8275 (tpp)
REVERT: A  200 MET cc_start: 0.9048 (tpp) cc_final: 0.8278 (mmm)
REVERT: A  210 MET cc_start: 0.8552 (tpp) cc_final: 0.8059 (tpp)
REVERT: A  252 ASP cc_start: 0.9477 (m-30) cc_final: 0.9200 (t0)
REVERT: A  295 MET cc_start: 0.8451 (ttt) cc_final: 0.8068 (tpp)
REVERT: A  359 LEU cc_start: 0.9585 (tp) cc_final: 0.9234 (tt)
REVERT: A  402 MET cc_start: 0.8308 (tmm) cc_final: 0.7828 (tmm)
REVERT: A  418 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8565 (mm-40)
REVERT: A  456 MET cc_start: 0.9421 (ttp) cc_final: 0.9158 (tmm)
REVERT: A  460 MET cc_start: 0.8801 (mmm) cc_final: 0.8439 (mmm)
REVERT: B   88 CYS cc_start: 0.9363 (OUTLIER) cc_final: 0.8788 (t)
REVERT: B  295 MET cc_start: 0.9253 (tpp) cc_final: 0.8784 (ttt)
REVERT: B  402 MET cc_start: 0.9099 (tmm) cc_final: 0.8709 (tmm)
REVERT: B  456 MET cc_start: 0.9358 (ttp) cc_final: 0.8931 (tmm)
  outliers start: 23
  outliers final: 16
  residues processed: 101
  average time/residue: 0.1697
  time to fit residues: 26.4895
Evaluate side-chains
  98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  555 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 88 optimal weight:    8.9990
   chunk 100 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
** B 326 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 = 0.3277 r_free = 0.3277 target = 0.043808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.034825 restraints weight = 70534.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.035822 restraints weight = 41803.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.036538 restraints weight = 29365.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   8950  Z= 0.134
  Angle     :  0.686  12.836  12092  Z= 0.328
  Chirality :  0.041   0.196   1440
  Planarity :  0.005   0.098   1532
  Dihedral  :  4.112  20.467   1238
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.23 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 22.62 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.26), residues: 1134
  helix:  1.88 (0.19), residues: 730
  sheet:  1.75 (1.04), residues: 32
  loop : -0.97 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  17 
 HIS   0.004   0.001   HIS A 568 
 PHE   0.012   0.001   PHE B 230 
 TYR   0.009   0.001   TYR B 268 
 ARG   0.006   0.000   ARG B 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03881 (  560)
  hydrogen bonds       : angle       4.11349 ( 1662)
  covalent geometry    : bond        0.00295 ( 8950)
  covalent geometry    : angle       0.68594 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LEU cc_start: 0.9682 (mt) cc_final: 0.9457 (tp)
REVERT: A   44 MET cc_start: 0.9077 (tmm) cc_final: 0.8634 (tmm)
REVERT: A   64 LEU cc_start: 0.9529 (tp) cc_final: 0.9278 (tp)
REVERT: A   88 CYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8691 (t)
REVERT: A   98 MET cc_start: 0.8858 (tpp) cc_final: 0.8212 (tpp)
REVERT: A  210 MET cc_start: 0.8459 (tpp) cc_final: 0.8029 (tpp)
REVERT: A  252 ASP cc_start: 0.9441 (m-30) cc_final: 0.9179 (t0)
REVERT: A  295 MET cc_start: 0.8431 (ttt) cc_final: 0.8088 (tpp)
REVERT: A  359 LEU cc_start: 0.9578 (tp) cc_final: 0.9250 (tt)
REVERT: A  402 MET cc_start: 0.8367 (tmm) cc_final: 0.7866 (tmm)
REVERT: A  418 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8547 (mm-40)
REVERT: A  456 MET cc_start: 0.9349 (ttp) cc_final: 0.9105 (tmm)
REVERT: A  460 MET cc_start: 0.8785 (mmm) cc_final: 0.8426 (mmm)
REVERT: B   88 CYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8761 (t)
REVERT: B  295 MET cc_start: 0.9204 (tpp) cc_final: 0.8762 (ttt)
REVERT: B  402 MET cc_start: 0.9127 (tmm) cc_final: 0.8732 (tmm)
  outliers start: 20
  outliers final: 16
  residues processed: 99
  average time/residue: 0.1774
  time to fit residues: 26.9043
Evaluate side-chains
  99 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  555 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 37 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 111 optimal weight:   30.0000
   chunk 102 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
** B 326 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 = 0.3279 r_free = 0.3279 target = 0.043879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.034901 restraints weight = 70654.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.035917 restraints weight = 41776.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.036632 restraints weight = 29356.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   8950  Z= 0.132
  Angle     :  0.682  12.727  12092  Z= 0.328
  Chirality :  0.041   0.201   1440
  Planarity :  0.005   0.093   1532
  Dihedral  :  4.172  25.646   1238
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.32 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 22.62 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.26), residues: 1134
  helix:  1.89 (0.19), residues: 730
  sheet:  1.79 (1.04), residues: 32
  loop : -0.99 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  17 
 HIS   0.004   0.001   HIS A 568 
 PHE   0.012   0.001   PHE B 230 
 TYR   0.010   0.001   TYR B 268 
 ARG   0.006   0.000   ARG B 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03913 (  560)
  hydrogen bonds       : angle       4.14254 ( 1662)
  covalent geometry    : bond        0.00290 ( 8950)
  covalent geometry    : angle       0.68200 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3032.34 seconds
wall clock time: 54 minutes 24.28 seconds (3264.28 seconds total)