Starting phenix.real_space_refine
on Sat Aug 23 01:09:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fv6_50790/08_2025/9fv6_50790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fv6_50790/08_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_50790/08_2025/9fv6_50790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fv6_50790/08_2025/9fv6_50790.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fv6_50790/08_2025/9fv6_50790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fv6_50790/08_2025/9fv6_50790.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.65, per 1000 atoms: 0.30
  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: 0.70
  Conformation dependent library (CDL) restraints added in 265.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.32
  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: 1.31

  Time building geometry restraints manager: 0.89 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: 0.02
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:             4.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.660
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.450
-------------------------------------------------------------------------------
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 : 6.26
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.25), 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
 ARG   0.005   0.001   ARG A 488 
 TYR   0.017   0.001   TYR A 439 
 PHE   0.015   0.002   PHE A 429 
 TRP   0.011   0.001   TRP B  17 
 HIS   0.007   0.001   HIS A 427 

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

*********************** 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  : 0.279 
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: 0.0958
  time to fit residues: 10.9044
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  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    0.0010
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    0.5980
   chunk 106 optimal weight:    9.9990
   overall best weight:    2.1192

-------------------------------------------------------------------------------
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**
B 363 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.042957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.034081 restraints weight = 70009.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.035109 restraints weight = 39569.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.035829 restraints weight = 27105.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.036318 restraints weight = 20737.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.036710 restraints weight = 17147.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   8950  Z= 0.173
  Angle     :  0.615  10.021  12092  Z= 0.321
  Chirality :  0.040   0.140   1440
  Planarity :  0.005   0.086   1532
  Dihedral  :  4.317  22.740   1238
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.67 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 19.11 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.25), residues: 1134
  helix:  1.64 (0.19), residues: 736
  sheet:  0.52 (0.86), residues: 32
  loop : -0.92 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 569 
 TYR   0.012   0.001   TYR A 351 
 PHE   0.020   0.002   PHE B 230 
 TRP   0.009   0.001   TRP B  17 
 HIS   0.005   0.001   HIS B 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 8950)
  covalent geometry    : angle       0.61503 (12092)
  hydrogen bonds       : bond        0.04707 (  560)
  hydrogen bonds       : angle       4.63298 ( 1662)

*********************** 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
  95 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9052 (tmm) cc_final: 0.8547 (tmm)
REVERT: A   64 LEU cc_start: 0.9499 (tp) cc_final: 0.9167 (tp)
REVERT: A   98 MET cc_start: 0.8838 (tpp) cc_final: 0.8284 (tpp)
REVERT: A  111 MET cc_start: 0.8441 (tmm) cc_final: 0.8221 (tmm)
REVERT: A  200 MET cc_start: 0.9239 (tpp) cc_final: 0.8935 (mmm)
REVERT: A  210 MET cc_start: 0.8596 (tpp) cc_final: 0.8365 (tpp)
REVERT: A  252 ASP cc_start: 0.9466 (m-30) cc_final: 0.9233 (t0)
REVERT: A  402 MET cc_start: 0.8474 (tmm) cc_final: 0.8027 (tmm)
REVERT: A  460 MET cc_start: 0.8633 (tpp) cc_final: 0.8411 (mmm)
REVERT: B  210 MET cc_start: 0.8886 (mmm) cc_final: 0.8660 (tpp)
REVERT: B  295 MET cc_start: 0.9264 (mmp) cc_final: 0.8984 (mmm)
REVERT: B  319 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8353 (m-80)
REVERT: B  402 MET cc_start: 0.9036 (tmm) cc_final: 0.8419 (tmm)
REVERT: B  456 MET cc_start: 0.9324 (ttp) cc_final: 0.8472 (tpp)
  outliers start: 21
  outliers final: 10
  residues processed: 90
  average time/residue: 0.0885
  time to fit residues: 11.5281
Evaluate side-chains
  81 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  319 PHE
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 51 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 73 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 55 optimal weight:   20.0000
   chunk 38 optimal weight:    0.1980
   chunk 96 optimal weight:    9.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3257 r_free = 0.3257 target = 0.043079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.034321 restraints weight = 69667.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.035311 restraints weight = 39444.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.036032 restraints weight = 27115.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.036492 restraints weight = 20679.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.036896 restraints weight = 17182.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.1706

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= 0.129
  Angle     :  0.562   9.777  12092  Z= 0.291
  Chirality :  0.039   0.141   1440
  Planarity :  0.004   0.086   1532
  Dihedral  :  4.162  20.329   1238
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.79 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 20.66 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.25), residues: 1134
  helix:  1.77 (0.19), residues: 734
  sheet:  1.07 (0.96), residues: 32
  loop : -1.04 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 569 
 TYR   0.010   0.001   TYR A 572 
 PHE   0.015   0.001   PHE B 230 
 TRP   0.009   0.001   TRP B  66 
 HIS   0.004   0.001   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8950)
  covalent geometry    : angle       0.56208 (12092)
  hydrogen bonds       : bond        0.04324 (  560)
  hydrogen bonds       : angle       4.33624 ( 1662)

*********************** 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
  97 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9074 (tmm) cc_final: 0.8565 (tmm)
REVERT: A   64 LEU cc_start: 0.9512 (tp) cc_final: 0.9306 (tp)
REVERT: A   98 MET cc_start: 0.8894 (tpp) cc_final: 0.8267 (tpp)
REVERT: A  196 MET cc_start: 0.8882 (tmm) cc_final: 0.7952 (tmm)
REVERT: A  200 MET cc_start: 0.9286 (tpp) cc_final: 0.9003 (mmm)
REVERT: A  210 MET cc_start: 0.8597 (tpp) cc_final: 0.8320 (tpp)
REVERT: A  252 ASP cc_start: 0.9489 (m-30) cc_final: 0.9240 (t0)
REVERT: A  402 MET cc_start: 0.8384 (tmm) cc_final: 0.7903 (tmm)
REVERT: A  460 MET cc_start: 0.8681 (tpp) cc_final: 0.8448 (mmm)
REVERT: B  319 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8370 (m-80)
REVERT: B  402 MET cc_start: 0.9066 (tmm) cc_final: 0.8499 (tmm)
  outliers start: 22
  outliers final: 11
  residues processed: 95
  average time/residue: 0.0886
  time to fit residues: 12.2849
Evaluate side-chains
  81 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
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  171 LEU
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  319 PHE
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 13 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 66 optimal weight:    0.1980
   chunk 36 optimal weight:    9.9990
   chunk 81 optimal weight:    0.9990
   chunk 53 optimal weight:    8.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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 = 0.3267 r_free = 0.3267 target = 0.043353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.034481 restraints weight = 70808.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.035506 restraints weight = 40667.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.036221 restraints weight = 28024.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.036727 restraints weight = 21557.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.037066 restraints weight = 17797.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.1994

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= 0.126
  Angle     :  0.560   8.465  12092  Z= 0.289
  Chirality :  0.039   0.143   1440
  Planarity :  0.004   0.083   1532
  Dihedral  :  4.104  20.947   1238
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.06 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.76 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.25), residues: 1134
  helix:  1.77 (0.19), residues: 734
  sheet:  1.20 (0.96), residues: 32
  loop : -1.05 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  14 
 TYR   0.009   0.001   TYR B 268 
 PHE   0.015   0.001   PHE B 429 
 TRP   0.009   0.001   TRP B  17 
 HIS   0.006   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8950)
  covalent geometry    : angle       0.55954 (12092)
  hydrogen bonds       : bond        0.04097 (  560)
  hydrogen bonds       : angle       4.25209 ( 1662)

*********************** 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
  104 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 74
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9046 (tmm) cc_final: 0.8540 (tmm)
REVERT: A   64 LEU cc_start: 0.9516 (tp) cc_final: 0.9301 (tp)
REVERT: A   88 CYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8749 (t)
REVERT: A   98 MET cc_start: 0.8882 (tpp) cc_final: 0.8235 (tpp)
REVERT: A  252 ASP cc_start: 0.9473 (m-30) cc_final: 0.9215 (t0)
REVERT: A  402 MET cc_start: 0.8380 (tmm) cc_final: 0.7876 (tmm)
REVERT: B  319 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8362 (m-80)
REVERT: B  402 MET cc_start: 0.9106 (tmm) cc_final: 0.7604 (tmm)
REVERT: B  456 MET cc_start: 0.9304 (ttp) cc_final: 0.8941 (tmm)
  outliers start: 30
  outliers final: 13
  residues processed: 101
  average time/residue: 0.0976
  time to fit residues: 13.8438
Evaluate side-chains
  87 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
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  174 LEU
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   35 ILE
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  252 ASP
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  319 PHE
Chi-restraints excluded: chain B residue  441 ARG
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 96 optimal weight:    3.9990
   chunk 111 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 83 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3266 r_free = 0.3266 target = 0.043313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.034537 restraints weight = 70368.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.035565 restraints weight = 40100.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.036286 restraints weight = 27368.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.036774 restraints weight = 20825.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.037149 restraints weight = 17147.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.2215

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     :  0.604  12.493  12092  Z= 0.298
  Chirality :  0.039   0.174   1440
  Planarity :  0.004   0.081   1532
  Dihedral  :  4.090  20.852   1238
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.88 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 20.97 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.25), residues: 1134
  helix:  1.86 (0.19), residues: 730
  sheet:  1.44 (0.99), residues: 32
  loop : -0.99 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 236 
 TYR   0.008   0.001   TYR B 268 
 PHE   0.015   0.001   PHE B 230 
 TRP   0.008   0.001   TRP B  66 
 HIS   0.006   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8950)
  covalent geometry    : angle       0.60374 (12092)
  hydrogen bonds       : bond        0.03972 (  560)
  hydrogen bonds       : angle       4.18643 ( 1662)

*********************** 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
  106 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 78
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9080 (tmm) cc_final: 0.8580 (tmm)
REVERT: A   64 LEU cc_start: 0.9526 (tp) cc_final: 0.9296 (tp)
REVERT: A   88 CYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8747 (t)
REVERT: A   98 MET cc_start: 0.8880 (tpp) cc_final: 0.8253 (tpp)
REVERT: A  210 MET cc_start: 0.8568 (tpp) cc_final: 0.7999 (tpp)
REVERT: A  252 ASP cc_start: 0.9484 (m-30) cc_final: 0.9207 (t0)
REVERT: A  257 LEU cc_start: 0.9767 (tt) cc_final: 0.9502 (pp)
REVERT: A  359 LEU cc_start: 0.9610 (tp) cc_final: 0.9215 (tt)
REVERT: A  460 MET cc_start: 0.8641 (mmm) cc_final: 0.8297 (mmm)
REVERT: B   88 CYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8759 (t)
REVERT: B  319 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8374 (m-80)
REVERT: B  402 MET cc_start: 0.9105 (tmm) cc_final: 0.8573 (tmm)
  outliers start: 28
  outliers final: 15
  residues processed: 102
  average time/residue: 0.0985
  time to fit residues: 14.2568
Evaluate side-chains
  93 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
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  174 LEU
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   88 CYS
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  252 ASP
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  319 PHE
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 109 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 53 optimal weight:    8.9990
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    1.1988

-------------------------------------------------------------------------------
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 = 0.3264 r_free = 0.3264 target = 0.043286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.034530 restraints weight = 70177.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.035531 restraints weight = 40076.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.036238 restraints weight = 27536.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.036771 restraints weight = 21144.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.037114 restraints weight = 17281.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.2400

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= 0.124
  Angle     :  0.607  11.016  12092  Z= 0.299
  Chirality :  0.039   0.142   1440
  Planarity :  0.004   0.079   1532
  Dihedral  :  4.083  20.938   1238
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.79 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 20.97 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.25), residues: 1134
  helix:  1.90 (0.19), residues: 730
  sheet:  1.60 (1.00), residues: 32
  loop : -0.96 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 441 
 TYR   0.009   0.001   TYR B 268 
 PHE   0.014   0.001   PHE B 230 
 TRP   0.008   0.001   TRP B  66 
 HIS   0.005   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8950)
  covalent geometry    : angle       0.60706 (12092)
  hydrogen bonds       : bond        0.03918 (  560)
  hydrogen bonds       : angle       4.12934 ( 1662)

*********************** 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
  110 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9086 (tmm) cc_final: 0.8584 (tmm)
REVERT: A   88 CYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8744 (t)
REVERT: A   98 MET cc_start: 0.8880 (tpp) cc_final: 0.8238 (tpp)
REVERT: A  210 MET cc_start: 0.8527 (tpp) cc_final: 0.8048 (tpp)
REVERT: A  252 ASP cc_start: 0.9476 (m-30) cc_final: 0.9184 (t0)
REVERT: A  359 LEU cc_start: 0.9589 (tp) cc_final: 0.9197 (tt)
REVERT: A  460 MET cc_start: 0.8659 (mmm) cc_final: 0.8282 (mmm)
REVERT: B   88 CYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8757 (t)
REVERT: B  319 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8396 (m-80)
REVERT: B  402 MET cc_start: 0.9146 (tmm) cc_final: 0.8688 (tmm)
  outliers start: 32
  outliers final: 16
  residues processed: 108
  average time/residue: 0.0944
  time to fit residues: 14.3732
Evaluate side-chains
  93 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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  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   35 ILE
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  252 ASP
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  319 PHE
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 64 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 60 optimal weight:    0.0030
   chunk 57 optimal weight:    8.9990
   chunk 104 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 88 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 109 optimal weight:    9.9990
   chunk 36 optimal weight:    0.0980
   chunk 93 optimal weight:    6.9990
   overall best weight:    2.0196

-------------------------------------------------------------------------------
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 = 0.3240 r_free = 0.3240 target = 0.042717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.033872 restraints weight = 71214.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.034877 restraints weight = 40803.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.035597 restraints weight = 28140.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.036087 restraints weight = 21621.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.036464 restraints weight = 17882.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.2634

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= 0.159
  Angle     :  0.636  11.529  12092  Z= 0.316
  Chirality :  0.040   0.174   1440
  Planarity :  0.004   0.077   1532
  Dihedral  :  4.127  21.048   1238
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.14 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 22.31 %
    Favored  : 74.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.25), residues: 1134
  helix:  1.87 (0.19), residues: 730
  sheet:  1.71 (1.01), residues: 32
  loop : -0.92 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 354 
 TYR   0.011   0.001   TYR B 268 
 PHE   0.016   0.001   PHE B 429 
 TRP   0.011   0.001   TRP B  17 
 HIS   0.005   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8950)
  covalent geometry    : angle       0.63579 (12092)
  hydrogen bonds       : bond        0.04000 (  560)
  hydrogen bonds       : angle       4.18118 ( 1662)

*********************** 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
  100 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9091 (tmm) cc_final: 0.8575 (tmm)
REVERT: A   88 CYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8726 (t)
REVERT: A   98 MET cc_start: 0.8871 (tpp) cc_final: 0.8247 (tpp)
REVERT: A  210 MET cc_start: 0.8471 (tpp) cc_final: 0.8007 (tpp)
REVERT: A  252 ASP cc_start: 0.9485 (m-30) cc_final: 0.9201 (t0)
REVERT: A  359 LEU cc_start: 0.9599 (tp) cc_final: 0.9220 (tt)
REVERT: A  460 MET cc_start: 0.8712 (mmm) cc_final: 0.8316 (mmm)
REVERT: B  319 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8398 (m-80)
REVERT: B  402 MET cc_start: 0.9090 (tmm) cc_final: 0.8708 (tmm)
  outliers start: 27
  outliers final: 19
  residues processed: 98
  average time/residue: 0.0899
  time to fit residues: 12.8528
Evaluate side-chains
  94 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
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  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   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  319 PHE
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  555 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 99 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    0.1980
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3261 r_free = 0.3261 target = 0.043256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.034453 restraints weight = 70023.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.035448 restraints weight = 40349.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.036175 restraints weight = 28011.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.036668 restraints weight = 21436.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.037047 restraints weight = 17700.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.2780

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= 0.123
  Angle     :  0.654  11.511  12092  Z= 0.316
  Chirality :  0.040   0.180   1440
  Planarity :  0.004   0.076   1532
  Dihedral  :  4.090  21.230   1238
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.79 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 22.93 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.25), residues: 1134
  helix:  1.86 (0.19), residues: 730
  sheet:  1.92 (1.05), residues: 32
  loop : -0.98 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 441 
 TYR   0.008   0.001   TYR B 268 
 PHE   0.013   0.001   PHE B 230 
 TRP   0.010   0.001   TRP B  17 
 HIS   0.005   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8950)
  covalent geometry    : angle       0.65366 (12092)
  hydrogen bonds       : bond        0.03898 (  560)
  hydrogen bonds       : angle       4.14984 ( 1662)

*********************** 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
  104 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9102 (tmm) cc_final: 0.8595 (tmm)
REVERT: A   88 CYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8727 (t)
REVERT: A   98 MET cc_start: 0.8883 (tpp) cc_final: 0.8254 (tpp)
REVERT: A  210 MET cc_start: 0.8508 (tpp) cc_final: 0.8021 (tpp)
REVERT: A  252 ASP cc_start: 0.9477 (m-30) cc_final: 0.9185 (t0)
REVERT: A  295 MET cc_start: 0.8426 (ttt) cc_final: 0.8083 (tpp)
REVERT: A  359 LEU cc_start: 0.9581 (tp) cc_final: 0.9207 (tt)
REVERT: A  460 MET cc_start: 0.8728 (mmm) cc_final: 0.8315 (mmm)
REVERT: B   88 CYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8762 (t)
REVERT: B  319 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8421 (m-80)
REVERT: B  402 MET cc_start: 0.9122 (tmm) cc_final: 0.8722 (tmm)
REVERT: B  456 MET cc_start: 0.9384 (ttp) cc_final: 0.8805 (tmm)
  outliers start: 24
  outliers final: 17
  residues processed: 101
  average time/residue: 0.0812
  time to fit residues: 12.0006
Evaluate side-chains
  98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
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  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   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  319 PHE
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 109 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 1 optimal weight:    0.0870
   chunk 105 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.7360

-------------------------------------------------------------------------------
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 = 0.043695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.034910 restraints weight = 69778.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.035933 restraints weight = 40540.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.036634 restraints weight = 28137.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.037175 restraints weight = 21631.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.037533 restraints weight = 17733.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2929

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= 0.117
  Angle     :  0.667  10.720  12092  Z= 0.318
  Chirality :  0.040   0.176   1440
  Planarity :  0.004   0.075   1532
  Dihedral  :  4.065  21.185   1238
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.88 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 23.45 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.26), residues: 1134
  helix:  1.90 (0.19), residues: 730
  sheet:  2.05 (1.06), residues: 32
  loop : -0.97 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 441 
 TYR   0.007   0.001   TYR B 268 
 PHE   0.011   0.001   PHE B 230 
 TRP   0.010   0.001   TRP B  17 
 HIS   0.005   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8950)
  covalent geometry    : angle       0.66697 (12092)
  hydrogen bonds       : bond        0.03828 (  560)
  hydrogen bonds       : angle       4.10787 ( 1662)

*********************** 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
  104 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9103 (tmm) cc_final: 0.8794 (tmm)
REVERT: A   88 CYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8764 (t)
REVERT: A   98 MET cc_start: 0.8879 (tpp) cc_final: 0.8202 (tpp)
REVERT: A  210 MET cc_start: 0.8493 (tpp) cc_final: 0.8036 (tpp)
REVERT: A  252 ASP cc_start: 0.9472 (m-30) cc_final: 0.9163 (t0)
REVERT: A  295 MET cc_start: 0.8392 (ttt) cc_final: 0.8053 (tpp)
REVERT: A  359 LEU cc_start: 0.9551 (tp) cc_final: 0.9178 (tt)
REVERT: A  460 MET cc_start: 0.8735 (mmm) cc_final: 0.8333 (mmm)
REVERT: B   88 CYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8747 (t)
REVERT: B  319 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8429 (m-80)
REVERT: B  402 MET cc_start: 0.9130 (tmm) cc_final: 0.8737 (tmm)
REVERT: B  456 MET cc_start: 0.9385 (ttp) cc_final: 0.9113 (tmm)
  outliers start: 22
  outliers final: 15
  residues processed: 102
  average time/residue: 0.0846
  time to fit residues: 12.8016
Evaluate side-chains
  98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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  388 LEU
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   88 CYS
Chi-restraints excluded: chain B residue   97 VAL
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  319 PHE
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 47 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   chunk 82 optimal weight:    0.0870
   chunk 3 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 108 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 109 optimal weight:    6.9990
   overall best weight:    0.6760

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

Flipped N/Q/H residues before XYZ refinement:
B  37 ASN
** 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 = 0.3289 r_free = 0.3289 target = 0.044145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.035149 restraints weight = 69977.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.036180 restraints weight = 40871.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.036919 restraints weight = 28508.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.037448 restraints weight = 21995.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.037805 restraints weight = 18155.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.3039

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= 0.119
  Angle     :  0.686  11.089  12092  Z= 0.327
  Chirality :  0.040   0.181   1440
  Planarity :  0.004   0.074   1532
  Dihedral  :  4.038  20.901   1238
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.70 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 24.07 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.26), residues: 1134
  helix:  1.89 (0.19), residues: 730
  sheet:  2.05 (1.07), residues: 32
  loop : -0.98 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 441 
 TYR   0.008   0.001   TYR B 268 
 PHE   0.011   0.001   PHE B 230 
 TRP   0.011   0.001   TRP B  17 
 HIS   0.005   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8950)
  covalent geometry    : angle       0.68592 (12092)
  hydrogen bonds       : bond        0.03834 (  560)
  hydrogen bonds       : angle       4.08718 ( 1662)

********************** 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
  99 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9082 (tmm) cc_final: 0.8766 (tmm)
REVERT: A   88 CYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8739 (t)
REVERT: A   98 MET cc_start: 0.8861 (tpp) cc_final: 0.8182 (tpp)
REVERT: A  210 MET cc_start: 0.8488 (tpp) cc_final: 0.8041 (tpp)
REVERT: A  252 ASP cc_start: 0.9457 (m-30) cc_final: 0.9145 (t0)
REVERT: A  295 MET cc_start: 0.8370 (ttt) cc_final: 0.8050 (tpp)
REVERT: A  359 LEU cc_start: 0.9544 (tp) cc_final: 0.9184 (tt)
REVERT: A  456 MET cc_start: 0.9386 (ttp) cc_final: 0.9093 (tmm)
REVERT: A  460 MET cc_start: 0.8736 (mmm) cc_final: 0.8319 (mmm)
REVERT: B   88 CYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8721 (t)
REVERT: B  291 MET cc_start: 0.9429 (tpp) cc_final: 0.9122 (tpp)
REVERT: B  319 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8457 (m-80)
REVERT: B  402 MET cc_start: 0.9149 (tmm) cc_final: 0.8752 (tmm)
REVERT: B  456 MET cc_start: 0.9393 (ttp) cc_final: 0.9122 (tmm)
  outliers start: 16
  outliers final: 11
  residues processed: 97
  average time/residue: 0.0797
  time to fit residues: 11.7612
Evaluate side-chains
  94 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
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  426 VAL
Chi-restraints excluded: chain A residue  556 ILE
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  164 SER
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  319 PHE
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 80 optimal weight:    0.9990
   chunk 104 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0570
   chunk 49 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0000
   chunk 65 optimal weight:    4.9990
   chunk 94 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.5302

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3298 r_free = 0.3298 target = 0.044419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.035650 restraints weight = 68772.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.036656 restraints weight = 40488.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.037382 restraints weight = 28339.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.037877 restraints weight = 21864.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.038252 restraints weight = 18124.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.3193

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= 0.117
  Angle     :  0.690  10.873  12092  Z= 0.323
  Chirality :  0.041   0.240   1440
  Planarity :  0.004   0.073   1532
  Dihedral  :  3.981  20.670   1238
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.06 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 23.66 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.26), residues: 1134
  helix:  1.88 (0.19), residues: 732
  sheet:  2.12 (1.08), residues: 32
  loop : -0.98 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 441 
 TYR   0.008   0.001   TYR B 268 
 PHE   0.010   0.001   PHE B 230 
 TRP   0.009   0.001   TRP B  17 
 HIS   0.005   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8950)
  covalent geometry    : angle       0.68957 (12092)
  hydrogen bonds       : bond        0.03796 (  560)
  hydrogen bonds       : angle       4.06449 ( 1662)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1543.96 seconds
wall clock time: 27 minutes 28.73 seconds (1648.73 seconds total)