Starting phenix.real_space_refine
on Mon Apr 28 09:08:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qv6_4645/04_2025/6qv6_4645.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qv6_4645/04_2025/6qv6_4645.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qv6_4645/04_2025/6qv6_4645.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qv6_4645/04_2025/6qv6_4645.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qv6_4645/04_2025/6qv6_4645.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qv6_4645/04_2025/6qv6_4645.cif"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      58      5.16       5
     C    4814      2.51       5
     N    1138      2.21       5
     O    1198      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7208
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3604
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 25, 'TRANS': 443}
          Chain breaks: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.49, per 1000 atoms: 0.90
  Number of scatterers: 7208
  At special positions: 0
  Unit cell: (105.93, 82.39, 75.97, 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      58     16.00
     O    1198      8.00
     N    1138      7.00
     C    4814      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: 1.72
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1720

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 2 sheets defined
      74.8% alpha, 0.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'B' and resid 116 through 153
      removed outlier: 4.096A  pdb=" N   PHE B 120 " --> pdb=" O   GLU B 116 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU B 130 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL B 131 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 181
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 190 through 198
      removed outlier: 4.209A  pdb=" N   MET B 194 " --> pdb=" O   GLY B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 207
      removed outlier: 3.852A  pdb=" N   LEU B 207 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 204 through 207'
    Processing helix  chain 'B' and resid 208 through 224
      removed outlier: 3.962A  pdb=" N   PHE B 212 " --> pdb=" O   THR B 208 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL B 213 " --> pdb=" O   MET B 209 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   VAL B 217 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   ALA B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 250
      removed outlier: 3.644A  pdb=" N   PHE B 235 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 280
    Processing helix  chain 'B' and resid 281 through 291
    Processing helix  chain 'B' and resid 298 through 323
      removed outlier: 3.879A  pdb=" N   ALA B 320 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   VAL B 321 " --> pdb=" O   ARG B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 377
      removed outlier: 3.899A  pdb=" N   PHE B 351 " --> pdb=" O   GLU B 347 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   CYS B 358 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   GLY B 375 " --> pdb=" O   GLN B 371 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 389
      removed outlier: 3.585A  pdb=" N   HIS B 389 " --> pdb=" O   PHE B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 404
      removed outlier: 3.645A  pdb=" N   GLY B 395 " --> pdb=" O   LEU B 391 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   VAL B 397 " --> pdb=" O   TYR B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 427
    Processing helix  chain 'B' and resid 434 through 438
      removed outlier: 3.806A  pdb=" N   GLY B 438 " --> pdb=" O   LYS B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 450
      removed outlier: 3.682A  pdb=" N   ALA B 447 " --> pdb=" O   GLY B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 477
      removed outlier: 3.597A  pdb=" N   ILE B 459 " --> pdb=" O   ASN B 455 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ILE B 472 " --> pdb=" O   PHE B 468 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL B 473 " --> pdb=" O   TRP B 469 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   MET B 477 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 506
    Processing helix  chain 'B' and resid 521 through 537
      removed outlier: 4.761A  pdb=" N   THR B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 541 through 551
      removed outlier: 3.903A  pdb=" N   ILE B 545 " --> pdb=" O   SER B 541 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 574
      removed outlier: 3.731A  pdb=" N   GLN B 574 " --> pdb=" O   ALA B 570 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 576 through 586
    Processing helix  chain 'A' and resid 116 through 153
      removed outlier: 4.097A  pdb=" N   PHE A 120 " --> pdb=" O   GLU A 116 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 181
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 190 through 198
      removed outlier: 4.209A  pdb=" N   MET A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 207
      removed outlier: 3.852A  pdb=" N   LEU A 207 " --> pdb=" O   LYS A 204 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 204 through 207'
    Processing helix  chain 'A' and resid 208 through 224
      removed outlier: 3.963A  pdb=" N   PHE A 212 " --> pdb=" O   THR A 208 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL A 213 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   VAL A 217 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   ALA A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 250
      removed outlier: 3.644A  pdb=" N   PHE A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 280
    Processing helix  chain 'A' and resid 281 through 291
    Processing helix  chain 'A' and resid 298 through 323
      removed outlier: 3.879A  pdb=" N   ALA A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   VAL A 321 " --> pdb=" O   ARG A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 377
      removed outlier: 3.900A  pdb=" N   PHE A 351 " --> pdb=" O   GLU A 347 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   CYS A 358 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   GLY A 375 " --> pdb=" O   GLN A 371 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 389
      removed outlier: 3.585A  pdb=" N   HIS A 389 " --> pdb=" O   PHE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 404
      removed outlier: 3.645A  pdb=" N   GLY A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   VAL A 397 " --> pdb=" O   TYR A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 427
    Processing helix  chain 'A' and resid 434 through 438
      removed outlier: 3.807A  pdb=" N   GLY A 438 " --> pdb=" O   LYS A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 3.681A  pdb=" N   ALA A 447 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 477
      removed outlier: 3.598A  pdb=" N   ILE A 459 " --> pdb=" O   ASN A 455 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ILE A 472 " --> pdb=" O   PHE A 468 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL A 473 " --> pdb=" O   TRP A 469 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   MET A 477 " --> pdb=" O   VAL A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 506
    Processing helix  chain 'A' and resid 521 through 537
      removed outlier: 4.761A  pdb=" N   THR A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 551
      removed outlier: 3.904A  pdb=" N   ILE A 545 " --> pdb=" O   SER A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 574
      removed outlier: 3.732A  pdb=" N   GLN A 574 " --> pdb=" O   ALA A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 586
    Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512
    Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 512

    486 hydrogen bonds defined for protein.
    1422 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.03

  Time building geometry restraints manager: 2.03 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2036
        1.34 -     1.46: 1662
        1.46 -     1.58: 3614
        1.58 -     1.69: 0
        1.69 -     1.81: 98
  Bond restraints: 7410
  Sorted by residual:
  bond pdb=" CB  PRO B 408 "
       pdb=" CG  PRO B 408 "
    ideal  model  delta    sigma   weight residual
    1.492  1.400  0.092 5.00e-02 4.00e+02 3.37e+00
  bond pdb=" CB  PRO A 408 "
       pdb=" CG  PRO A 408 "
    ideal  model  delta    sigma   weight residual
    1.492  1.401  0.091 5.00e-02 4.00e+02 3.31e+00
  bond pdb=" CB  GLU B 347 "
       pdb=" CG  GLU B 347 "
    ideal  model  delta    sigma   weight residual
    1.520  1.575 -0.055 3.00e-02 1.11e+03 3.30e+00
  bond pdb=" CB  GLU A 347 "
       pdb=" CG  GLU A 347 "
    ideal  model  delta    sigma   weight residual
    1.520  1.574 -0.054 3.00e-02 1.11e+03 3.26e+00
  bond pdb=" CG1 ILE A 564 "
       pdb=" CD1 ILE A 564 "
    ideal  model  delta    sigma   weight residual
    1.513  1.443  0.070 3.90e-02 6.57e+02 3.24e+00
  ... (remaining 7405 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.00: 9692
        3.00 -     6.00: 330
        6.00 -     9.00: 36
        9.00 -    12.00: 20
       12.00 -    15.00: 6
  Bond angle restraints: 10084
  Sorted by residual:
  angle pdb=" CA  GLU B 347 "
        pdb=" CB  GLU B 347 "
        pdb=" CG  GLU B 347 "
      ideal   model   delta    sigma   weight residual
     114.10  129.10  -15.00 2.00e+00 2.50e-01 5.62e+01
  angle pdb=" CA  GLU A 347 "
        pdb=" CB  GLU A 347 "
        pdb=" CG  GLU A 347 "
      ideal   model   delta    sigma   weight residual
     114.10  129.07  -14.97 2.00e+00 2.50e-01 5.60e+01
  angle pdb=" CB  GLU A 347 "
        pdb=" CG  GLU A 347 "
        pdb=" CD  GLU A 347 "
      ideal   model   delta    sigma   weight residual
     112.60  122.08   -9.48 1.70e+00 3.46e-01 3.11e+01
  angle pdb=" CB  GLU B 347 "
        pdb=" CG  GLU B 347 "
        pdb=" CD  GLU B 347 "
      ideal   model   delta    sigma   weight residual
     112.60  122.03   -9.43 1.70e+00 3.46e-01 3.08e+01
  angle pdb=" N   VAL A 252 "
        pdb=" CA  VAL A 252 "
        pdb=" C   VAL A 252 "
      ideal   model   delta    sigma   weight residual
     113.20  107.91    5.29 9.60e-01 1.09e+00 3.03e+01
  ... (remaining 10079 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.85: 3848
       13.85 -    27.70: 328
       27.70 -    41.56: 86
       41.56 -    55.41: 16
       55.41 -    69.26: 4
  Dihedral angle restraints: 4282
    sinusoidal: 1600
      harmonic: 2682
  Sorted by residual:
  dihedral pdb=" CA  ALA A 326 "
           pdb=" C   ALA A 326 "
           pdb=" N   VAL A 327 "
           pdb=" CA  VAL A 327 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -134.24  -45.76     0      5.00e+00 4.00e-02 8.37e+01
  dihedral pdb=" CA  ALA B 326 "
           pdb=" C   ALA B 326 "
           pdb=" N   VAL B 327 "
           pdb=" CA  VAL B 327 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -134.27  -45.73     0      5.00e+00 4.00e-02 8.36e+01
  dihedral pdb=" CA  ILE A 290 "
           pdb=" C   ILE A 290 "
           pdb=" N   GLU A 291 "
           pdb=" CA  GLU A 291 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.85  -28.15     0      5.00e+00 4.00e-02 3.17e+01
  ... (remaining 4279 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 718
       0.053 -    0.107: 318
       0.107 -    0.160: 101
       0.160 -    0.214: 37
       0.214 -    0.267: 4
  Chirality restraints: 1178
  Sorted by residual:
  chirality pdb=" CB  ILE A 329 "
            pdb=" CA  ILE A 329 "
            pdb=" CG1 ILE A 329 "
            pdb=" CG2 ILE A 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.91   -0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" CB  ILE B 329 "
            pdb=" CA  ILE B 329 "
            pdb=" CG1 ILE B 329 "
            pdb=" CG2 ILE B 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.91   -0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CA  LEU B 557 "
            pdb=" N   LEU B 557 "
            pdb=" C   LEU B 557 "
            pdb=" CB  LEU B 557 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  ... (remaining 1175 not shown)

  Planarity restraints: 1234
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 365 "    0.015 2.00e-02 2.50e+03   3.04e-02 9.26e+00
        pdb=" C   PHE B 365 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   PHE B 365 "    0.020 2.00e-02 2.50e+03
        pdb=" N   VAL B 366 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 365 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.21e+00
        pdb=" C   PHE A 365 "    0.052 2.00e-02 2.50e+03
        pdb=" O   PHE A 365 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   VAL A 366 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 370 "    0.015 2.00e-02 2.50e+03   2.90e-02 8.40e+00
        pdb=" C   ARG A 370 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ARG A 370 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLN A 371 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1231 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2041
        2.81 -     3.33: 7042
        3.33 -     3.85: 12078
        3.85 -     4.38: 12824
        4.38 -     4.90: 22442
  Nonbonded interactions: 56427
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 472 "
            pdb=" OG1 THR A 476 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   ILE B 472 "
            pdb=" OG1 THR B 476 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OE2 GLU B 193 "
            pdb=" OH  TYR B 206 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OE2 GLU A 193 "
            pdb=" OH  TYR A 206 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OE2 GLU B 291 "
            pdb=" OG  SER B 541 "
     model   vdw
     2.296 3.040
  ... (remaining 56422 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             3.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.020
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
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      :  0.010   0.092   7410  Z= 0.399
  Angle     :  1.309  14.996  10084  Z= 0.693
  Chirality :  0.070   0.267   1178
  Planarity :  0.011   0.059   1234
  Dihedral  : 11.643  69.261   2562
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  7.96 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  6.77 %
    Favored  : 92.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.57 (0.21), residues: 930
  helix: -2.34 (0.16), residues: 672
  sheet:  None (None), residues: 0
  loop : -4.55 (0.28), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP B 133 
 HIS   0.009   0.002   HIS B 237 
 PHE   0.026   0.004   PHE B 547 
 TYR   0.035   0.003   TYR B 146 
 ARG   0.008   0.001   ARG B 390 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17130 (  486)
  hydrogen bonds       : angle       7.14507 ( 1422)
  covalent geometry    : bond        0.00969 ( 7410)
  covalent geometry    : angle       1.30897 (10084)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 156
  time to evaluate  : 0.824 
Fit side-chains
REVERT: B  194 MET cc_start: 0.8534 (ppp) cc_final: 0.8309 (ppp)
REVERT: B  209 MET cc_start: 0.8955 (tmt) cc_final: 0.8635 (tmm)
REVERT: B  291 GLU cc_start: 0.8040 (pm20) cc_final: 0.7626 (pm20)
REVERT: B  417 GLU cc_start: 0.8383 (tt0) cc_final: 0.8007 (tm-30)
REVERT: B  571 GLN cc_start: 0.8664 (tt0) cc_final: 0.8003 (tp40)
REVERT: B  589 TYR cc_start: 0.8083 (t80) cc_final: 0.7697 (t80)
REVERT: A  206 TYR cc_start: 0.6453 (t80) cc_final: 0.6240 (t80)
REVERT: A  209 MET cc_start: 0.8905 (tmt) cc_final: 0.8545 (tmm)
REVERT: A  589 TYR cc_start: 0.8060 (t80) cc_final: 0.7589 (t80)
  outliers start: 8
  outliers final: 4
  residues processed: 162
  average time/residue: 0.1869
  time to fit residues: 41.5136
Evaluate side-chains
  108 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  347 GLU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  347 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 53 optimal weight:    0.2980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 451 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.109549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.092313 restraints weight = 14483.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.096026 restraints weight = 6557.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.098417 restraints weight = 3845.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7410  Z= 0.156
  Angle     :  0.784  10.353  10084  Z= 0.396
  Chirality :  0.044   0.160   1178
  Planarity :  0.006   0.051   1234
  Dihedral  :  6.381  39.595    996
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 15.76 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.27), residues: 930
  helix: -0.07 (0.20), residues: 652
  sheet:  None (None), residues: 0
  loop : -3.76 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 469 
 HIS   0.004   0.001   HIS A 237 
 PHE   0.034   0.002   PHE A 547 
 TYR   0.017   0.001   TYR B 206 
 ARG   0.004   0.001   ARG B 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05389 (  486)
  hydrogen bonds       : angle       4.42758 ( 1422)
  covalent geometry    : bond        0.00340 ( 7410)
  covalent geometry    : angle       0.78442 (10084)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 158
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
REVERT: B  194 MET cc_start: 0.8415 (ppp) cc_final: 0.8154 (ppp)
REVERT: B  209 MET cc_start: 0.8884 (tmt) cc_final: 0.8394 (tmm)
REVERT: B  291 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7637 (pm20)
REVERT: B  340 ASP cc_start: 0.7604 (m-30) cc_final: 0.7327 (m-30)
REVERT: B  344 ASP cc_start: 0.8647 (p0) cc_final: 0.8380 (p0)
REVERT: B  466 MET cc_start: 0.7683 (mmt) cc_final: 0.7465 (mmt)
REVERT: B  571 GLN cc_start: 0.8574 (tt0) cc_final: 0.7916 (tp40)
REVERT: A  209 MET cc_start: 0.8901 (tmt) cc_final: 0.8431 (tmm)
REVERT: A  291 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7852 (pm20)
REVERT: A  340 ASP cc_start: 0.8049 (m-30) cc_final: 0.7835 (m-30)
REVERT: A  344 ASP cc_start: 0.8796 (p0) cc_final: 0.8532 (p0)
REVERT: A  373 MET cc_start: 0.8606 (mmt) cc_final: 0.8394 (mmt)
REVERT: A  466 MET cc_start: 0.7717 (mmt) cc_final: 0.7377 (mmt)
REVERT: A  524 TYR cc_start: 0.8387 (m-80) cc_final: 0.7936 (m-10)
REVERT: A  571 GLN cc_start: 0.8467 (tt0) cc_final: 0.7838 (tp40)
  outliers start: 32
  outliers final: 13
  residues processed: 178
  average time/residue: 0.2091
  time to fit residues: 54.7013
Evaluate side-chains
  136 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain B residue  389 HIS
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  403 SER
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  389 HIS
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  567 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 HIS
** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 HIS ** 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 = 0.3428 r_free = 0.3428 target = 0.103747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.086335 restraints weight = 15081.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.089730 restraints weight = 6992.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.092212 restraints weight = 4202.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7410  Z= 0.215
  Angle     :  0.836  11.186  10084  Z= 0.416
  Chirality :  0.046   0.171   1178
  Planarity :  0.005   0.047   1234
  Dihedral  :  5.571  38.227    986
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 18.36 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.28), residues: 930
  helix:  0.61 (0.20), residues: 670
  sheet:  None (None), residues: 0
  loop : -3.99 (0.34), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 164 
 HIS   0.017   0.002   HIS B 379 
 PHE   0.030   0.002   PHE A 547 
 TYR   0.017   0.002   TYR A 146 
 ARG   0.003   0.001   ARG B 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05529 (  486)
  hydrogen bonds       : angle       4.23140 ( 1422)
  covalent geometry    : bond        0.00508 ( 7410)
  covalent geometry    : angle       0.83567 (10084)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 122
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8937 (tp)
REVERT: B  178 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7921 (t80)
REVERT: B  209 MET cc_start: 0.8868 (tmt) cc_final: 0.8325 (tmm)
REVERT: B  291 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7687 (pm20)
REVERT: B  303 TRP cc_start: 0.8369 (m-10) cc_final: 0.8126 (m-10)
REVERT: B  391 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8773 (pp)
REVERT: B  571 GLN cc_start: 0.8704 (tt0) cc_final: 0.7948 (tp40)
REVERT: A  127 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8951 (tp)
REVERT: A  178 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7918 (t80)
REVERT: A  209 MET cc_start: 0.8900 (tmt) cc_final: 0.8417 (tmm)
REVERT: A  303 TRP cc_start: 0.8345 (m-10) cc_final: 0.8124 (m-10)
REVERT: A  344 ASP cc_start: 0.8860 (p0) cc_final: 0.8566 (p0)
REVERT: A  391 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8558 (pp)
REVERT: A  571 GLN cc_start: 0.8597 (tt0) cc_final: 0.7895 (tp40)
  outliers start: 47
  outliers final: 30
  residues processed: 150
  average time/residue: 0.1735
  time to fit residues: 39.9029
Evaluate side-chains
  153 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 116
  time to evaluate  : 2.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  389 HIS
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  389 HIS
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  567 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0980
   chunk 77 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 451 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.108792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.091117 restraints weight = 14640.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.094844 restraints weight = 6674.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.097255 restraints weight = 3940.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7410  Z= 0.138
  Angle     :  0.736  11.977  10084  Z= 0.360
  Chirality :  0.043   0.179   1178
  Planarity :  0.005   0.048   1234
  Dihedral  :  5.172  33.690    986
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 19.14 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.29), residues: 930
  helix:  1.07 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.83 (0.33), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 469 
 HIS   0.009   0.001   HIS A 379 
 PHE   0.029   0.001   PHE A 547 
 TYR   0.015   0.001   TYR B 524 
 ARG   0.003   0.000   ARG B 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04463 (  486)
  hydrogen bonds       : angle       3.94015 ( 1422)
  covalent geometry    : bond        0.00303 ( 7410)
  covalent geometry    : angle       0.73566 (10084)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 129
  time to evaluate  : 1.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8843 (tp)
REVERT: B  178 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7992 (t80)
REVERT: B  209 MET cc_start: 0.8856 (tmt) cc_final: 0.8315 (tmm)
REVERT: B  302 TYR cc_start: 0.9088 (t80) cc_final: 0.8317 (t80)
REVERT: B  368 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9190 (mm)
REVERT: B  389 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7846 (m-70)
REVERT: B  391 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8638 (pp)
REVERT: B  466 MET cc_start: 0.7671 (mmt) cc_final: 0.7329 (mmp)
REVERT: B  571 GLN cc_start: 0.8578 (tt0) cc_final: 0.7962 (tp40)
REVERT: A  127 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8883 (tp)
REVERT: A  178 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7958 (t80)
REVERT: A  209 MET cc_start: 0.8869 (tmt) cc_final: 0.8339 (tmm)
REVERT: A  302 TYR cc_start: 0.9119 (t80) cc_final: 0.8346 (t80)
REVERT: A  344 ASP cc_start: 0.8854 (p0) cc_final: 0.8582 (p0)
REVERT: A  391 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8477 (pp)
REVERT: A  571 GLN cc_start: 0.8552 (tt0) cc_final: 0.7872 (tp40)
  outliers start: 46
  outliers final: 25
  residues processed: 158
  average time/residue: 0.1818
  time to fit residues: 42.5948
Evaluate side-chains
  146 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 113
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  389 HIS
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  403 SER
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  206 TYR
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  567 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 71 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 301 ASN ** 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 = 0.3501 r_free = 0.3501 target = 0.109039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.091536 restraints weight = 14387.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.095092 restraints weight = 6542.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.097622 restraints weight = 3880.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7410  Z= 0.138
  Angle     :  0.723  11.890  10084  Z= 0.353
  Chirality :  0.043   0.175   1178
  Planarity :  0.005   0.047   1234
  Dihedral  :  4.965  30.300    986
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  7.03 %
    Allowed  : 19.66 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.29), residues: 930
  helix:  1.28 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.65 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 469 
 HIS   0.008   0.001   HIS A 379 
 PHE   0.028   0.001   PHE A 547 
 TYR   0.013   0.001   TYR B 524 
 ARG   0.002   0.000   ARG B 496 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04341 (  486)
  hydrogen bonds       : angle       3.80378 ( 1422)
  covalent geometry    : bond        0.00309 ( 7410)
  covalent geometry    : angle       0.72335 (10084)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 128
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8830 (tp)
REVERT: B  178 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.8007 (t80)
REVERT: B  209 MET cc_start: 0.8873 (tmt) cc_final: 0.8358 (tmm)
REVERT: B  302 TYR cc_start: 0.9096 (t80) cc_final: 0.8189 (t80)
REVERT: B  368 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9192 (mm)
REVERT: B  389 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7883 (m-70)
REVERT: B  391 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8704 (pp)
REVERT: B  436 HIS cc_start: 0.8020 (m-70) cc_final: 0.7614 (m170)
REVERT: B  466 MET cc_start: 0.7808 (mmt) cc_final: 0.7605 (mmp)
REVERT: B  571 GLN cc_start: 0.8591 (tt0) cc_final: 0.7941 (tp40)
REVERT: A  127 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8839 (tp)
REVERT: A  178 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7948 (t80)
REVERT: A  201 VAL cc_start: 0.8910 (t) cc_final: 0.8475 (t)
REVERT: A  209 MET cc_start: 0.8859 (tmt) cc_final: 0.8324 (tmm)
REVERT: A  302 TYR cc_start: 0.9141 (t80) cc_final: 0.8271 (t80)
REVERT: A  391 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8569 (pp)
REVERT: A  571 GLN cc_start: 0.8584 (tt0) cc_final: 0.7894 (tp40)
  outliers start: 54
  outliers final: 30
  residues processed: 162
  average time/residue: 0.1622
  time to fit residues: 39.9402
Evaluate side-chains
  157 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 119
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  389 HIS
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  567 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 55 optimal weight:    0.3980
   chunk 21 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 61 optimal weight:    0.3980
   chunk 80 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 301 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.109228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.091563 restraints weight = 14402.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.095120 restraints weight = 6613.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.097648 restraints weight = 3946.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7410  Z= 0.142
  Angle     :  0.749  11.807  10084  Z= 0.363
  Chirality :  0.043   0.178   1178
  Planarity :  0.005   0.046   1234
  Dihedral  :  4.842  26.872    986
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  7.03 %
    Allowed  : 19.92 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.29), residues: 930
  helix:  1.37 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.50 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 469 
 HIS   0.007   0.001   HIS A 379 
 PHE   0.029   0.001   PHE B 547 
 TYR   0.017   0.001   TYR B 524 
 ARG   0.003   0.000   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04223 (  486)
  hydrogen bonds       : angle       3.72380 ( 1422)
  covalent geometry    : bond        0.00325 ( 7410)
  covalent geometry    : angle       0.74901 (10084)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 119
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8832 (tp)
REVERT: B  178 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7975 (t80)
REVERT: B  209 MET cc_start: 0.8882 (tmt) cc_final: 0.8376 (tmm)
REVERT: B  287 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8677 (mp)
REVERT: B  302 TYR cc_start: 0.9093 (t80) cc_final: 0.8132 (t80)
REVERT: B  368 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9187 (mm)
REVERT: B  389 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7921 (m-70)
REVERT: B  391 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8712 (pp)
REVERT: B  436 HIS cc_start: 0.8024 (m-70) cc_final: 0.7592 (m170)
REVERT: B  466 MET cc_start: 0.7740 (mmt) cc_final: 0.7436 (mmp)
REVERT: B  571 GLN cc_start: 0.8563 (tt0) cc_final: 0.7921 (tp40)
REVERT: A  127 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8835 (tp)
REVERT: A  178 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7946 (t80)
REVERT: A  209 MET cc_start: 0.8864 (tmt) cc_final: 0.8329 (tmm)
REVERT: A  302 TYR cc_start: 0.9141 (t80) cc_final: 0.8187 (t80)
REVERT: A  391 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8552 (pp)
REVERT: A  571 GLN cc_start: 0.8473 (tt0) cc_final: 0.7887 (tp40)
  outliers start: 54
  outliers final: 34
  residues processed: 153
  average time/residue: 0.1284
  time to fit residues: 29.3704
Evaluate side-chains
  154 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 111
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  389 HIS
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  567 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 90 optimal weight:    0.6980
   chunk 89 optimal weight:    0.3980
   chunk 63 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 86 optimal weight:    0.4980
   chunk 68 optimal weight:    0.0570
   chunk 46 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.4698

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.110811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.092982 restraints weight = 14282.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.096620 restraints weight = 6595.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.099142 restraints weight = 3937.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7410  Z= 0.134
  Angle     :  0.736  16.006  10084  Z= 0.354
  Chirality :  0.042   0.180   1178
  Planarity :  0.005   0.048   1234
  Dihedral  :  4.721  23.342    986
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 21.35 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.29), residues: 930
  helix:  1.50 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -3.35 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 469 
 HIS   0.007   0.001   HIS A 379 
 PHE   0.027   0.001   PHE A 547 
 TYR   0.018   0.001   TYR A 524 
 ARG   0.002   0.000   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04020 (  486)
  hydrogen bonds       : angle       3.63193 ( 1422)
  covalent geometry    : bond        0.00298 ( 7410)
  covalent geometry    : angle       0.73551 (10084)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 130
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7930 (t80)
REVERT: B  209 MET cc_start: 0.8880 (tmt) cc_final: 0.8383 (tmm)
REVERT: B  287 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8491 (mp)
REVERT: B  302 TYR cc_start: 0.9084 (t80) cc_final: 0.8066 (t80)
REVERT: B  391 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8706 (pp)
REVERT: B  436 HIS cc_start: 0.8029 (m-70) cc_final: 0.7582 (m170)
REVERT: B  466 MET cc_start: 0.7690 (mmt) cc_final: 0.7207 (mmp)
REVERT: B  571 GLN cc_start: 0.8514 (tt0) cc_final: 0.7893 (tp40)
REVERT: A  178 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7968 (t80)
REVERT: A  209 MET cc_start: 0.8888 (tmt) cc_final: 0.8344 (tmm)
REVERT: A  302 TYR cc_start: 0.9141 (t80) cc_final: 0.8230 (t80)
REVERT: A  368 LEU cc_start: 0.9314 (mt) cc_final: 0.9090 (mm)
REVERT: A  391 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8553 (pp)
REVERT: A  571 GLN cc_start: 0.8398 (tt0) cc_final: 0.7841 (tp40)
  outliers start: 48
  outliers final: 32
  residues processed: 160
  average time/residue: 0.1546
  time to fit residues: 36.8533
Evaluate side-chains
  161 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 124
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  477 MET
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  564 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 15 optimal weight:    0.4980
   chunk 84 optimal weight:    0.9980
   chunk 13 optimal weight:    0.3980
   chunk 87 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.109974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.091994 restraints weight = 14618.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.095593 restraints weight = 6732.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.097976 restraints weight = 4043.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.4013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7410  Z= 0.143
  Angle     :  0.740  12.572  10084  Z= 0.360
  Chirality :  0.043   0.207   1178
  Planarity :  0.005   0.051   1234
  Dihedral  :  4.763  22.100    986
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 21.74 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.29), residues: 930
  helix:  1.57 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.30 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 469 
 HIS   0.007   0.001   HIS B 379 
 PHE   0.027   0.002   PHE B 547 
 TYR   0.012   0.001   TYR A 524 
 ARG   0.005   0.000   ARG B 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04154 (  486)
  hydrogen bonds       : angle       3.62222 ( 1422)
  covalent geometry    : bond        0.00325 ( 7410)
  covalent geometry    : angle       0.74021 (10084)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 125
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7932 (t80)
REVERT: B  209 MET cc_start: 0.8872 (tmt) cc_final: 0.8364 (tmm)
REVERT: B  302 TYR cc_start: 0.9087 (t80) cc_final: 0.8111 (t80)
REVERT: B  391 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8715 (pp)
REVERT: B  436 HIS cc_start: 0.8086 (m-70) cc_final: 0.7631 (m170)
REVERT: B  466 MET cc_start: 0.7778 (mmt) cc_final: 0.7491 (mmp)
REVERT: B  571 GLN cc_start: 0.8529 (tt0) cc_final: 0.7900 (tp40)
REVERT: A  178 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7974 (t80)
REVERT: A  209 MET cc_start: 0.8913 (tmt) cc_final: 0.8421 (tmm)
REVERT: A  302 TYR cc_start: 0.9138 (t80) cc_final: 0.8268 (t80)
REVERT: A  391 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8561 (pp)
REVERT: A  571 GLN cc_start: 0.8406 (tt0) cc_final: 0.7850 (tp40)
  outliers start: 47
  outliers final: 36
  residues processed: 155
  average time/residue: 0.1488
  time to fit residues: 34.3696
Evaluate side-chains
  159 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 119
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  477 MET
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 30 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 379 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.109630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.091497 restraints weight = 14534.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.095057 restraints weight = 6765.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.097574 restraints weight = 4092.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7410  Z= 0.147
  Angle     :  0.744  12.715  10084  Z= 0.364
  Chirality :  0.043   0.208   1178
  Planarity :  0.005   0.052   1234
  Dihedral  :  4.796  26.224    986
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 21.48 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.29), residues: 930
  helix:  1.63 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -3.24 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 469 
 HIS   0.008   0.001   HIS A 379 
 PHE   0.028   0.002   PHE B 547 
 TYR   0.015   0.001   TYR B 524 
 ARG   0.003   0.000   ARG B 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04261 (  486)
  hydrogen bonds       : angle       3.64406 ( 1422)
  covalent geometry    : bond        0.00341 ( 7410)
  covalent geometry    : angle       0.74412 (10084)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 122
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.8947 (tpp) cc_final: 0.8706 (tpt)
REVERT: B  178 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7974 (t80)
REVERT: B  209 MET cc_start: 0.8871 (tmt) cc_final: 0.8364 (tmm)
REVERT: B  302 TYR cc_start: 0.9097 (t80) cc_final: 0.8104 (t80)
REVERT: B  391 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8653 (pp)
REVERT: B  436 HIS cc_start: 0.8118 (m-70) cc_final: 0.7694 (m170)
REVERT: B  466 MET cc_start: 0.7708 (mmt) cc_final: 0.7231 (mmp)
REVERT: B  557 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8036 (mt)
REVERT: B  571 GLN cc_start: 0.8536 (tt0) cc_final: 0.7897 (tp40)
REVERT: A  128 MET cc_start: 0.8904 (tpp) cc_final: 0.8643 (tpt)
REVERT: A  178 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7990 (t80)
REVERT: A  209 MET cc_start: 0.8926 (tmt) cc_final: 0.8441 (tmm)
REVERT: A  302 TYR cc_start: 0.9139 (t80) cc_final: 0.8269 (t80)
REVERT: A  328 THR cc_start: 0.6729 (OUTLIER) cc_final: 0.6364 (t)
REVERT: A  391 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8552 (pp)
REVERT: A  571 GLN cc_start: 0.8472 (tt0) cc_final: 0.7871 (tp40)
  outliers start: 48
  outliers final: 38
  residues processed: 149
  average time/residue: 0.1376
  time to fit residues: 30.5412
Evaluate side-chains
  161 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 117
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  477 MET
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  414 MET
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  513 ASP
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 83 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 81 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 84 optimal weight:    0.0670
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 HIS ** 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 = 0.3521 r_free = 0.3521 target = 0.110077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.091993 restraints weight = 14695.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.095639 restraints weight = 6786.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.097981 restraints weight = 4075.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.4163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7410  Z= 0.144
  Angle     :  0.737  12.459  10084  Z= 0.359
  Chirality :  0.043   0.193   1178
  Planarity :  0.005   0.052   1234
  Dihedral  :  4.767  27.251    986
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 21.74 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.29), residues: 930
  helix:  1.61 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -3.22 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 469 
 HIS   0.007   0.001   HIS A 379 
 PHE   0.029   0.002   PHE B 174 
 TYR   0.011   0.001   TYR B 524 
 ARG   0.004   0.000   ARG B 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04151 (  486)
  hydrogen bonds       : angle       3.63440 ( 1422)
  covalent geometry    : bond        0.00329 ( 7410)
  covalent geometry    : angle       0.73664 (10084)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 122
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.8908 (tpp) cc_final: 0.8639 (tpt)
REVERT: B  178 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7958 (t80)
REVERT: B  209 MET cc_start: 0.8857 (tmt) cc_final: 0.8362 (tmm)
REVERT: B  302 TYR cc_start: 0.9114 (t80) cc_final: 0.8136 (t80)
REVERT: B  328 THR cc_start: 0.6384 (m) cc_final: 0.6099 (t)
REVERT: B  391 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8656 (pp)
REVERT: B  436 HIS cc_start: 0.8143 (m-70) cc_final: 0.7732 (m170)
REVERT: B  466 MET cc_start: 0.7745 (mmt) cc_final: 0.7482 (mmp)
REVERT: B  557 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8049 (mt)
REVERT: B  571 GLN cc_start: 0.8463 (tt0) cc_final: 0.7866 (tp40)
REVERT: A  128 MET cc_start: 0.8900 (tpp) cc_final: 0.8615 (tpt)
REVERT: A  178 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.8006 (t80)
REVERT: A  209 MET cc_start: 0.8907 (tmt) cc_final: 0.8446 (tmm)
REVERT: A  302 TYR cc_start: 0.9133 (t80) cc_final: 0.8333 (t80)
REVERT: A  328 THR cc_start: 0.6802 (OUTLIER) cc_final: 0.6424 (t)
REVERT: A  391 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8545 (pp)
REVERT: A  436 HIS cc_start: 0.8044 (m-70) cc_final: 0.7766 (m-70)
REVERT: A  571 GLN cc_start: 0.8441 (tt0) cc_final: 0.7837 (tp40)
  outliers start: 46
  outliers final: 36
  residues processed: 148
  average time/residue: 0.1346
  time to fit residues: 29.9265
Evaluate side-chains
  161 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 119
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  477 MET
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  414 MET
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  513 ASP
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 83 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 HIS ** 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 = 0.3500 r_free = 0.3500 target = 0.108704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.090600 restraints weight = 14502.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.094195 restraints weight = 6774.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.096526 restraints weight = 4098.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.4145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7410  Z= 0.158
  Angle     :  0.761  12.353  10084  Z= 0.372
  Chirality :  0.044   0.185   1178
  Planarity :  0.005   0.050   1234
  Dihedral  :  4.798  28.017    986
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 21.22 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.29), residues: 930
  helix:  1.58 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -3.20 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 469 
 HIS   0.007   0.001   HIS A 379 
 PHE   0.029   0.002   PHE B 174 
 TYR   0.014   0.001   TYR B 524 
 ARG   0.003   0.000   ARG B 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04397 (  486)
  hydrogen bonds       : angle       3.66829 ( 1422)
  covalent geometry    : bond        0.00369 ( 7410)
  covalent geometry    : angle       0.76055 (10084)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2701.15 seconds
wall clock time: 50 minutes 9.95 seconds (3009.95 seconds total)