Starting phenix.real_space_refine
on Wed Feb 12 05:00:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qv6_4645/02_2025/6qv6_4645.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qv6_4645/02_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_4645/02_2025/6qv6_4645.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qv6_4645/02_2025/6qv6_4645.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qv6_4645/02_2025/6qv6_4645.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qv6_4645/02_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-5592/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: 6.33, per 1000 atoms: 0.88
  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: 2.01
  Conformation dependent library (CDL) restraints added in 1.2 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: 0.68
  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: 2.08

  Time building geometry restraints manager: 2.31 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:             2.490
  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:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     22.110
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.000
-------------------------------------------------------------------------------
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= 0.624
  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 

*********************** 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  : 0.775 
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: 0.1839
  time to fit residues: 40.4376
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  : 0.795 
-------------------------------------------------------------------------------
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 = 33)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.092312 restraints weight = 14483.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.095944 restraints weight = 6554.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.098492 restraints weight = 3877.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
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= 0.220
  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 

*********************** 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  : 0.771 
Fit side-chains
   revert: symmetry clash
REVERT: B  194 MET cc_start: 0.8420 (ppp) cc_final: 0.8157 (ppp)
REVERT: B  209 MET cc_start: 0.8888 (tmt) cc_final: 0.8397 (tmm)
REVERT: B  291 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7640 (pm20)
REVERT: B  340 ASP cc_start: 0.7614 (m-30) cc_final: 0.7337 (m-30)
REVERT: B  344 ASP cc_start: 0.8646 (p0) cc_final: 0.8373 (p0)
REVERT: B  466 MET cc_start: 0.7686 (mmt) cc_final: 0.7467 (mmt)
REVERT: B  571 GLN cc_start: 0.8573 (tt0) cc_final: 0.7910 (tp40)
REVERT: A  209 MET cc_start: 0.8906 (tmt) cc_final: 0.8437 (tmm)
REVERT: A  291 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7853 (pm20)
REVERT: A  340 ASP cc_start: 0.8053 (m-30) cc_final: 0.7840 (m-30)
REVERT: A  344 ASP cc_start: 0.8795 (p0) cc_final: 0.8529 (p0)
REVERT: A  373 MET cc_start: 0.8602 (mmt) cc_final: 0.8390 (mmt)
REVERT: A  466 MET cc_start: 0.7718 (mmt) cc_final: 0.7376 (mmt)
REVERT: A  524 TYR cc_start: 0.8388 (m-80) cc_final: 0.7939 (m-10)
REVERT: A  571 GLN cc_start: 0.8466 (tt0) cc_final: 0.7833 (tp40)
  outliers start: 32
  outliers final: 13
  residues processed: 178
  average time/residue: 0.1499
  time to fit residues: 39.0810
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  : 0.921 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
B 301 ASN
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.108451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.091081 restraints weight = 14613.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.094651 restraints weight = 6653.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.097173 restraints weight = 3950.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2885

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= 0.224
  Angle     :  0.777  12.090  10084  Z= 0.382
  Chirality :  0.044   0.171   1178
  Planarity :  0.005   0.046   1234
  Dihedral  :  5.403  36.061    986
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 19.14 %
    Favored  : 75.65 %
  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: -0.73 (0.28), residues: 930
  helix:  0.79 (0.21), residues: 662
  sheet:  None (None), residues: 0
  loop : -3.88 (0.32), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 164 
 HIS   0.010   0.001   HIS B 379 
 PHE   0.031   0.002   PHE A 547 
 TYR   0.013   0.001   TYR A 146 
 ARG   0.003   0.000   ARG B 199 

*********************** 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
  168 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 128
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8842 (tp)
REVERT: B  178 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7956 (t80)
REVERT: B  209 MET cc_start: 0.8850 (tmt) cc_final: 0.8312 (tmm)
REVERT: B  291 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7735 (pm20)
REVERT: B  391 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8793 (pp)
REVERT: B  466 MET cc_start: 0.7648 (mmt) cc_final: 0.7411 (mmp)
REVERT: B  571 GLN cc_start: 0.8573 (tt0) cc_final: 0.7921 (tp40)
REVERT: A  127 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8896 (tp)
REVERT: A  178 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7967 (t80)
REVERT: A  209 MET cc_start: 0.8884 (tmt) cc_final: 0.8383 (tmm)
REVERT: A  303 TRP cc_start: 0.8326 (m-10) cc_final: 0.8121 (m-10)
REVERT: A  344 ASP cc_start: 0.8839 (p0) cc_final: 0.8604 (p0)
REVERT: A  391 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8568 (pp)
REVERT: A  466 MET cc_start: 0.7769 (mmt) cc_final: 0.7453 (mmt)
REVERT: A  571 GLN cc_start: 0.8532 (tt0) cc_final: 0.7864 (tp40)
  outliers start: 40
  outliers final: 25
  residues processed: 150
  average time/residue: 0.1413
  time to fit residues: 31.2972
Evaluate side-chains
  150 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 118
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
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  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  429 ASP
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  559 MET
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  178 PHE
Chi-restraints excluded: chain A residue  194 MET
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  422 GLU
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  454 VAL
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:   10.0000
   chunk 79 optimal weight:    2.9990
   chunk 22 optimal weight:    0.4980
   chunk 47 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
B 451 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.107261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.089468 restraints weight = 14700.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.093118 restraints weight = 6760.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.095498 restraints weight = 4024.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7410  Z= 0.244
  Angle     :  0.757  11.140  10084  Z= 0.371
  Chirality :  0.044   0.176   1178
  Planarity :  0.005   0.048   1234
  Dihedral  :  5.157  33.409    986
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  7.42 %
    Allowed  : 17.45 %
    Favored  : 75.13 %
  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:  1.06 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.80 (0.33), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 148 
 HIS   0.008   0.001   HIS A 379 
 PHE   0.028   0.002   PHE A 547 
 TYR   0.015   0.001   TYR B 524 
 ARG   0.003   0.000   ARG B 199 

*********************** 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
  180 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 123
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8878 (tp)
REVERT: B  178 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7999 (t80)
REVERT: B  209 MET cc_start: 0.8855 (tmt) cc_final: 0.8317 (tmm)
REVERT: B  302 TYR cc_start: 0.9110 (t80) cc_final: 0.8311 (t80)
REVERT: B  368 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9231 (mm)
REVERT: B  389 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.7866 (m-70)
REVERT: B  391 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8707 (pp)
REVERT: B  466 MET cc_start: 0.7602 (mmt) cc_final: 0.7390 (mmp)
REVERT: B  571 GLN cc_start: 0.8674 (tt0) cc_final: 0.7981 (tp40)
REVERT: A  127 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8883 (tp)
REVERT: A  178 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7967 (t80)
REVERT: A  209 MET cc_start: 0.8887 (tmt) cc_final: 0.8370 (tmm)
REVERT: A  302 TYR cc_start: 0.9153 (t80) cc_final: 0.8401 (t80)
REVERT: A  344 ASP cc_start: 0.8979 (p0) cc_final: 0.8636 (p0)
REVERT: A  368 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9139 (mm)
REVERT: A  391 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8481 (pp)
REVERT: A  466 MET cc_start: 0.7792 (mmt) cc_final: 0.7491 (mmt)
REVERT: A  485 MET cc_start: 0.8757 (mmm) cc_final: 0.8535 (mmm)
REVERT: A  571 GLN cc_start: 0.8587 (tt0) cc_final: 0.7892 (tp40)
  outliers start: 57
  outliers final: 31
  residues processed: 159
  average time/residue: 0.1326
  time to fit residues: 31.3332
Evaluate side-chains
  153 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 113
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
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  173 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  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  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  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  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  368 LEU
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  414 MET
Chi-restraints excluded: chain A residue  429 ASP
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 71 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 77 optimal weight:    0.4980
   chunk 69 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 567 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.108016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.090608 restraints weight = 14448.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.094140 restraints weight = 6575.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.096544 restraints weight = 3902.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.3485

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= 0.211
  Angle     :  0.730  11.935  10084  Z= 0.358
  Chirality :  0.043   0.178   1178
  Planarity :  0.005   0.048   1234
  Dihedral  :  4.958  30.083    986
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 19.14 %
    Favored  : 73.70 %
  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: -0.05 (0.29), residues: 930
  helix:  1.27 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -3.61 (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   0.028   0.001   PHE A 547 
 TYR   0.014   0.001   TYR B 524 
 ARG   0.002   0.000   ARG B 199 

*********************** 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
  178 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 123
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8848 (tp)
REVERT: B  178 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7966 (t80)
REVERT: B  209 MET cc_start: 0.8862 (tmt) cc_final: 0.8361 (tmm)
REVERT: B  302 TYR cc_start: 0.9090 (t80) cc_final: 0.8306 (t80)
REVERT: B  389 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7924 (m-70)
REVERT: B  391 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8704 (pp)
REVERT: B  436 HIS cc_start: 0.8081 (m-70) cc_final: 0.7664 (m170)
REVERT: B  466 MET cc_start: 0.7601 (mmt) cc_final: 0.7243 (mmp)
REVERT: B  571 GLN cc_start: 0.8575 (tt0) cc_final: 0.7911 (tp40)
REVERT: A  127 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8848 (tp)
REVERT: A  178 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7948 (t80)
REVERT: A  209 MET cc_start: 0.8865 (tmt) cc_final: 0.8339 (tmm)
REVERT: A  302 TYR cc_start: 0.9140 (t80) cc_final: 0.8244 (t80)
REVERT: A  368 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9140 (mm)
REVERT: A  391 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8533 (pp)
REVERT: A  571 GLN cc_start: 0.8549 (tt0) cc_final: 0.7890 (tp40)
  outliers start: 55
  outliers final: 33
  residues processed: 158
  average time/residue: 0.1336
  time to fit residues: 31.5179
Evaluate side-chains
  152 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 111
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
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  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  290 ILE
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  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  196 THR
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  368 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  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  519 ILE
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:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0030
   chunk 78 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 53 optimal weight:    0.2980
   chunk 24 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 83 optimal weight:    0.5980
   overall best weight:    0.4590

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

Flipped N/Q/H residues before XYZ refinement:
B 567 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.110741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.093133 restraints weight = 14214.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.096809 restraints weight = 6471.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.099200 restraints weight = 3821.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.3740

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= 0.192
  Angle     :  0.741  11.872  10084  Z= 0.359
  Chirality :  0.043   0.182   1178
  Planarity :  0.005   0.045   1234
  Dihedral  :  4.831  26.114    986
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  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:  0.15 (0.29), residues: 930
  helix:  1.39 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.48 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 469 
 HIS   0.006   0.001   HIS A 379 
 PHE   0.029   0.001   PHE B 547 
 TYR   0.018   0.001   TYR B 524 
 ARG   0.003   0.000   ARG B 496 

*********************** 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
  176 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 122
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8849 (tp)
REVERT: B  178 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7979 (t80)
REVERT: B  209 MET cc_start: 0.8891 (tmt) cc_final: 0.8392 (tmm)
REVERT: B  302 TYR cc_start: 0.9086 (t80) cc_final: 0.8207 (t80)
REVERT: B  339 MET cc_start: 0.8540 (ptp) cc_final: 0.8332 (ptp)
REVERT: B  389 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7907 (m-70)
REVERT: B  391 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8748 (pp)
REVERT: B  436 HIS cc_start: 0.8024 (m-70) cc_final: 0.7580 (m170)
REVERT: B  571 GLN cc_start: 0.8557 (tt0) cc_final: 0.7869 (tp40)
REVERT: A  127 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8829 (tp)
REVERT: A  178 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7945 (t80)
REVERT: A  209 MET cc_start: 0.8883 (tmt) cc_final: 0.8340 (tmm)
REVERT: A  302 TYR cc_start: 0.9147 (t80) cc_final: 0.8226 (t80)
REVERT: A  368 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9138 (mm)
REVERT: A  391 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8582 (pp)
REVERT: A  571 GLN cc_start: 0.8530 (tt0) cc_final: 0.7900 (tp40)
  outliers start: 54
  outliers final: 32
  residues processed: 156
  average time/residue: 0.1385
  time to fit residues: 31.8900
Evaluate side-chains
  153 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 113
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
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  385 PHE
Chi-restraints excluded: chain B residue  389 HIS
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  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  207 LEU
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 MET
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  477 MET
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
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:    0.9980
   chunk 89 optimal weight:    0.9980
   chunk 63 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 86 optimal weight:    0.5980
   chunk 68 optimal weight:    0.1980
   chunk 46 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 567 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.110930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.092863 restraints weight = 14264.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.096441 restraints weight = 6630.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.099003 restraints weight = 3986.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.3916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7410  Z= 0.197
  Angle     :  0.741  16.611  10084  Z= 0.355
  Chirality :  0.043   0.181   1178
  Planarity :  0.005   0.046   1234
  Dihedral  :  4.760  24.517    986
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  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:  0.23 (0.29), residues: 930
  helix:  1.44 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -3.41 (0.33), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 469 
 HIS   0.006   0.001   HIS A 379 
 PHE   0.038   0.002   PHE B 333 
 TYR   0.014   0.001   TYR A 206 
 ARG   0.002   0.000   ARG A 199 

*********************** 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
  169 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 121
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7987 (t80)
REVERT: B  209 MET cc_start: 0.8877 (tmt) cc_final: 0.8382 (tmm)
REVERT: B  302 TYR cc_start: 0.9078 (t80) cc_final: 0.8144 (t80)
REVERT: B  391 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8718 (pp)
REVERT: B  436 HIS cc_start: 0.8030 (m-70) cc_final: 0.7610 (m170)
REVERT: B  466 MET cc_start: 0.7674 (mmt) cc_final: 0.7349 (mmp)
REVERT: B  571 GLN cc_start: 0.8547 (tt0) cc_final: 0.7871 (tp40)
REVERT: A  178 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7980 (t80)
REVERT: A  209 MET cc_start: 0.8889 (tmt) cc_final: 0.8349 (tmm)
REVERT: A  302 TYR cc_start: 0.9143 (t80) cc_final: 0.8280 (t80)
REVERT: A  368 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9162 (mm)
REVERT: A  391 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8540 (pp)
REVERT: A  524 TYR cc_start: 0.7815 (m-10) cc_final: 0.7581 (m-10)
REVERT: A  571 GLN cc_start: 0.8429 (tt0) cc_final: 0.7816 (tp40)
  outliers start: 48
  outliers final: 34
  residues processed: 149
  average time/residue: 0.1430
  time to fit residues: 31.5244
Evaluate side-chains
  155 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 116
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
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  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  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  368 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  410 MET
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  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:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 87 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0370
   chunk 70 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
B 379 HIS
B 567 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.110097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.092165 restraints weight = 14613.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.095737 restraints weight = 6765.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.098319 restraints weight = 4056.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.3997

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= 0.204
  Angle     :  0.731  12.488  10084  Z= 0.355
  Chirality :  0.043   0.238   1178
  Planarity :  0.005   0.050   1234
  Dihedral  :  4.748  22.054    986
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 20.96 %
    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:  0.37 (0.29), residues: 930
  helix:  1.53 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -3.31 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 469 
 HIS   0.007   0.001   HIS A 379 
 PHE   0.029   0.002   PHE B 333 
 TYR   0.013   0.001   TYR A 524 
 ARG   0.002   0.000   ARG A 199 

*********************** 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: 51
    poor density    : 121
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.8868 (tpp) cc_final: 0.8581 (tpt)
REVERT: B  178 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7941 (t80)
REVERT: B  209 MET cc_start: 0.8871 (tmt) cc_final: 0.8382 (tmm)
REVERT: B  302 TYR cc_start: 0.9075 (t80) cc_final: 0.8186 (t80)
REVERT: B  391 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8703 (pp)
REVERT: B  422 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7991 (pm20)
REVERT: B  436 HIS cc_start: 0.8067 (m-70) cc_final: 0.7633 (m170)
REVERT: B  466 MET cc_start: 0.7692 (mmt) cc_final: 0.7359 (mmp)
REVERT: B  571 GLN cc_start: 0.8540 (tt0) cc_final: 0.7869 (tp40)
REVERT: A  178 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7988 (t80)
REVERT: A  209 MET cc_start: 0.8886 (tmt) cc_final: 0.8355 (tmm)
REVERT: A  302 TYR cc_start: 0.9126 (t80) cc_final: 0.8287 (t80)
REVERT: A  368 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9151 (mm)
REVERT: A  391 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8539 (pp)
REVERT: A  571 GLN cc_start: 0.8410 (tt0) cc_final: 0.7810 (tp40)
  outliers start: 51
  outliers final: 39
  residues processed: 152
  average time/residue: 0.1409
  time to fit residues: 31.3785
Evaluate side-chains
  162 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 117
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
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  422 GLU
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  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  207 LEU
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  368 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  410 MET
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  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:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 62 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 567 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.109736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.091621 restraints weight = 14538.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.095262 restraints weight = 6771.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.097718 restraints weight = 4070.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.4019

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= 0.217
  Angle     :  0.738  12.411  10084  Z= 0.359
  Chirality :  0.044   0.247   1178
  Planarity :  0.005   0.049   1234
  Dihedral  :  4.793  27.128    986
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 21.09 %
    Favored  : 72.66 %
  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:  0.38 (0.29), residues: 930
  helix:  1.50 (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   0.011   0.001   TRP B 469 
 HIS   0.007   0.001   HIS A 379 
 PHE   0.028   0.002   PHE B 174 
 TYR   0.017   0.001   TYR B 524 
 ARG   0.002   0.000   ARG A 199 

*********************** 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  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.8893 (tpp) cc_final: 0.8600 (tpt)
REVERT: B  178 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7935 (t80)
REVERT: B  209 MET cc_start: 0.8889 (tmt) cc_final: 0.8391 (tmm)
REVERT: B  302 TYR cc_start: 0.9101 (t80) cc_final: 0.8123 (t80)
REVERT: B  391 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8703 (pp)
REVERT: B  422 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8018 (pm20)
REVERT: B  436 HIS cc_start: 0.8094 (m-70) cc_final: 0.7658 (m170)
REVERT: B  466 MET cc_start: 0.7705 (mmt) cc_final: 0.7349 (mmp)
REVERT: B  571 GLN cc_start: 0.8554 (tt0) cc_final: 0.7934 (tp40)
REVERT: A  128 MET cc_start: 0.8878 (tpp) cc_final: 0.8587 (tpt)
REVERT: A  178 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7976 (t80)
REVERT: A  209 MET cc_start: 0.8898 (tmt) cc_final: 0.8434 (tmm)
REVERT: A  302 TYR cc_start: 0.9131 (t80) cc_final: 0.8260 (t80)
REVERT: A  328 THR cc_start: 0.6767 (OUTLIER) cc_final: 0.6410 (t)
REVERT: A  368 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9160 (mm)
REVERT: A  391 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8537 (pp)
REVERT: A  571 GLN cc_start: 0.8423 (tt0) cc_final: 0.7836 (tp40)
  outliers start: 48
  outliers final: 38
  residues processed: 150
  average time/residue: 0.1385
  time to fit residues: 30.7569
Evaluate side-chains
  165 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 120
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
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  385 PHE
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  422 GLU
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  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  207 LEU
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  368 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 MET
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  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:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 83 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 81 optimal weight:    0.0370
   chunk 13 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
B 567 ASN
** 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 = 0.3532 r_free = 0.3532 target = 0.110936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.092746 restraints weight = 14698.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.096340 restraints weight = 6847.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.098914 restraints weight = 4128.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.4143

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= 0.202
  Angle     :  0.735  12.455  10084  Z= 0.358
  Chirality :  0.043   0.236   1178
  Planarity :  0.005   0.051   1234
  Dihedral  :  4.764  26.464    986
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  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:  0.39 (0.29), residues: 930
  helix:  1.50 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -3.16 (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   0.018   0.001   TYR A 524 
 ARG   0.002   0.000   ARG B 496 

********************** 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
  172 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 124
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.8937 (tpp) cc_final: 0.8648 (tpt)
REVERT: B  178 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7969 (t80)
REVERT: B  209 MET cc_start: 0.8889 (tmt) cc_final: 0.8404 (tmm)
REVERT: B  302 TYR cc_start: 0.9096 (t80) cc_final: 0.8121 (t80)
REVERT: B  391 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8664 (pp)
REVERT: B  422 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7997 (pm20)
REVERT: B  436 HIS cc_start: 0.8085 (m-70) cc_final: 0.7661 (m170)
REVERT: B  466 MET cc_start: 0.7683 (mmt) cc_final: 0.7349 (mmp)
REVERT: B  557 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8118 (mt)
REVERT: B  571 GLN cc_start: 0.8507 (tt0) cc_final: 0.7886 (tp40)
REVERT: A  128 MET cc_start: 0.8901 (tpp) cc_final: 0.8615 (tpt)
REVERT: A  178 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7972 (t80)
REVERT: A  209 MET cc_start: 0.8898 (tmt) cc_final: 0.8447 (tmm)
REVERT: A  302 TYR cc_start: 0.9122 (t80) cc_final: 0.8272 (t80)
REVERT: A  328 THR cc_start: 0.6816 (OUTLIER) cc_final: 0.6424 (t)
REVERT: A  368 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9164 (mm)
REVERT: A  391 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8552 (pp)
REVERT: A  571 GLN cc_start: 0.8401 (tt0) cc_final: 0.7816 (tp40)
  outliers start: 48
  outliers final: 35
  residues processed: 152
  average time/residue: 0.1456
  time to fit residues: 32.7212
Evaluate side-chains
  161 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 118
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
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  385 PHE
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  422 GLU
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  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  207 LEU
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  368 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  410 MET
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  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:    0.0570
   chunk 27 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 83 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.3539 r_free = 0.3539 target = 0.111222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.093070 restraints weight = 14392.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.096627 restraints weight = 6757.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.099202 restraints weight = 4086.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.4198

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= 0.199
  Angle     :  0.740  12.534  10084  Z= 0.360
  Chirality :  0.043   0.227   1178
  Planarity :  0.005   0.052   1234
  Dihedral  :  4.735  25.967    986
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 21.48 %
    Favored  : 72.66 %
  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:  0.57 (0.29), residues: 930
  helix:  1.64 (0.21), residues: 654
  sheet:  None (None), residues: 0
  loop : -2.91 (0.34), residues: 276

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   0.017   0.001   TYR A 524 
 ARG   0.002   0.000   ARG A 199 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2087.01 seconds
wall clock time: 38 minutes 26.72 seconds (2306.72 seconds total)