Starting phenix.real_space_refine
on Tue Jul 29 19:09:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wcc_21606/07_2025/6wcc_21606.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wcc_21606/07_2025/6wcc_21606.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wcc_21606/07_2025/6wcc_21606.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wcc_21606/07_2025/6wcc_21606.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wcc_21606/07_2025/6wcc_21606.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wcc_21606/07_2025/6wcc_21606.cif"
  }
  resolution = 3.24
  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
-------------------------------------------------------------------------------
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=   1.000
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: 6
    Type Number    sf(0)   Gaussians
     Cs      5     16.47       5
     S      38      5.16       5
     C    3758      2.51       5
     N     940      2.21       5
     O     980      1.98       5
     H    5908      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11629
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 5806
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 16, 'TRANS': 350}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 5806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 5806
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 16, 'TRANS': 350}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CS': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CS': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 5.79, per 1000 atoms: 0.50
  Number of scatterers: 11629
  At special positions: 0
  Unit cell: (107.712, 66.368, 78.336, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cs      5     54.66
     S      38     16.00
     O     980      8.00
     N     940      7.00
     C    3758      6.00
     H    5908      1.00
    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: 3.24
  Conformation dependent library (CDL) restraints added in 860.0 milliseconds
  

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1404

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 0 sheets defined
      86.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 50
    Processing helix  chain 'A' and resid 52 through 57
    Processing helix  chain 'A' and resid 67 through 103
      removed outlier: 4.180A  pdb=" N   GLN A  71 " --> pdb=" O   ASP A  67 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL A 101 " --> pdb=" O   ARG A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 122
    Processing helix  chain 'A' and resid 122 through 133
    Processing helix  chain 'A' and resid 137 through 164
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 257 through 284
    Processing helix  chain 'A' and resid 287 through 295
    Processing helix  chain 'A' and resid 298 through 333
      removed outlier: 3.839A  pdb=" N   ALA A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
      Proline residue:  A 308  - end of helix
      removed outlier: 3.624A  pdb=" N   HIS A 333 " --> pdb=" O   SER A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 353
    Processing helix  chain 'A' and resid 354 through 359
      removed outlier: 3.544A  pdb=" N   ALA A 358 " --> pdb=" O   GLY A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 400
      removed outlier: 3.912A  pdb=" N   PHE A 389 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   GLN A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   HIS A 400 " --> pdb=" O   THR A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 405
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 415 through 440
      removed outlier: 4.951A  pdb=" N   TYR A 426 " --> pdb=" O   LYS A 422 " (cutoff:3.500A)
      Proline residue:  A 427  - end of helix
    Processing helix  chain 'A' and resid 443 through 461
      Proline residue:  A 456  - end of helix
    Processing helix  chain 'A' and resid 461 through 476
    Processing helix  chain 'B' and resid 33 through 50
    Processing helix  chain 'B' and resid 52 through 57
    Processing helix  chain 'B' and resid 67 through 103
      removed outlier: 4.180A  pdb=" N   GLN B  71 " --> pdb=" O   ASP B  67 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL B 101 " --> pdb=" O   ARG B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 122
    Processing helix  chain 'B' and resid 122 through 133
    Processing helix  chain 'B' and resid 137 through 164
    Processing helix  chain 'B' and resid 165 through 168
    Processing helix  chain 'B' and resid 257 through 284
    Processing helix  chain 'B' and resid 287 through 295
    Processing helix  chain 'B' and resid 298 through 333
      removed outlier: 3.840A  pdb=" N   ALA B 302 " --> pdb=" O   SER B 298 " (cutoff:3.500A)
      Proline residue:  B 308  - end of helix
      removed outlier: 3.624A  pdb=" N   HIS B 333 " --> pdb=" O   SER B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 353
    Processing helix  chain 'B' and resid 354 through 359
      removed outlier: 3.544A  pdb=" N   ALA B 358 " --> pdb=" O   GLY B 354 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 400
      removed outlier: 3.912A  pdb=" N   PHE B 389 " --> pdb=" O   LEU B 385 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   GLN B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   HIS B 400 " --> pdb=" O   THR B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 405
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 415 through 440
      removed outlier: 4.952A  pdb=" N   TYR B 426 " --> pdb=" O   LYS B 422 " (cutoff:3.500A)
      Proline residue:  B 427  - end of helix
    Processing helix  chain 'B' and resid 443 through 461
      Proline residue:  B 456  - end of helix
    Processing helix  chain 'B' and resid 461 through 476

    462 hydrogen bonds defined for protein.
    1368 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: 4.43

  Time building geometry restraints manager: 3.85 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5890
        1.03 -     1.23: 18
        1.23 -     1.42: 2386
        1.42 -     1.61: 3394
        1.61 -     1.81: 58
  Bond restraints: 11746
  Sorted by residual:
  bond pdb=" CG  LEU B 470 "
       pdb=" CD1 LEU B 470 "
    ideal  model  delta    sigma   weight residual
    1.521  1.559 -0.038 3.30e-02 9.18e+02 1.31e+00
  bond pdb=" CG  PHE A 295 "
       pdb=" CD2 PHE A 295 "
    ideal  model  delta    sigma   weight residual
    1.384  1.360  0.024 2.10e-02 2.27e+03 1.26e+00
  bond pdb=" CG  LEU A 470 "
       pdb=" CD1 LEU A 470 "
    ideal  model  delta    sigma   weight residual
    1.521  1.558 -0.037 3.30e-02 9.18e+02 1.24e+00
  bond pdb=" CG  PHE B 295 "
       pdb=" CD2 PHE B 295 "
    ideal  model  delta    sigma   weight residual
    1.384  1.361  0.023 2.10e-02 2.27e+03 1.17e+00
  bond pdb=" CB  GLU B  59 "
       pdb=" CG  GLU B  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.96e-01
  ... (remaining 11741 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 21172
        2.12 -     4.24: 111
        4.24 -     6.37: 8
        6.37 -     8.49: 3
        8.49 -    10.61: 2
  Bond angle restraints: 21296
  Sorted by residual:
  angle pdb=" CG  LEU A 470 "
        pdb=" CD2 LEU A 470 "
        pdb="HD23 LEU A 470 "
      ideal   model   delta    sigma   weight residual
     109.00   98.39   10.61 3.00e+00 1.11e-01 1.25e+01
  angle pdb="HD21 LEU A 470 "
        pdb=" CD2 LEU A 470 "
        pdb="HD23 LEU A 470 "
      ideal   model   delta    sigma   weight residual
     110.00  100.10    9.90 3.00e+00 1.11e-01 1.09e+01
  angle pdb=" CG  LEU A 470 "
        pdb=" CD2 LEU A 470 "
        pdb="HD21 LEU A 470 "
      ideal   model   delta    sigma   weight residual
     109.00  117.41   -8.41 3.00e+00 1.11e-01 7.85e+00
  angle pdb=" CD2 LEU B 470 "
        pdb=" CG  LEU B 470 "
        pdb=" HG  LEU B 470 "
      ideal   model   delta    sigma   weight residual
     108.00  100.28    7.72 3.00e+00 1.11e-01 6.63e+00
  angle pdb="HD22 LEU A 470 "
        pdb=" CD2 LEU A 470 "
        pdb="HD23 LEU A 470 "
      ideal   model   delta    sigma   weight residual
     110.00  116.89   -6.89 3.00e+00 1.11e-01 5.28e+00
  ... (remaining 21291 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.97: 4918
       16.97 -    33.93: 428
       33.93 -    50.90: 118
       50.90 -    67.86: 58
       67.86 -    84.83: 6
  Dihedral angle restraints: 5528
    sinusoidal: 2936
      harmonic: 2592
  Sorted by residual:
  dihedral pdb=" CA  ASP A 283 "
           pdb=" C   ASP A 283 "
           pdb=" N   ASN A 284 "
           pdb=" CA  ASN A 284 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.43  -16.57     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  ASP B 283 "
           pdb=" C   ASP B 283 "
           pdb=" N   ASN B 284 "
           pdb=" CA  ASN B 284 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.43  -16.57     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  ASN B 284 "
           pdb=" CB  ASN B 284 "
           pdb=" CG  ASN B 284 "
           pdb=" OD1 ASN B 284 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -162.72   72.72     2      2.00e+01 2.50e-03 1.09e+01
  ... (remaining 5525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 721
       0.027 -    0.053: 128
       0.053 -    0.080: 84
       0.080 -    0.107: 34
       0.107 -    0.134: 11
  Chirality restraints: 978
  Sorted by residual:
  chirality pdb=" CG  LEU A 470 "
            pdb=" CB  LEU A 470 "
            pdb=" CD1 LEU A 470 "
            pdb=" CD2 LEU A 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.47e-01
  chirality pdb=" CG  LEU B 470 "
            pdb=" CB  LEU B 470 "
            pdb=" CD1 LEU B 470 "
            pdb=" CD2 LEU B 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.23e-01
  chirality pdb=" CA  VAL A 285 "
            pdb=" N   VAL A 285 "
            pdb=" C   VAL A 285 "
            pdb=" CB  VAL A 285 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.93e-01
  ... (remaining 975 not shown)

  Planarity restraints: 1674
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 295 "   -0.028 2.00e-02 2.50e+03   1.82e-02 9.89e+00
        pdb=" CG  PHE A 295 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 295 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 295 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 295 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 295 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 295 "   -0.002 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 295 "    0.006 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 295 "    0.005 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 295 "   -0.004 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 295 "   -0.005 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 295 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 295 "    0.022 2.00e-02 2.50e+03   1.78e-02 9.48e+00
        pdb=" CG  PHE B 295 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 295 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 295 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 295 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 295 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 295 "    0.003 2.00e-02 2.50e+03
        pdb=" HD1 PHE B 295 "    0.002 2.00e-02 2.50e+03
        pdb=" HD2 PHE B 295 "    0.001 2.00e-02 2.50e+03
        pdb=" HE1 PHE B 295 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 PHE B 295 "    0.005 2.00e-02 2.50e+03
        pdb=" HZ  PHE B 295 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 123 "   -0.025 5.00e-02 4.00e+02   3.78e-02 2.29e+00
        pdb=" N   PRO B 124 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B 124 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 124 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1671 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.60: 12042
        2.60 -     3.41: 46823
        3.41 -     4.23: 62751
        4.23 -     5.04: 110077
        5.04 -     5.86: 145341
  Nonbonded interactions: 377034
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 123 "
            pdb=" HG1 THR B 126 "
     model   vdw
     1.784 2.450
  nonbonded pdb=" O   LEU A 123 "
            pdb=" HG1 THR A 126 "
     model   vdw
     1.784 2.450
  nonbonded pdb=" OD1 ASP A 266 "
            pdb="HH21 ARG B  35 "
     model   vdw
     1.812 2.450
  nonbonded pdb=" O   ALA A  93 "
            pdb=" HG1 THR A  96 "
     model   vdw
     1.812 2.450
  nonbonded pdb=" O   ALA B  93 "
            pdb=" HG1 THR B  96 "
     model   vdw
     1.813 2.450
  ... (remaining 377029 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 30 through 476 or resid 701 through 702))
  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 individual isotropic
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:             0.140
  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:             0.200
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     28.170
  Find NCS groups from input model:        0.330
  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:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
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      :  0.003   0.038   5838  Z= 0.134
  Angle     :  0.510   4.479   7956  Z= 0.278
  Chirality :  0.033   0.134    978
  Planarity :  0.004   0.038    976
  Dihedral  : 15.734  84.831   2040
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 10.32 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.28), residues: 726
  helix:  1.59 (0.19), residues: 590
  sheet:  None (None), residues: 0
  loop : -1.76 (0.44), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 394 
 HIS   0.003   0.001   HIS B 328 
 PHE   0.053   0.001   PHE A 295 
 TYR   0.008   0.001   TYR A 313 
 ARG   0.001   0.000   ARG B  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10621 (  462)
  hydrogen bonds       : angle       4.28443 ( 1368)
  covalent geometry    : bond        0.00266 ( 5838)
  covalent geometry    : angle       0.51011 ( 7956)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  143 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  335 ARG cc_start: 0.8477 (mtp180) cc_final: 0.8276 (mtp180)
REVERT: B  335 ARG cc_start: 0.8501 (mtp180) cc_final: 0.8301 (mtp180)
REVERT: B  418 LEU cc_start: 0.8247 (tp) cc_final: 0.7967 (mp)
  outliers start: 14
  outliers final: 12
  residues processed: 143
  average time/residue: 0.4007
  time to fit residues: 74.1156
Evaluate side-chains
  104 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 GLU
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue  279 ASP
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  470 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 18 optimal weight:   30.0000
   chunk 36 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 333 HIS
B 113 ASN
** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 333 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.168225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.119678 restraints weight = 9290.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 1.60
r_work: 0.3068 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5838  Z= 0.167
  Angle     :  0.536   5.522   7956  Z= 0.273
  Chirality :  0.036   0.128    978
  Planarity :  0.004   0.045    976
  Dihedral  :  7.968  70.280    804
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 14.03 %
    Favored  : 83.06 %
  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:  3.34 (0.30), residues: 726
  helix:  2.84 (0.20), residues: 598
  sheet:  None (None), residues: 0
  loop : -1.12 (0.49), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 394 
 HIS   0.005   0.001   HIS A 328 
 PHE   0.018   0.002   PHE A  99 
 TYR   0.012   0.002   TYR A 313 
 ARG   0.003   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05251 (  462)
  hydrogen bonds       : angle       3.79657 ( 1368)
  covalent geometry    : bond        0.00383 ( 5838)
  covalent geometry    : angle       0.53641 ( 7956)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7939 (mtt90)
REVERT: A  117 MET cc_start: 0.8033 (mmt) cc_final: 0.7787 (mmp)
REVERT: A  314 PHE cc_start: 0.8210 (m-80) cc_final: 0.7994 (m-80)
REVERT: B   77 ARG cc_start: 0.8257 (mtt90) cc_final: 0.7986 (mtt90)
REVERT: B  117 MET cc_start: 0.8209 (mmp) cc_final: 0.7990 (mmt)
REVERT: B  418 LEU cc_start: 0.8505 (tp) cc_final: 0.7952 (mp)
  outliers start: 18
  outliers final: 16
  residues processed: 121
  average time/residue: 0.3893
  time to fit residues: 61.8350
Evaluate side-chains
  114 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   63 GLU
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  279 ASP
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  436 SER
Chi-restraints excluded: chain B residue  470 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    2.7988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.165585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.116209 restraints weight = 9834.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.65
r_work: 0.3022 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.2648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5838  Z= 0.181
  Angle     :  0.527   5.998   7956  Z= 0.272
  Chirality :  0.036   0.136    978
  Planarity :  0.004   0.049    976
  Dihedral  :  7.086  58.392    802
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.52 %
    Favored  : 82.26 %
  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:  3.60 (0.31), residues: 726
  helix:  3.09 (0.20), residues: 586
  sheet:  None (None), residues: 0
  loop : -0.94 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 394 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.017   0.002   PHE A  99 
 TYR   0.014   0.002   TYR B 160 
 ARG   0.003   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05148 (  462)
  hydrogen bonds       : angle       3.76603 ( 1368)
  covalent geometry    : bond        0.00415 ( 5838)
  covalent geometry    : angle       0.52733 ( 7956)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  118 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.6163 (tp40) cc_final: 0.5800 (tm-30)
REVERT: A   77 ARG cc_start: 0.8252 (mtt90) cc_final: 0.7993 (mtt90)
REVERT: A  160 TYR cc_start: 0.8849 (t80) cc_final: 0.8583 (t80)
REVERT: B  117 MET cc_start: 0.8302 (mmp) cc_final: 0.8054 (mmt)
  outliers start: 20
  outliers final: 18
  residues processed: 114
  average time/residue: 0.3571
  time to fit residues: 54.2741
Evaluate side-chains
  107 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   63 GLU
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue  279 ASP
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  345 ASN
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  436 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 56 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 65 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.166196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.116639 restraints weight = 9612.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 1.64
r_work: 0.3032 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5838  Z= 0.149
  Angle     :  0.490   4.046   7956  Z= 0.252
  Chirality :  0.035   0.123    978
  Planarity :  0.004   0.046    976
  Dihedral  :  6.399  56.682    800
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.84 %
    Favored  : 81.94 %
  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:  3.78 (0.31), residues: 726
  helix:  3.13 (0.20), residues: 598
  sheet:  None (None), residues: 0
  loop : -0.89 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 394 
 HIS   0.003   0.001   HIS B 328 
 PHE   0.016   0.001   PHE B  99 
 TYR   0.011   0.002   TYR B 160 
 ARG   0.002   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04725 (  462)
  hydrogen bonds       : angle       3.67893 ( 1368)
  covalent geometry    : bond        0.00336 ( 5838)
  covalent geometry    : angle       0.49001 ( 7956)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.6182 (tp40) cc_final: 0.5767 (tm-30)
REVERT: A   77 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7915 (mtt90)
REVERT: A  160 TYR cc_start: 0.8775 (t80) cc_final: 0.8569 (t80)
REVERT: A  303 LEU cc_start: 0.4366 (OUTLIER) cc_final: 0.4159 (tp)
REVERT: B   71 GLN cc_start: 0.6225 (tp40) cc_final: 0.5849 (tm-30)
REVERT: B   77 ARG cc_start: 0.8227 (mtt90) cc_final: 0.7997 (mtt90)
  outliers start: 20
  outliers final: 16
  residues processed: 110
  average time/residue: 0.3663
  time to fit residues: 53.5342
Evaluate side-chains
  113 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  279 ASP
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  345 ASN
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  436 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    3.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.163853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.114325 restraints weight = 9459.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 1.61
r_work: 0.2989 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5838  Z= 0.220
  Angle     :  0.536   4.444   7956  Z= 0.282
  Chirality :  0.037   0.135    978
  Planarity :  0.004   0.044    976
  Dihedral  :  5.733  56.449    792
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 15.16 %
    Favored  : 81.45 %
  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:  3.52 (0.31), residues: 726
  helix:  3.00 (0.20), residues: 588
  sheet:  None (None), residues: 0
  loop : -0.87 (0.51), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 394 
 HIS   0.005   0.001   HIS B 328 
 PHE   0.017   0.002   PHE A  99 
 TYR   0.010   0.002   TYR B 313 
 ARG   0.003   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05331 (  462)
  hydrogen bonds       : angle       3.82625 ( 1368)
  covalent geometry    : bond        0.00516 ( 5838)
  covalent geometry    : angle       0.53602 ( 7956)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  120 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.6312 (tp40) cc_final: 0.5855 (tm-30)
REVERT: A   77 ARG cc_start: 0.8198 (mtt90) cc_final: 0.7935 (mtt90)
REVERT: A  160 TYR cc_start: 0.8911 (t80) cc_final: 0.8562 (t80)
REVERT: B   71 GLN cc_start: 0.6319 (tp40) cc_final: 0.5805 (tm-30)
  outliers start: 21
  outliers final: 18
  residues processed: 112
  average time/residue: 0.3664
  time to fit residues: 54.3930
Evaluate side-chains
  115 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  430 SER
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  279 ASP
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  345 ASN
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  436 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 31 optimal weight:    0.2980
   chunk 34 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 18 optimal weight:   20.0000
   chunk 55 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
A 345 ASN
B 345 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.165176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.114871 restraints weight = 9795.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.66
r_work: 0.3006 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5838  Z= 0.162
  Angle     :  0.495   4.125   7956  Z= 0.256
  Chirality :  0.035   0.127    978
  Planarity :  0.004   0.044    976
  Dihedral  :  5.128  55.878    788
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 15.97 %
    Favored  : 80.65 %
  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:  3.69 (0.31), residues: 726
  helix:  3.15 (0.20), residues: 586
  sheet:  None (None), residues: 0
  loop : -0.93 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 394 
 HIS   0.004   0.001   HIS B 328 
 PHE   0.016   0.001   PHE A  99 
 TYR   0.009   0.002   TYR A 313 
 ARG   0.002   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04844 (  462)
  hydrogen bonds       : angle       3.73261 ( 1368)
  covalent geometry    : bond        0.00370 ( 5838)
  covalent geometry    : angle       0.49451 ( 7956)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  119 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.6289 (tp40) cc_final: 0.5785 (tm-30)
REVERT: A  160 TYR cc_start: 0.8879 (t80) cc_final: 0.8634 (t80)
REVERT: A  282 GLU cc_start: 0.4441 (mm-30) cc_final: 0.3391 (mm-30)
REVERT: B   71 GLN cc_start: 0.6299 (tp40) cc_final: 0.5804 (tm-30)
REVERT: B  282 GLU cc_start: 0.4446 (mm-30) cc_final: 0.3413 (mm-30)
  outliers start: 21
  outliers final: 20
  residues processed: 112
  average time/residue: 0.3598
  time to fit residues: 53.7470
Evaluate side-chains
  115 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  113 ASN
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  279 ASP
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  345 ASN
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  436 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0670
   chunk 56 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.6126

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.165976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.115731 restraints weight = 9803.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 1.68
r_work: 0.3029 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5838  Z= 0.131
  Angle     :  0.486   4.093   7956  Z= 0.251
  Chirality :  0.035   0.123    978
  Planarity :  0.004   0.044    976
  Dihedral  :  5.022  55.327    788
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.42 %
    Favored  : 80.97 %
  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:  3.82 (0.31), residues: 726
  helix:  3.25 (0.20), residues: 586
  sheet:  None (None), residues: 0
  loop : -0.92 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 394 
 HIS   0.003   0.001   HIS B 328 
 PHE   0.015   0.001   PHE B  99 
 TYR   0.009   0.002   TYR B 160 
 ARG   0.003   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04597 (  462)
  hydrogen bonds       : angle       3.67524 ( 1368)
  covalent geometry    : bond        0.00286 ( 5838)
  covalent geometry    : angle       0.48647 ( 7956)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  104 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.6284 (tp40) cc_final: 0.5768 (tm-30)
REVERT: A  160 TYR cc_start: 0.8858 (t80) cc_final: 0.8612 (t80)
REVERT: A  282 GLU cc_start: 0.4448 (mm-30) cc_final: 0.3442 (mm-30)
REVERT: A  314 PHE cc_start: 0.8342 (m-80) cc_final: 0.8129 (m-80)
REVERT: B   71 GLN cc_start: 0.6298 (tp40) cc_final: 0.5798 (tm-30)
REVERT: B  282 GLU cc_start: 0.4426 (mm-30) cc_final: 0.3415 (mm-30)
  outliers start: 10
  outliers final: 10
  residues processed: 100
  average time/residue: 0.3825
  time to fit residues: 50.4062
Evaluate side-chains
  102 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  279 ASP
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  436 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.165764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.114834 restraints weight = 9888.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 1.69
r_work: 0.3014 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5838  Z= 0.148
  Angle     :  0.482   4.228   7956  Z= 0.248
  Chirality :  0.035   0.125    978
  Planarity :  0.004   0.043    976
  Dihedral  :  4.907  55.222    786
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.61 %
    Favored  : 81.13 %
  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:  3.93 (0.31), residues: 726
  helix:  3.29 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -0.91 (0.52), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 394 
 HIS   0.004   0.001   HIS B 328 
 PHE   0.015   0.001   PHE A  99 
 TYR   0.009   0.002   TYR A 313 
 ARG   0.003   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04580 (  462)
  hydrogen bonds       : angle       3.64380 ( 1368)
  covalent geometry    : bond        0.00337 ( 5838)
  covalent geometry    : angle       0.48209 ( 7956)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  107 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.6319 (tp40) cc_final: 0.5779 (tm-30)
REVERT: A  160 TYR cc_start: 0.8896 (t80) cc_final: 0.8651 (t80)
REVERT: A  282 GLU cc_start: 0.4640 (mm-30) cc_final: 0.3613 (mm-30)
REVERT: B   71 GLN cc_start: 0.6327 (tp40) cc_final: 0.5815 (tm-30)
REVERT: B  282 GLU cc_start: 0.4471 (mm-30) cc_final: 0.3480 (mm-30)
  outliers start: 14
  outliers final: 12
  residues processed: 102
  average time/residue: 0.3755
  time to fit residues: 50.4261
Evaluate side-chains
  105 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  113 ASN
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  279 ASP
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  348 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 0 optimal weight:    6.9990
   chunk 71 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    2.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.164904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.114040 restraints weight = 9882.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.69
r_work: 0.2999 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5838  Z= 0.186
  Angle     :  0.503   4.262   7956  Z= 0.261
  Chirality :  0.036   0.129    978
  Planarity :  0.004   0.043    976
  Dihedral  :  4.844  55.543    784
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.77 %
    Favored  : 80.97 %
  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:  3.80 (0.31), residues: 726
  helix:  3.21 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -0.97 (0.52), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 394 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.015   0.001   PHE B  99 
 TYR   0.009   0.002   TYR A 426 
 ARG   0.003   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04839 (  462)
  hydrogen bonds       : angle       3.70720 ( 1368)
  covalent geometry    : bond        0.00432 ( 5838)
  covalent geometry    : angle       0.50317 ( 7956)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.6355 (tp40) cc_final: 0.5792 (tm-30)
REVERT: A  160 TYR cc_start: 0.8860 (t80) cc_final: 0.8642 (t80)
REVERT: A  282 GLU cc_start: 0.4711 (mm-30) cc_final: 0.3706 (mm-30)
REVERT: B   71 GLN cc_start: 0.6362 (tp40) cc_final: 0.5826 (tm-30)
REVERT: B  282 GLU cc_start: 0.4577 (mm-30) cc_final: 0.3559 (mm-30)
  outliers start: 14
  outliers final: 13
  residues processed: 103
  average time/residue: 0.3683
  time to fit residues: 49.8831
Evaluate side-chains
  107 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  279 ASP
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  436 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 68 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 54 optimal weight:    7.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.165779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.115017 restraints weight = 9880.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.68
r_work: 0.3013 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5838  Z= 0.149
  Angle     :  0.481   4.395   7956  Z= 0.247
  Chirality :  0.035   0.124    978
  Planarity :  0.004   0.043    976
  Dihedral  :  4.799  55.342    784
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.42 %
    Favored  : 80.48 %
  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:  3.97 (0.31), residues: 726
  helix:  3.33 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -0.97 (0.53), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 394 
 HIS   0.004   0.001   HIS B 328 
 PHE   0.015   0.001   PHE A  99 
 TYR   0.008   0.002   TYR B 313 
 ARG   0.003   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04521 (  462)
  hydrogen bonds       : angle       3.63743 ( 1368)
  covalent geometry    : bond        0.00340 ( 5838)
  covalent geometry    : angle       0.48136 ( 7956)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR   81 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  104 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.6249 (tp40) cc_final: 0.5714 (tm-30)
REVERT: A  160 TYR cc_start: 0.8849 (t80) cc_final: 0.8630 (t80)
REVERT: A  282 GLU cc_start: 0.4669 (mm-30) cc_final: 0.3619 (mm-30)
REVERT: B   71 GLN cc_start: 0.6254 (tp40) cc_final: 0.5746 (tm-30)
REVERT: B  282 GLU cc_start: 0.4600 (mm-30) cc_final: 0.3590 (mm-30)
  outliers start: 13
  outliers final: 13
  residues processed: 99
  average time/residue: 0.3865
  time to fit residues: 50.6783
Evaluate side-chains
  104 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  113 ASN
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  279 ASP
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  436 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 61 optimal weight:    7.9990
   chunk 60 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 68 optimal weight:    7.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.166686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.115855 restraints weight = 10010.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 1.69
r_work: 0.3023 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5838  Z= 0.122
  Angle     :  0.473   4.501   7956  Z= 0.241
  Chirality :  0.034   0.122    978
  Planarity :  0.004   0.045    976
  Dihedral  :  4.757  55.095    784
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 18.06 %
    Favored  : 80.16 %
  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:  4.06 (0.31), residues: 726
  helix:  3.40 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -0.95 (0.53), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 394 
 HIS   0.003   0.001   HIS B 328 
 PHE   0.014   0.001   PHE B  99 
 TYR   0.008   0.002   TYR A 313 
 ARG   0.002   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04339 (  462)
  hydrogen bonds       : angle       3.57961 ( 1368)
  covalent geometry    : bond        0.00268 ( 5838)
  covalent geometry    : angle       0.47291 ( 7956)

===============================================================================
Job complete
usr+sys time: 6012.89 seconds
wall clock time: 102 minutes 35.44 seconds (6155.44 seconds total)