Starting phenix.real_space_refine
on Tue Mar 11 15:12:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gyw_34378/03_2025/8gyw_34378.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gyw_34378/03_2025/8gyw_34378.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gyw_34378/03_2025/8gyw_34378.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gyw_34378/03_2025/8gyw_34378.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gyw_34378/03_2025/8gyw_34378.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gyw_34378/03_2025/8gyw_34378.cif"
  }
  resolution = 3.9
  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=   0.005 sd=   0.102
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
     P       4      5.49       5
     Mg      4      5.21       5
     S      48      5.16       5
     C    3994      2.51       5
     N     984      2.21       5
     O    1042      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6076
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3005
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3005
          Classifications: {'peptide': 380}
          Link IDs: {'PTRANS': 17, 'TRANS': 362}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'CDC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.13, per 1000 atoms: 0.84
  Number of scatterers: 6076
  At special positions: 0
  Unit cell: (97.37, 101.65, 71.69, 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)
     S      48     16.00
     P       4     15.00
     Mg      4     11.99
     O    1042      8.00
     N     984      7.00
     C    3994      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.52
  Conformation dependent library (CDL) restraints added in 738.9 milliseconds
  

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1424

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 4 sheets defined
      80.7% alpha, 1.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 37
    Processing helix  chain 'B' and resid 44 through 53
    Processing helix  chain 'B' and resid 64 through 79
      removed outlier: 3.539A  pdb=" N   MET B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLY B  70 " --> pdb=" O   PRO B  66 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   TYR B  71 " --> pdb=" O   LEU B  67 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ARG B  77 " --> pdb=" O   GLU B  73 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ARG B  78 " --> pdb=" O   TRP B  74 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   VAL B  79 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 107
      removed outlier: 3.756A  pdb=" N   ILE B  88 " --> pdb=" O   ALA B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 143
      removed outlier: 3.904A  pdb=" N   TYR B 119 " --> pdb=" O   PRO B 115 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   GLY B 137 " --> pdb=" O   ASP B 133 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   LYS B 138 " --> pdb=" O   ALA B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 173
      removed outlier: 3.583A  pdb=" N   LEU B 160 " --> pdb=" O   GLY B 156 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   VAL B 163 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   PHE B 164 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 177
      removed outlier: 3.663A  pdb=" N   THR B 177 " --> pdb=" O   GLN B 174 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 174 through 177'
    Processing helix  chain 'B' and resid 178 through 204
    Processing helix  chain 'B' and resid 212 through 237
      Proline residue:  B 232  - end of helix
    Processing helix  chain 'B' and resid 247 through 272
      removed outlier: 4.189A  pdb=" N   ALA B 251 " --> pdb=" O   LYS B 247 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   VAL B 268 " --> pdb=" O   ASN B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 279
    Processing helix  chain 'B' and resid 287 through 307
      removed outlier: 3.883A  pdb=" N   LEU B 291 " --> pdb=" O   LEU B 287 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   HIS B 292 " --> pdb=" O   SER B 288 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE B 293 " --> pdb=" O   PRO B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 315
    Processing helix  chain 'B' and resid 315 through 341
    Processing helix  chain 'B' and resid 348 through 350
      No H-bonds generated for 'chain 'B' and resid 348 through 350'
    Processing helix  chain 'B' and resid 351 through 363
    Processing helix  chain 'B' and resid 368 through 400
    Processing helix  chain 'A' and resid 29 through 37
    Processing helix  chain 'A' and resid 44 through 53
    Processing helix  chain 'A' and resid 64 through 79
      removed outlier: 3.539A  pdb=" N   MET A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLY A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   TYR A  71 " --> pdb=" O   LEU A  67 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ARG A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ARG A  78 " --> pdb=" O   TRP A  74 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   VAL A  79 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 107
      removed outlier: 3.756A  pdb=" N   ILE A  88 " --> pdb=" O   ALA A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 143
      removed outlier: 3.904A  pdb=" N   TYR A 119 " --> pdb=" O   PRO A 115 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   GLY A 137 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   LYS A 138 " --> pdb=" O   ALA A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 173
      removed outlier: 3.583A  pdb=" N   LEU A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   VAL A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   PHE A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 177
      removed outlier: 3.663A  pdb=" N   THR A 177 " --> pdb=" O   GLN A 174 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 174 through 177'
    Processing helix  chain 'A' and resid 178 through 204
    Processing helix  chain 'A' and resid 212 through 237
      Proline residue:  A 232  - end of helix
    Processing helix  chain 'A' and resid 247 through 272
      removed outlier: 4.190A  pdb=" N   ALA A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   VAL A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 287 through 307
      removed outlier: 3.883A  pdb=" N   LEU A 291 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   HIS A 292 " --> pdb=" O   SER A 288 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 315
    Processing helix  chain 'A' and resid 315 through 341
    Processing helix  chain 'A' and resid 348 through 350
      No H-bonds generated for 'chain 'A' and resid 348 through 350'
    Processing helix  chain 'A' and resid 351 through 363
    Processing helix  chain 'A' and resid 368 through 400
    Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 59
    Processing sheet with id=AA2, first strand: chain 'B' and resid 238 through 239
      removed outlier: 3.703A  pdb=" N   ILE B 239 " --> pdb=" O   ILE B 244 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   ILE B 244 " --> pdb=" O   ILE B 239 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59
    Processing sheet with id=AA4, first strand: chain 'A' and resid 238 through 239
      removed outlier: 3.703A  pdb=" N   ILE A 239 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    441 hydrogen bonds defined for protein.
    1311 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.65

  Time building geometry restraints manager: 1.77 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: 1379
        1.34 -     1.45: 1411
        1.45 -     1.57: 3380
        1.57 -     1.69: 12
        1.69 -     1.81: 66
  Bond restraints: 6248
  Sorted by residual:
  bond pdb=" CB  PRO A 115 "
       pdb=" CG  PRO A 115 "
    ideal  model  delta    sigma   weight residual
    1.492  1.638 -0.146 5.00e-02 4.00e+02 8.56e+00
  bond pdb=" CB  PRO B 115 "
       pdb=" CG  PRO B 115 "
    ideal  model  delta    sigma   weight residual
    1.492  1.638 -0.146 5.00e-02 4.00e+02 8.55e+00
  bond pdb=" CA  PRO A 108 "
       pdb=" C   PRO A 108 "
    ideal  model  delta    sigma   weight residual
    1.517  1.559 -0.042 1.54e-02 4.22e+03 7.49e+00
  bond pdb=" CA  PRO B 108 "
       pdb=" C   PRO B 108 "
    ideal  model  delta    sigma   weight residual
    1.517  1.558 -0.042 1.54e-02 4.22e+03 7.39e+00
  bond pdb=" CB  PRO B 108 "
       pdb=" CG  PRO B 108 "
    ideal  model  delta    sigma   weight residual
    1.492  1.612 -0.120 5.00e-02 4.00e+02 5.74e+00
  ... (remaining 6243 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.79: 8287
        3.79 -     7.58: 197
        7.58 -    11.38: 26
       11.38 -    15.17: 12
       15.17 -    18.96: 2
  Bond angle restraints: 8524
  Sorted by residual:
  angle pdb=" CA  PRO A 115 "
        pdb=" N   PRO A 115 "
        pdb=" CD  PRO A 115 "
      ideal   model   delta    sigma   weight residual
     112.00   99.70   12.30 1.40e+00 5.10e-01 7.72e+01
  angle pdb=" CA  PRO B 115 "
        pdb=" N   PRO B 115 "
        pdb=" CD  PRO B 115 "
      ideal   model   delta    sigma   weight residual
     112.00   99.71   12.29 1.40e+00 5.10e-01 7.71e+01
  angle pdb=" CA  PRO A 108 "
        pdb=" N   PRO A 108 "
        pdb=" CD  PRO A 108 "
      ideal   model   delta    sigma   weight residual
     112.00  100.26   11.74 1.40e+00 5.10e-01 7.03e+01
  angle pdb=" CA  PRO B 108 "
        pdb=" N   PRO B 108 "
        pdb=" CD  PRO B 108 "
      ideal   model   delta    sigma   weight residual
     112.00  100.28   11.72 1.40e+00 5.10e-01 7.01e+01
  angle pdb=" CA  LEU A  48 "
        pdb=" CB  LEU A  48 "
        pdb=" CG  LEU A  48 "
      ideal   model   delta    sigma   weight residual
     116.30  135.26  -18.96 3.50e+00 8.16e-02 2.93e+01
  ... (remaining 8519 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.52: 3182
       16.52 -    33.04: 286
       33.04 -    49.56: 98
       49.56 -    66.08: 54
       66.08 -    82.61: 14
  Dihedral angle restraints: 3634
    sinusoidal: 1426
      harmonic: 2208
  Sorted by residual:
  dihedral pdb=" C   PRO B 108 "
           pdb=" N   PRO B 108 "
           pdb=" CA  PRO B 108 "
           pdb=" CB  PRO B 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -129.60    8.90     0      2.50e+00 1.60e-01 1.27e+01
  dihedral pdb=" C   PRO A 108 "
           pdb=" N   PRO A 108 "
           pdb=" CA  PRO A 108 "
           pdb=" CB  PRO A 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -129.55    8.85     0      2.50e+00 1.60e-01 1.25e+01
  dihedral pdb=" CA  ASP A 348 "
           pdb=" CB  ASP A 348 "
           pdb=" CG  ASP A 348 "
           pdb=" OD1 ASP A 348 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.32   59.32     1      2.00e+01 2.50e-03 1.18e+01
  ... (remaining 3631 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 758
       0.081 -    0.162: 188
       0.162 -    0.244: 30
       0.244 -    0.325: 6
       0.325 -    0.406: 2
  Chirality restraints: 984
  Sorted by residual:
  chirality pdb=" CA  PRO B 108 "
            pdb=" N   PRO B 108 "
            pdb=" C   PRO B 108 "
            pdb=" CB  PRO B 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.31    0.41 2.00e-01 2.50e+01 4.12e+00
  chirality pdb=" CA  PRO A 108 "
            pdb=" N   PRO A 108 "
            pdb=" C   PRO A 108 "
            pdb=" CB  PRO A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.32    0.40 2.00e-01 2.50e+01 4.04e+00
  chirality pdb=" CB  THR A 214 "
            pdb=" CA  THR A 214 "
            pdb=" OG1 THR A 214 "
            pdb=" CG2 THR A 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.26    0.29 2.00e-01 2.50e+01 2.13e+00
  ... (remaining 981 not shown)

  Planarity restraints: 1036
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 114 "    0.103 5.00e-02 4.00e+02   1.45e-01 3.39e+01
        pdb=" N   PRO A 115 "   -0.251 5.00e-02 4.00e+02
        pdb=" CA  PRO A 115 "    0.074 5.00e-02 4.00e+02
        pdb=" CD  PRO A 115 "    0.075 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 114 "    0.102 5.00e-02 4.00e+02   1.45e-01 3.37e+01
        pdb=" N   PRO B 115 "   -0.251 5.00e-02 4.00e+02
        pdb=" CA  PRO B 115 "    0.073 5.00e-02 4.00e+02
        pdb=" CD  PRO B 115 "    0.075 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 107 "   -0.094 5.00e-02 4.00e+02   1.33e-01 2.83e+01
        pdb=" N   PRO A 108 "    0.230 5.00e-02 4.00e+02
        pdb=" CA  PRO A 108 "   -0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO A 108 "   -0.071 5.00e-02 4.00e+02
  ... (remaining 1033 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 38
        2.59 -     3.17: 5029
        3.17 -     3.74: 9890
        3.74 -     4.32: 12054
        4.32 -     4.90: 20504
  Nonbonded interactions: 47515
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 154 "
            pdb="MG    MG B 502 "
     model   vdw
     2.008 2.170
  nonbonded pdb=" OD1 ASP A 154 "
            pdb="MG    MG A 502 "
     model   vdw
     2.009 2.170
  nonbonded pdb="MG    MG B 502 "
            pdb=" O2B CDC B 503 "
     model   vdw
     2.085 2.170
  nonbonded pdb="MG    MG A 502 "
            pdb=" O2B CDC A 503 "
     model   vdw
     2.086 2.170
  nonbonded pdb=" OD1 ASP A 180 "
            pdb=" OH  TYR A 304 "
     model   vdw
     2.269 3.040
  ... (remaining 47510 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: 0.03
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:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.590
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
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      :  0.008   0.146   6248  Z= 0.534
  Angle     :  1.459  18.960   8524  Z= 0.833
  Chirality :  0.077   0.406    984
  Planarity :  0.015   0.199   1036
  Dihedral  : 16.780  82.606   2210
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 19.94 %
    Favored  : 79.76 %
  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:  1.24 (0.29), residues: 756
  helix:  0.99 (0.20), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.67 (0.47), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.004   TRP B 181 
 HIS   0.007   0.002   HIS A  46 
 PHE   0.069   0.004   PHE B 234 
 TYR   0.047   0.006   TYR A 362 
 ARG   0.010   0.002   ARG A  77 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 190
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 GLN cc_start: 0.8807 (mt0) cc_final: 0.8524 (mt0)
REVERT: B   82 TRP cc_start: 0.8514 (p90) cc_final: 0.8297 (p90)
REVERT: B  130 GLN cc_start: 0.8216 (tp40) cc_final: 0.7863 (tp-100)
REVERT: B  344 MET cc_start: 0.7872 (mtp) cc_final: 0.7572 (mtt)
REVERT: B  361 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8108 (mm-40)
REVERT: A   82 TRP cc_start: 0.8500 (p90) cc_final: 0.8279 (p90)
REVERT: A  130 GLN cc_start: 0.8265 (tp40) cc_final: 0.7914 (tp-100)
REVERT: A  361 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8294 (mm-40)
  outliers start: 2
  outliers final: 0
  residues processed: 192
  average time/residue: 0.1938
  time to fit residues: 47.2177
Evaluate side-chains
  172 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.0970
   chunk 57 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN
A 197 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.184061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.143730 restraints weight = 7854.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.148802 restraints weight = 4387.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.152330 restraints weight = 2982.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6248  Z= 0.196
  Angle     :  0.631   8.729   8524  Z= 0.330
  Chirality :  0.042   0.132    984
  Planarity :  0.005   0.051   1036
  Dihedral  :  7.521  52.373    874
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 16.47 %
    Favored  : 79.46 %
  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:  2.74 (0.29), residues: 756
  helix:  2.16 (0.20), residues: 558
  sheet:  None (None), residues: 0
  loop :  0.99 (0.48), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 117 
 HIS   0.004   0.001   HIS B 315 
 PHE   0.017   0.002   PHE B 358 
 TYR   0.012   0.002   TYR B 387 
 ARG   0.007   0.001   ARG B 141 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 177
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   68 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8548 (mmm)
REVERT: B  142 ARG cc_start: 0.8128 (tpt90) cc_final: 0.7791 (tpt90)
REVERT: B  260 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8217 (t80)
REVERT: A  142 ARG cc_start: 0.8221 (tpt90) cc_final: 0.7845 (tpt90)
REVERT: A  260 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8231 (t80)
REVERT: A  302 MET cc_start: 0.8756 (mmm) cc_final: 0.8555 (mmt)
  outliers start: 27
  outliers final: 16
  residues processed: 191
  average time/residue: 0.1981
  time to fit residues: 48.2119
Evaluate side-chains
  175 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 156
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  260 PHE
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  378 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0370
   chunk 58 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.1462

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

Flipped N/Q/H residues before XYZ refinement:
B  69 GLN
A  69 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.178622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.137172 restraints weight = 8079.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.142076 restraints weight = 4617.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.145502 restraints weight = 3196.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6248  Z= 0.223
  Angle     :  0.589   6.054   8524  Z= 0.309
  Chirality :  0.042   0.151    984
  Planarity :  0.004   0.036   1036
  Dihedral  :  6.079  45.430    874
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 18.88 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.05 (0.30), residues: 756
  helix:  2.35 (0.20), residues: 558
  sheet:  None (None), residues: 0
  loop :  1.21 (0.50), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 117 
 HIS   0.004   0.001   HIS A 315 
 PHE   0.016   0.002   PHE B 187 
 TYR   0.011   0.002   TYR B  56 
 ARG   0.002   0.000   ARG B 141 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 165
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  142 ARG cc_start: 0.8265 (tpt90) cc_final: 0.7924 (tpt90)
REVERT: B  193 PHE cc_start: 0.8274 (t80) cc_final: 0.8060 (t80)
REVERT: B  260 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8121 (t80)
REVERT: B  306 LYS cc_start: 0.8170 (tppt) cc_final: 0.7922 (tppt)
REVERT: A   45 ARG cc_start: 0.7247 (ttt90) cc_final: 0.6912 (tmm160)
REVERT: A  142 ARG cc_start: 0.8311 (tpt90) cc_final: 0.7949 (tpt90)
REVERT: A  193 PHE cc_start: 0.8327 (t80) cc_final: 0.8093 (t80)
REVERT: A  260 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8084 (t80)
REVERT: A  302 MET cc_start: 0.8773 (mmm) cc_final: 0.8268 (mtt)
REVERT: A  306 LYS cc_start: 0.8113 (tppt) cc_final: 0.7855 (tppt)
  outliers start: 32
  outliers final: 23
  residues processed: 180
  average time/residue: 0.2006
  time to fit residues: 46.3313
Evaluate side-chains
  189 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 164
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  170 CYS
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  260 PHE
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 56 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 21 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 62 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
B  69 GLN
A  69 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.175030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.135759 restraints weight = 8393.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.140911 restraints weight = 4617.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.144448 restraints weight = 3119.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.3407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6248  Z= 0.223
  Angle     :  0.582   9.260   8524  Z= 0.302
  Chirality :  0.042   0.141    984
  Planarity :  0.004   0.038   1036
  Dihedral  :  5.805  43.494    874
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 19.49 %
    Favored  : 74.47 %
  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:  2.86 (0.30), residues: 756
  helix:  2.23 (0.20), residues: 560
  sheet:  None (None), residues: 0
  loop :  1.05 (0.49), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 374 
 HIS   0.005   0.001   HIS B 197 
 PHE   0.023   0.002   PHE B 234 
 TYR   0.020   0.002   TYR A 362 
 ARG   0.006   0.000   ARG B  55 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 179
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 PHE cc_start: 0.8798 (t80) cc_final: 0.8566 (t80)
REVERT: B  174 GLN cc_start: 0.9161 (mt0) cc_final: 0.8708 (mt0)
REVERT: B  260 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8053 (t80)
REVERT: A   38 LEU cc_start: 0.7865 (tp) cc_final: 0.7659 (tp)
REVERT: A   55 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7548 (mmt-90)
REVERT: A  127 PHE cc_start: 0.8850 (t80) cc_final: 0.8619 (t80)
REVERT: A  174 GLN cc_start: 0.9173 (mt0) cc_final: 0.8720 (mt0)
REVERT: A  302 MET cc_start: 0.8804 (mmm) cc_final: 0.8335 (mtp)
  outliers start: 40
  outliers final: 27
  residues processed: 198
  average time/residue: 0.2170
  time to fit residues: 54.0464
Evaluate side-chains
  191 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 163
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  170 CYS
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  260 PHE
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain B residue  388 CYS
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 61 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4017 r_free = 0.4017 target = 0.175600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.136590 restraints weight = 8157.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.141822 restraints weight = 4478.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.145300 restraints weight = 3000.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6248  Z= 0.194
  Angle     :  0.588  10.802   8524  Z= 0.302
  Chirality :  0.041   0.126    984
  Planarity :  0.004   0.038   1036
  Dihedral  :  5.571  41.231    874
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 23.56 %
    Favored  : 71.60 %
  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:  2.87 (0.30), residues: 756
  helix:  2.26 (0.20), residues: 560
  sheet:  None (None), residues: 0
  loop :  1.02 (0.49), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 235 
 HIS   0.004   0.001   HIS B 197 
 PHE   0.014   0.001   PHE B 187 
 TYR   0.016   0.001   TYR A 362 
 ARG   0.006   0.000   ARG B 141 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 172
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   55 ARG cc_start: 0.8159 (mmt-90) cc_final: 0.7791 (tpp80)
REVERT: B  127 PHE cc_start: 0.8801 (t80) cc_final: 0.8583 (t80)
REVERT: B  141 ARG cc_start: 0.8380 (mmt90) cc_final: 0.8069 (mpt-90)
REVERT: B  174 GLN cc_start: 0.9135 (mt0) cc_final: 0.8924 (mt0)
REVERT: B  182 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8254 (ttp)
REVERT: B  260 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7944 (t80)
REVERT: B  306 LYS cc_start: 0.8083 (tppt) cc_final: 0.7833 (tppt)
REVERT: B  367 ILE cc_start: 0.8276 (mm) cc_final: 0.8025 (tt)
REVERT: A   38 LEU cc_start: 0.7895 (tp) cc_final: 0.7645 (tp)
REVERT: A  127 PHE cc_start: 0.8854 (t80) cc_final: 0.8587 (t80)
REVERT: A  182 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8305 (ttp)
REVERT: A  260 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7973 (t80)
REVERT: A  302 MET cc_start: 0.8787 (mmm) cc_final: 0.8457 (mtp)
REVERT: A  367 ILE cc_start: 0.8267 (mm) cc_final: 0.7993 (tt)
  outliers start: 32
  outliers final: 22
  residues processed: 187
  average time/residue: 0.2165
  time to fit residues: 50.7891
Evaluate side-chains
  189 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 163
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  170 CYS
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  260 PHE
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   chunk 16 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 59 optimal weight:    7.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 174 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.173113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.134204 restraints weight = 8267.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.139374 restraints weight = 4578.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.142837 restraints weight = 3080.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.3873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6248  Z= 0.216
  Angle     :  0.597  11.592   8524  Z= 0.305
  Chirality :  0.041   0.129    984
  Planarity :  0.004   0.038   1036
  Dihedral  :  5.413  38.218    874
  Min Nonbonded Distance : 1.603

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 23.72 %
    Favored  : 70.69 %
  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:  2.87 (0.30), residues: 756
  helix:  2.22 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  1.12 (0.49), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 117 
 HIS   0.004   0.001   HIS B 197 
 PHE   0.018   0.001   PHE A 234 
 TYR   0.016   0.001   TYR A 362 
 ARG   0.005   0.000   ARG B 141 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 170
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   55 ARG cc_start: 0.8048 (mmt-90) cc_final: 0.7780 (tpp80)
REVERT: B  127 PHE cc_start: 0.8791 (t80) cc_final: 0.8566 (t80)
REVERT: B  174 GLN cc_start: 0.9172 (mt0) cc_final: 0.8963 (mt0)
REVERT: B  182 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8243 (ttp)
REVERT: B  260 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7987 (t80)
REVERT: B  307 SER cc_start: 0.9017 (t) cc_final: 0.8605 (t)
REVERT: B  367 ILE cc_start: 0.8251 (mm) cc_final: 0.7937 (tt)
REVERT: A   38 LEU cc_start: 0.7905 (tp) cc_final: 0.7638 (tp)
REVERT: A  127 PHE cc_start: 0.8868 (t80) cc_final: 0.8606 (t80)
REVERT: A  182 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8260 (ttp)
REVERT: A  260 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7998 (t80)
REVERT: A  302 MET cc_start: 0.8766 (mmm) cc_final: 0.8402 (mtp)
REVERT: A  307 SER cc_start: 0.9012 (t) cc_final: 0.8756 (t)
  outliers start: 37
  outliers final: 28
  residues processed: 187
  average time/residue: 0.2074
  time to fit residues: 48.8543
Evaluate side-chains
  196 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 164
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  170 CYS
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  260 PHE
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain B residue  388 CYS
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 54 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   chunk 29 optimal weight:    0.6980
   chunk 25 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  69 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.174329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.135147 restraints weight = 8391.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.140497 restraints weight = 4634.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.144056 restraints weight = 3106.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.4065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6248  Z= 0.212
  Angle     :  0.613  12.008   8524  Z= 0.311
  Chirality :  0.041   0.132    984
  Planarity :  0.004   0.038   1036
  Dihedral  :  5.462  38.636    874
  Min Nonbonded Distance : 1.461

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 24.92 %
    Favored  : 69.94 %
  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:  2.88 (0.30), residues: 756
  helix:  2.23 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  1.11 (0.49), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 235 
 HIS   0.004   0.001   HIS B 197 
 PHE   0.013   0.001   PHE B 187 
 TYR   0.019   0.001   TYR A 362 
 ARG   0.005   0.000   ARG B  55 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 172
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
REVERT: B   57 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7442 (mm-40)
REVERT: B   61 ARG cc_start: 0.7094 (mtp-110) cc_final: 0.6790 (mmm160)
REVERT: B  127 PHE cc_start: 0.8859 (t80) cc_final: 0.8631 (t80)
REVERT: B  141 ARG cc_start: 0.8627 (mmt90) cc_final: 0.8302 (mmt90)
REVERT: B  182 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8219 (ttp)
REVERT: B  260 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7922 (t80)
REVERT: B  307 SER cc_start: 0.8984 (t) cc_final: 0.8732 (t)
REVERT: B  367 ILE cc_start: 0.8242 (mm) cc_final: 0.7987 (tt)
REVERT: A  127 PHE cc_start: 0.8953 (t80) cc_final: 0.8709 (t80)
REVERT: A  182 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8238 (ttp)
REVERT: A  260 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.7979 (t80)
REVERT: A  302 MET cc_start: 0.8723 (mmm) cc_final: 0.8426 (mtp)
REVERT: A  307 SER cc_start: 0.9011 (t) cc_final: 0.8684 (t)
REVERT: A  361 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7919 (mm110)
  outliers start: 34
  outliers final: 24
  residues processed: 186
  average time/residue: 0.2040
  time to fit residues: 48.2471
Evaluate side-chains
  196 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 168
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  170 CYS
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain B residue  260 PHE
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  388 CYS
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0980
   chunk 27 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   chunk 37 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 56 optimal weight:   10.0000
   chunk 26 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B 174 GLN
A 130 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.176632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.137528 restraints weight = 8297.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.142842 restraints weight = 4554.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.146142 restraints weight = 3053.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.4289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6248  Z= 0.198
  Angle     :  0.631  12.223   8524  Z= 0.314
  Chirality :  0.040   0.120    984
  Planarity :  0.004   0.038   1036
  Dihedral  :  5.517  40.905    874
  Min Nonbonded Distance : 1.471

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 25.98 %
    Favored  : 69.18 %
  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:  2.83 (0.30), residues: 756
  helix:  2.21 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop :  1.04 (0.48), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 197 
 PHE   0.019   0.001   PHE A 234 
 TYR   0.020   0.001   TYR A 362 
 ARG   0.006   0.000   ARG B  55 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 166
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
REVERT: B   55 ARG cc_start: 0.7991 (mmt-90) cc_final: 0.7258 (tpp80)
REVERT: B   57 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7258 (mm-40)
REVERT: B   61 ARG cc_start: 0.7052 (mtp-110) cc_final: 0.6834 (mmm160)
REVERT: B  119 TYR cc_start: 0.8272 (m-80) cc_final: 0.8006 (m-80)
REVERT: B  260 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.7921 (t80)
REVERT: B  307 SER cc_start: 0.9017 (t) cc_final: 0.8775 (t)
REVERT: A   61 ARG cc_start: 0.7193 (mtp-110) cc_final: 0.6930 (mmm160)
REVERT: A  127 PHE cc_start: 0.8930 (t80) cc_final: 0.8699 (t80)
REVERT: A  130 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7718 (tp-100)
REVERT: A  260 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7959 (t80)
REVERT: A  302 MET cc_start: 0.8689 (mmm) cc_final: 0.8457 (mtp)
REVERT: A  307 SER cc_start: 0.9001 (t) cc_final: 0.8739 (t)
  outliers start: 32
  outliers final: 25
  residues processed: 179
  average time/residue: 0.2102
  time to fit residues: 47.2824
Evaluate side-chains
  188 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 160
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  170 CYS
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  260 PHE
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 3 optimal weight:    0.1980
   chunk 39 optimal weight:   20.0000
   chunk 48 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 6 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.3992 r_free = 0.3992 target = 0.173011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.133564 restraints weight = 8309.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.138868 restraints weight = 4615.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.142453 restraints weight = 3112.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.4308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6248  Z= 0.238
  Angle     :  0.651  13.057   8524  Z= 0.328
  Chirality :  0.042   0.141    984
  Planarity :  0.004   0.039   1036
  Dihedral  :  5.452  39.765    874
  Min Nonbonded Distance : 1.404

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 24.77 %
    Favored  : 69.79 %
  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:  2.82 (0.30), residues: 756
  helix:  2.20 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop :  1.05 (0.48), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 117 
 HIS   0.005   0.001   HIS B 197 
 PHE   0.013   0.001   PHE A 358 
 TYR   0.021   0.002   TYR A 362 
 ARG   0.006   0.000   ARG B  55 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 166
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
REVERT: B   55 ARG cc_start: 0.8056 (mmt-90) cc_final: 0.7777 (tpp80)
REVERT: B   61 ARG cc_start: 0.7127 (mtp-110) cc_final: 0.6907 (mmm160)
REVERT: B  260 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7878 (t80)
REVERT: A   98 CYS cc_start: 0.7593 (m) cc_final: 0.7285 (p)
REVERT: A  127 PHE cc_start: 0.8923 (t80) cc_final: 0.8677 (t80)
REVERT: A  260 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.7950 (t80)
REVERT: A  302 MET cc_start: 0.8765 (mmm) cc_final: 0.8479 (mtp)
REVERT: A  307 SER cc_start: 0.9101 (t) cc_final: 0.8809 (t)
REVERT: A  361 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7917 (mm110)
  outliers start: 36
  outliers final: 32
  residues processed: 181
  average time/residue: 0.1972
  time to fit residues: 45.8487
Evaluate side-chains
  196 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 162
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  170 CYS
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  260 PHE
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain B residue  388 CYS
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  390 SER
Chi-restraints excluded: chain A residue  392 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0050
   chunk 30 optimal weight:    0.6980
   chunk 49 optimal weight:    9.9990
   chunk 55 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
A 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.175754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.137305 restraints weight = 8289.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.142565 restraints weight = 4589.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.146103 restraints weight = 3076.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.4525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6248  Z= 0.207
  Angle     :  0.644  13.304   8524  Z= 0.324
  Chirality :  0.041   0.170    984
  Planarity :  0.004   0.039   1036
  Dihedral  :  5.473  40.383    874
  Min Nonbonded Distance : 1.348

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 26.28 %
    Favored  : 68.88 %
  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:  2.68 (0.30), residues: 756
  helix:  2.10 (0.21), residues: 574
  sheet:  None (None), residues: 0
  loop :  0.87 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 117 
 HIS   0.004   0.001   HIS B 197 
 PHE   0.024   0.001   PHE A 234 
 TYR   0.021   0.001   TYR A 362 
 ARG   0.006   0.000   ARG B  55 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 166
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   55 ARG cc_start: 0.8028 (mmt-90) cc_final: 0.7442 (tpp80)
REVERT: B  223 MET cc_start: 0.8398 (ttm) cc_final: 0.8093 (ttm)
REVERT: B  247 LYS cc_start: 0.7964 (ttpt) cc_final: 0.7674 (ttpt)
REVERT: B  260 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7929 (t80)
REVERT: B  405 ARG cc_start: 0.7263 (mtt180) cc_final: 0.6931 (mtt90)
REVERT: A  127 PHE cc_start: 0.8930 (t80) cc_final: 0.8694 (t80)
REVERT: A  260 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7983 (t80)
REVERT: A  302 MET cc_start: 0.8784 (mmm) cc_final: 0.8532 (mtp)
REVERT: A  307 SER cc_start: 0.9096 (t) cc_final: 0.8867 (t)
  outliers start: 32
  outliers final: 29
  residues processed: 178
  average time/residue: 0.2040
  time to fit residues: 46.7001
Evaluate side-chains
  194 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 163
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  170 CYS
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  260 PHE
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain B residue  388 CYS
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  390 SER
Chi-restraints excluded: chain A residue  392 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 46 optimal weight:    0.1980
   chunk 56 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4026 r_free = 0.4026 target = 0.176209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.137419 restraints weight = 8481.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.142719 restraints weight = 4578.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.146346 restraints weight = 3047.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.4511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6248  Z= 0.210
  Angle     :  0.646  13.305   8524  Z= 0.326
  Chirality :  0.041   0.172    984
  Planarity :  0.004   0.038   1036
  Dihedral  :  5.396  39.093    874
  Min Nonbonded Distance : 1.282

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 26.28 %
    Favored  : 69.03 %
  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:  2.74 (0.29), residues: 756
  helix:  2.17 (0.21), residues: 564
  sheet:  None (None), residues: 0
  loop :  0.88 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 117 
 HIS   0.003   0.001   HIS B 315 
 PHE   0.013   0.001   PHE A 323 
 TYR   0.021   0.001   TYR A 362 
 ARG   0.006   0.000   ARG B  55 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2134.54 seconds
wall clock time: 37 minutes 44.08 seconds (2264.08 seconds total)