Starting phenix.real_space_refine
on Fri Aug 22 16:55:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gyw_34378/08_2025/8gyw_34378.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gyw_34378/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gyw_34378/08_2025/8gyw_34378.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gyw_34378/08_2025/8gyw_34378.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gyw_34378/08_2025/8gyw_34378.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gyw_34378/08_2025/8gyw_34378.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6076
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      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: "B"
      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:
    A
  Time building chain proxies: 2.02, per 1000 atoms: 0.33
  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: 0.40
  Conformation dependent library (CDL) restraints added in 349.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.20
  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: 0.98

  Time building geometry restraints manager: 0.53 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}

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:             0.540
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     7.320
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.180
-------------------------------------------------------------------------------
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= 0.354
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (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
 ARG   0.010   0.002   ARG A  77 
 TYR   0.047   0.006   TYR A 362 
 PHE   0.069   0.004   PHE B 234 
 TRP   0.032   0.004   TRP B 181 
 HIS   0.007   0.002   HIS A  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00780 ( 6248)
  covalent geometry    : angle       1.45913 ( 8524)
  hydrogen bonds       : bond        0.22029 (  441)
  hydrogen bonds       : angle       6.72262 ( 1311)

*********************** 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  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 GLN cc_start: 0.8807 (mt0) cc_final: 0.8526 (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: 0.7861 (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: 0.7912 (tp-100)
REVERT: A  361 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8295 (mm-40)
  outliers start: 2
  outliers final: 0
  residues processed: 192
  average time/residue: 0.0890
  time to fit residues: 21.8667
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  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4032 r_free = 0.4032 target = 0.182220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.141664 restraints weight = 7976.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.146759 restraints weight = 4437.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.150308 restraints weight = 3005.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.152644 restraints weight = 2325.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.154018 restraints weight = 1967.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2308

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= 0.155
  Angle     :  0.641   8.702   8524  Z= 0.335
  Chirality :  0.043   0.130    984
  Planarity :  0.005   0.051   1036
  Dihedral  :  7.883  53.404    874
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 16.16 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.69 (0.29), residues: 756
  helix:  2.11 (0.20), residues: 558
  sheet:  None (None), residues: 0
  loop :  1.00 (0.48), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 141 
 TYR   0.011   0.002   TYR B 387 
 PHE   0.016   0.002   PHE B 358 
 TRP   0.012   0.001   TRP B 117 
 HIS   0.004   0.001   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6248)
  covalent geometry    : angle       0.64089 ( 8524)
  hydrogen bonds       : bond        0.05752 (  441)
  hydrogen bonds       : angle       4.44745 ( 1311)

*********************** 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
  201 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 174
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   68 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8497 (mmm)
REVERT: B  142 ARG cc_start: 0.8073 (tpt90) cc_final: 0.7785 (tpt90)
REVERT: B  260 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8206 (t80)
REVERT: A  142 ARG cc_start: 0.8142 (tpt90) cc_final: 0.7821 (tpt90)
REVERT: A  260 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8202 (t80)
  outliers start: 27
  outliers final: 16
  residues processed: 188
  average time/residue: 0.0873
  time to fit residues: 21.3191
Evaluate side-chains
  176 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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 71 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0980
   chunk 43 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 61 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.9586

-------------------------------------------------------------------------------
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 = 0.4007 r_free = 0.4007 target = 0.179366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.138238 restraints weight = 8023.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.143171 restraints weight = 4568.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.146616 restraints weight = 3150.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.148692 restraints weight = 2473.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.150302 restraints weight = 2122.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6248  Z= 0.148
  Angle     :  0.594   6.294   8524  Z= 0.308
  Chirality :  0.041   0.146    984
  Planarity :  0.004   0.036   1036
  Dihedral  :  6.180  46.189    874
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 19.79 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.93 (0.30), residues: 756
  helix:  2.31 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  1.00 (0.48), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  55 
 TYR   0.011   0.001   TYR B 387 
 PHE   0.016   0.002   PHE B 187 
 TRP   0.008   0.001   TRP B 117 
 HIS   0.004   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6248)
  covalent geometry    : angle       0.59441 ( 8524)
  hydrogen bonds       : bond        0.05219 (  441)
  hydrogen bonds       : angle       4.16351 ( 1311)

*********************** 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: 33
    poor density    : 164
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  193 PHE cc_start: 0.8240 (t80) cc_final: 0.8015 (t80)
REVERT: B  260 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8091 (t80)
REVERT: B  306 LYS cc_start: 0.8089 (tppt) cc_final: 0.7885 (tppt)
REVERT: A   45 ARG cc_start: 0.7156 (ttt90) cc_final: 0.6832 (tmm160)
REVERT: A  142 ARG cc_start: 0.8258 (tpt90) cc_final: 0.7899 (tpt90)
REVERT: A  193 PHE cc_start: 0.8297 (t80) cc_final: 0.8051 (t80)
REVERT: A  260 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8124 (t80)
  outliers start: 33
  outliers final: 22
  residues processed: 179
  average time/residue: 0.0897
  time to fit residues: 20.5589
Evaluate side-chains
  183 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 159
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
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  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  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 0 optimal weight:   10.0000
   chunk 64 optimal weight:    0.3980
   chunk 3 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4010 r_free = 0.4010 target = 0.179362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.136822 restraints weight = 8010.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.141961 restraints weight = 4467.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.145507 restraints weight = 3059.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.147613 restraints weight = 2386.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.149376 restraints weight = 2041.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.3227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6248  Z= 0.133
  Angle     :  0.564   9.689   8524  Z= 0.292
  Chirality :  0.041   0.148    984
  Planarity :  0.004   0.037   1036
  Dihedral  :  5.946  45.532    874
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 19.49 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.98 (0.30), residues: 756
  helix:  2.34 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  1.06 (0.49), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  50 
 TYR   0.013   0.001   TYR A 362 
 PHE   0.023   0.002   PHE B 234 
 TRP   0.007   0.001   TRP B 117 
 HIS   0.004   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6248)
  covalent geometry    : angle       0.56394 ( 8524)
  hydrogen bonds       : bond        0.04856 (  441)
  hydrogen bonds       : angle       4.06380 ( 1311)

*********************** 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
  207 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 171
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   55 ARG cc_start: 0.8016 (mpt-90) cc_final: 0.7815 (mmt-90)
REVERT: B  174 GLN cc_start: 0.9137 (mt0) cc_final: 0.8765 (mt0)
REVERT: B  260 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8030 (t80)
REVERT: A   50 ARG cc_start: 0.8562 (mtp85) cc_final: 0.8312 (mtp85)
REVERT: A  141 ARG cc_start: 0.8466 (mmt-90) cc_final: 0.8261 (mpt-90)
REVERT: A  174 GLN cc_start: 0.9144 (mt0) cc_final: 0.8747 (mt0)
  outliers start: 36
  outliers final: 23
  residues processed: 189
  average time/residue: 0.0989
  time to fit residues: 23.5326
Evaluate side-chains
  187 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 163
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
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  170 CYS
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  254 THR
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  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  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 65 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 42 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 57 optimal weight:    0.6980
   chunk 11 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 18 optimal weight:    8.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    2.7388

-------------------------------------------------------------------------------
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 = 0.3909 r_free = 0.3909 target = 0.165409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.127257 restraints weight = 8542.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.132060 restraints weight = 4759.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.135284 restraints weight = 3223.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.137502 restraints weight = 2493.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.138260 restraints weight = 2103.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.3884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   6248  Z= 0.273
  Angle     :  0.733  10.518   8524  Z= 0.377
  Chirality :  0.047   0.172    984
  Planarity :  0.005   0.050   1036
  Dihedral  :  5.794  41.326    874
  Min Nonbonded Distance : 1.539

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 21.75 %
    Favored  : 71.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.30), residues: 756
  helix:  1.90 (0.20), residues: 558
  sheet:  None (None), residues: 0
  loop :  1.13 (0.49), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 142 
 TYR   0.012   0.002   TYR B 362 
 PHE   0.017   0.002   PHE A 351 
 TRP   0.014   0.001   TRP B 374 
 HIS   0.005   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00621 ( 6248)
  covalent geometry    : angle       0.73324 ( 8524)
  hydrogen bonds       : bond        0.06031 (  441)
  hydrogen bonds       : angle       4.50191 ( 1311)

*********************** 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
  214 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 171
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   55 ARG cc_start: 0.8250 (mpt-90) cc_final: 0.7917 (tpp80)
REVERT: B   98 CYS cc_start: 0.7905 (m) cc_final: 0.7447 (p)
REVERT: B  127 PHE cc_start: 0.8863 (t80) cc_final: 0.8586 (t80)
REVERT: B  260 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.7970 (t80)
REVERT: B  306 LYS cc_start: 0.8055 (tppt) cc_final: 0.7086 (mmtt)
REVERT: A   50 ARG cc_start: 0.8649 (mtp85) cc_final: 0.8444 (mtp85)
REVERT: A   68 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8343 (mmm)
REVERT: A  127 PHE cc_start: 0.8886 (t80) cc_final: 0.8630 (t80)
REVERT: A  260 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.8040 (t80)
REVERT: A  306 LYS cc_start: 0.8049 (tppt) cc_final: 0.7078 (mmtt)
  outliers start: 43
  outliers final: 32
  residues processed: 192
  average time/residue: 0.0895
  time to fit residues: 22.0888
Evaluate side-chains
  196 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 161
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
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  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  254 THR
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  260 PHE
Chi-restraints excluded: chain B residue  336 VAL
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 B residue  391 VAL
Chi-restraints excluded: chain B residue  392 CYS
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  186 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  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
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  390 SER
Chi-restraints excluded: chain A residue  391 VAL
Chi-restraints excluded: chain A residue  392 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0010
   chunk 74 optimal weight:    0.8980
   chunk 2 optimal weight:    0.3980
   chunk 0 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.174310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.135229 restraints weight = 8337.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.140538 restraints weight = 4601.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.144116 restraints weight = 3085.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.146266 restraints weight = 2361.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.147898 restraints weight = 1997.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6248  Z= 0.134
  Angle     :  0.613  11.366   8524  Z= 0.310
  Chirality :  0.041   0.124    984
  Planarity :  0.004   0.041   1036
  Dihedral  :  5.766  42.535    874
  Min Nonbonded Distance : 1.370

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 27.64 %
    Favored  : 67.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.54 (0.30), residues: 756
  helix:  1.99 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.89 (0.50), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 142 
 TYR   0.016   0.001   TYR A 129 
 PHE   0.021   0.001   PHE B 234 
 TRP   0.005   0.001   TRP B 235 
 HIS   0.004   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6248)
  covalent geometry    : angle       0.61327 ( 8524)
  hydrogen bonds       : bond        0.04918 (  441)
  hydrogen bonds       : angle       4.14394 ( 1311)

*********************** 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
  210 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 181
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   55 ARG cc_start: 0.8201 (mpt-90) cc_final: 0.7842 (tpp80)
REVERT: B  127 PHE cc_start: 0.8812 (t80) cc_final: 0.8584 (t80)
REVERT: B  182 MET cc_start: 0.8660 (tpp) cc_final: 0.8430 (tpp)
REVERT: B  260 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7972 (t80)
REVERT: B  302 MET cc_start: 0.8593 (mmt) cc_final: 0.8062 (mmt)
REVERT: B  367 ILE cc_start: 0.8281 (mm) cc_final: 0.8040 (tt)
REVERT: A  127 PHE cc_start: 0.8802 (t80) cc_final: 0.8571 (t80)
REVERT: A  174 GLN cc_start: 0.9111 (mt0) cc_final: 0.8634 (mt0)
REVERT: A  260 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7979 (t80)
REVERT: A  302 MET cc_start: 0.8592 (mmt) cc_final: 0.8057 (mmt)
REVERT: A  367 ILE cc_start: 0.8237 (mm) cc_final: 0.7980 (tt)
  outliers start: 29
  outliers final: 20
  residues processed: 195
  average time/residue: 0.0941
  time to fit residues: 23.5026
Evaluate side-chains
  194 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 172
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  149 LEU
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  254 THR
Chi-restraints excluded: chain B residue  260 PHE
Chi-restraints excluded: chain B residue  349 THR
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   90 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  170 CYS
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  349 THR
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 14 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 58 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 46 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   chunk 13 optimal weight:    0.7980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B 174 GLN
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.172251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.132995 restraints weight = 8447.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.138194 restraints weight = 4684.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.141724 restraints weight = 3164.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.144073 restraints weight = 2442.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.145404 restraints weight = 2064.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.4269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6248  Z= 0.158
  Angle     :  0.674  12.380   8524  Z= 0.331
  Chirality :  0.042   0.128    984
  Planarity :  0.005   0.040   1036
  Dihedral  :  5.545  39.155    874
  Min Nonbonded Distance : 1.278

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 30.36 %
    Favored  : 65.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.30), residues: 756
  helix:  1.93 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  1.01 (0.50), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  61 
 TYR   0.018   0.002   TYR B 129 
 PHE   0.019   0.002   PHE A 234 
 TRP   0.005   0.001   TRP A 117 
 HIS   0.004   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6248)
  covalent geometry    : angle       0.67406 ( 8524)
  hydrogen bonds       : bond        0.05041 (  441)
  hydrogen bonds       : angle       4.17635 ( 1311)

*********************** 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
  202 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 176
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   55 ARG cc_start: 0.8090 (mpt-90) cc_final: 0.7756 (tpp80)
REVERT: B  127 PHE cc_start: 0.8814 (t80) cc_final: 0.8586 (t80)
REVERT: B  260 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7945 (t80)
REVERT: B  302 MET cc_start: 0.8612 (mmt) cc_final: 0.8227 (mmt)
REVERT: B  367 ILE cc_start: 0.8257 (mm) cc_final: 0.7995 (tt)
REVERT: A  127 PHE cc_start: 0.8878 (t80) cc_final: 0.8673 (t80)
REVERT: A  174 GLN cc_start: 0.9111 (mt0) cc_final: 0.8692 (mt0)
REVERT: A  260 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7930 (t80)
REVERT: A  302 MET cc_start: 0.8618 (mmt) cc_final: 0.8214 (mmt)
REVERT: A  361 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8109 (mm-40)
REVERT: A  367 ILE cc_start: 0.8307 (mm) cc_final: 0.8086 (tp)
  outliers start: 26
  outliers final: 23
  residues processed: 185
  average time/residue: 0.0862
  time to fit residues: 20.5914
Evaluate side-chains
  193 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 168
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  149 LEU
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  254 THR
Chi-restraints excluded: chain B residue  260 PHE
Chi-restraints excluded: chain B residue  349 THR
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   90 ILE
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  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  349 THR
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 28 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0070
   chunk 74 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 56 optimal weight:   10.0000
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.175570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.137031 restraints weight = 8350.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.142361 restraints weight = 4642.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.145850 restraints weight = 3119.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.148189 restraints weight = 2393.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.149508 restraints weight = 2016.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.4330

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= 0.139
  Angle     :  0.656  12.315   8524  Z= 0.322
  Chirality :  0.041   0.131    984
  Planarity :  0.004   0.040   1036
  Dihedral  :  5.584  39.068    874
  Min Nonbonded Distance : 1.257

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 30.66 %
    Favored  : 65.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.43 (0.30), residues: 756
  helix:  1.90 (0.21), residues: 574
  sheet:  None (None), residues: 0
  loop :  0.87 (0.50), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  61 
 TYR   0.017   0.002   TYR B 129 
 PHE   0.020   0.001   PHE B 234 
 TRP   0.006   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6248)
  covalent geometry    : angle       0.65616 ( 8524)
  hydrogen bonds       : bond        0.04809 (  441)
  hydrogen bonds       : angle       4.13718 ( 1311)

*********************** 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
  197 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 171
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   55 ARG cc_start: 0.8024 (mpt-90) cc_final: 0.7561 (tpp80)
REVERT: B  260 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7808 (t80)
REVERT: A  130 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7907 (tp-100)
REVERT: A  174 GLN cc_start: 0.9034 (mt0) cc_final: 0.8626 (mt0)
REVERT: A  260 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7942 (t80)
  outliers start: 26
  outliers final: 21
  residues processed: 180
  average time/residue: 0.0899
  time to fit residues: 20.8603
Evaluate side-chains
  193 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 169
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  170 CYS
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  244 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  349 THR
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   31 VAL
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  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  349 THR
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 7 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 62 optimal weight:    9.9990
   chunk 10 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 71 optimal weight:    0.4980
   chunk 32 optimal weight:    0.6980
   chunk 56 optimal weight:    0.1980
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B  57 GLN
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.175505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.136626 restraints weight = 8419.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.141985 restraints weight = 4605.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.145539 restraints weight = 3077.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.147678 restraints weight = 2352.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.149432 restraints weight = 1992.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.4575

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= 0.140
  Angle     :  0.664  12.897   8524  Z= 0.327
  Chirality :  0.041   0.133    984
  Planarity :  0.004   0.039   1036
  Dihedral  :  5.563  38.730    874
  Min Nonbonded Distance : 1.183

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 30.97 %
    Favored  : 65.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.30), residues: 756
  helix:  1.99 (0.21), residues: 574
  sheet:  None (None), residues: 0
  loop :  0.77 (0.49), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  61 
 TYR   0.025   0.001   TYR A 129 
 PHE   0.022   0.001   PHE A 234 
 TRP   0.004   0.001   TRP A 117 
 HIS   0.004   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6248)
  covalent geometry    : angle       0.66387 ( 8524)
  hydrogen bonds       : bond        0.04727 (  441)
  hydrogen bonds       : angle       4.10953 ( 1311)

*********************** 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
  197 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 172
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   55 ARG cc_start: 0.8101 (mpt-90) cc_final: 0.7689 (tpp80)
REVERT: B  153 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8241 (m-80)
REVERT: B  260 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7824 (t80)
REVERT: A  127 PHE cc_start: 0.8877 (t80) cc_final: 0.8652 (t80)
REVERT: A  128 ILE cc_start: 0.9433 (mt) cc_final: 0.9128 (mt)
REVERT: A  153 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8140 (m-80)
REVERT: A  174 GLN cc_start: 0.9047 (mt0) cc_final: 0.8652 (mt0)
REVERT: A  260 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7947 (t80)
REVERT: A  361 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8022 (mm110)
  outliers start: 25
  outliers final: 20
  residues processed: 179
  average time/residue: 0.0986
  time to fit residues: 22.3276
Evaluate side-chains
  193 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 169
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  349 THR
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   31 VAL
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  349 THR
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 39 optimal weight:   30.0000
   chunk 72 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 41 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 8 optimal weight:    0.3980
   chunk 63 optimal weight:   10.0000
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 155 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.169487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.130599 restraints weight = 8530.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.135520 restraints weight = 4849.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.138963 restraints weight = 3323.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.141207 restraints weight = 2579.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.142558 restraints weight = 2185.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.4713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6248  Z= 0.213
  Angle     :  0.738  13.329   8524  Z= 0.366
  Chirality :  0.044   0.149    984
  Planarity :  0.005   0.040   1036
  Dihedral  :  5.574  36.739    874
  Min Nonbonded Distance : 1.142

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 30.66 %
    Favored  : 65.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.30), residues: 756
  helix:  1.90 (0.21), residues: 566
  sheet:  None (None), residues: 0
  loop :  1.06 (0.49), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  55 
 TYR   0.019   0.002   TYR B 129 
 PHE   0.016   0.002   PHE B 358 
 TRP   0.006   0.001   TRP A 374 
 HIS   0.006   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 6248)
  covalent geometry    : angle       0.73801 ( 8524)
  hydrogen bonds       : bond        0.05463 (  441)
  hydrogen bonds       : angle       4.33953 ( 1311)

********************** 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
  197 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 169
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   55 ARG cc_start: 0.8202 (mpt-90) cc_final: 0.7851 (tpp80)
REVERT: B   98 CYS cc_start: 0.7671 (m) cc_final: 0.7361 (p)
REVERT: B  119 TYR cc_start: 0.8352 (m-80) cc_final: 0.7983 (m-80)
REVERT: B  128 ILE cc_start: 0.9502 (mt) cc_final: 0.9221 (mt)
REVERT: B  153 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8211 (m-80)
REVERT: B  260 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7919 (t80)
REVERT: A   45 ARG cc_start: 0.7195 (ttt90) cc_final: 0.6935 (tmm160)
REVERT: A  119 TYR cc_start: 0.8421 (m-80) cc_final: 0.8017 (m-80)
REVERT: A  127 PHE cc_start: 0.8950 (t80) cc_final: 0.8696 (t80)
REVERT: A  153 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8237 (m-80)
REVERT: A  174 GLN cc_start: 0.9164 (mt0) cc_final: 0.8277 (mm-40)
REVERT: A  260 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7970 (t80)
  outliers start: 28
  outliers final: 20
  residues processed: 178
  average time/residue: 0.0938
  time to fit residues: 21.4161
Evaluate side-chains
  188 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 164
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  346 LEU
Chi-restraints excluded: chain B residue  349 THR
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  132 LEU
Chi-restraints excluded: chain A residue  153 PHE
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  349 THR
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  57 GLN
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 130 GLN
A 197 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.174153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.135266 restraints weight = 8390.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.140393 restraints weight = 4690.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.143962 restraints weight = 3184.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.146128 restraints weight = 2454.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.147429 restraints weight = 2080.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.4788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6248  Z= 0.148
  Angle     :  0.685  13.355   8524  Z= 0.339
  Chirality :  0.041   0.147    984
  Planarity :  0.004   0.040   1036
  Dihedral  :  5.667  40.260    874
  Min Nonbonded Distance : 1.162

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 31.12 %
    Favored  : 64.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.30), residues: 756
  helix:  1.95 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.72 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  50 
 TYR   0.022   0.002   TYR A 129 
 PHE   0.024   0.001   PHE B 234 
 TRP   0.005   0.001   TRP B 117 
 HIS   0.004   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6248)
  covalent geometry    : angle       0.68496 ( 8524)
  hydrogen bonds       : bond        0.04910 (  441)
  hydrogen bonds       : angle       4.18585 ( 1311)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1153.78 seconds
wall clock time: 20 minutes 43.58 seconds (1243.58 seconds total)