Starting phenix.real_space_refine
on Thu Jul 31 11:39:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wu3_21904/07_2025/6wu3_21904_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wu3_21904/07_2025/6wu3_21904.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wu3_21904/07_2025/6wu3_21904.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wu3_21904/07_2025/6wu3_21904.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wu3_21904/07_2025/6wu3_21904_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wu3_21904/07_2025/6wu3_21904_neut.cif"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    4450      2.51       5
     N    1044      2.21       5
     O    1128      1.98       5
     H    6936      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13610
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 6805
          Classifications: {'peptide': 445}
          Link IDs: {'PTRANS': 15, 'TRANS': 429}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 6805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 6805
          Classifications: {'peptide': 445}
          Link IDs: {'PTRANS': 15, 'TRANS': 429}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 7.45, per 1000 atoms: 0.55
  Number of scatterers: 13610
  At special positions: 0
  Unit cell: (90.789, 97.641, 76.514, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     O    1128      8.00
     N    1044      7.00
     C    4450      6.00
     H    6936      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.34
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1656

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      82.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 38
      removed outlier: 3.596A  pdb=" N   LEU A  26 " --> pdb=" O   SER A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 62
    Processing helix  chain 'A' and resid 65 through 79
      Proline residue:  A  74  - end of helix
    Processing helix  chain 'A' and resid 84 through 90
    Processing helix  chain 'A' and resid 91 through 93
      No H-bonds generated for 'chain 'A' and resid 91 through 93'
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 3.795A  pdb=" N   PHE A  98 " --> pdb=" O   ASN A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 127
      removed outlier: 3.521A  pdb=" N   ALA A 127 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 147
    Processing helix  chain 'A' and resid 151 through 167
      removed outlier: 3.796A  pdb=" N   ALA A 155 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
      Proline residue:  A 160  - end of helix
    Processing helix  chain 'A' and resid 174 through 193
      removed outlier: 4.021A  pdb=" N   TYR A 178 " --> pdb=" O   GLN A 174 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   VAL A 185 " --> pdb=" O   VAL A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 211
      removed outlier: 3.907A  pdb=" N   ALA A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 240
      removed outlier: 4.372A  pdb=" N   PHE A 220 " --> pdb=" O   ASP A 216 " (cutoff:3.500A)
      Proline residue:  A 223  - end of helix
      Proline residue:  A 230  - end of helix
    Processing helix  chain 'A' and resid 260 through 277
    Processing helix  chain 'A' and resid 277 through 284
    Processing helix  chain 'A' and resid 290 through 306
    Processing helix  chain 'A' and resid 310 through 318
    Processing helix  chain 'A' and resid 319 through 339
      removed outlier: 3.680A  pdb=" N   LEU A 323 " --> pdb=" O   ASP A 319 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   GLY A 327 " --> pdb=" O   LEU A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 356
      removed outlier: 5.003A  pdb=" N   ASP A 351 " --> pdb=" O   ASN A 347 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   MET A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   MET A 356 " --> pdb=" O   MET A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 373
    Processing helix  chain 'A' and resid 377 through 392
      Proline residue:  A 387  - end of helix
    Processing helix  chain 'A' and resid 401 through 413
      removed outlier: 3.754A  pdb=" N   SER A 412 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 420
    Processing helix  chain 'A' and resid 421 through 429
    Processing helix  chain 'A' and resid 434 through 460
    Processing helix  chain 'C' and resid 19 through 38
      removed outlier: 3.596A  pdb=" N   LEU C  26 " --> pdb=" O   SER C  22 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 62
    Processing helix  chain 'C' and resid 65 through 79
      Proline residue:  C  74  - end of helix
    Processing helix  chain 'C' and resid 84 through 90
    Processing helix  chain 'C' and resid 91 through 93
      No H-bonds generated for 'chain 'C' and resid 91 through 93'
    Processing helix  chain 'C' and resid 94 through 113
      removed outlier: 3.795A  pdb=" N   PHE C  98 " --> pdb=" O   ASN C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 127
      removed outlier: 3.522A  pdb=" N   ALA C 127 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 147
    Processing helix  chain 'C' and resid 151 through 167
      removed outlier: 3.797A  pdb=" N   ALA C 155 " --> pdb=" O   ASN C 151 " (cutoff:3.500A)
      Proline residue:  C 160  - end of helix
    Processing helix  chain 'C' and resid 174 through 193
      removed outlier: 4.022A  pdb=" N   TYR C 178 " --> pdb=" O   GLN C 174 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   VAL C 185 " --> pdb=" O   VAL C 181 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 211
      removed outlier: 3.906A  pdb=" N   ALA C 204 " --> pdb=" O   SER C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 240
      removed outlier: 4.372A  pdb=" N   PHE C 220 " --> pdb=" O   ASP C 216 " (cutoff:3.500A)
      Proline residue:  C 223  - end of helix
      Proline residue:  C 230  - end of helix
    Processing helix  chain 'C' and resid 260 through 277
    Processing helix  chain 'C' and resid 277 through 284
    Processing helix  chain 'C' and resid 290 through 306
    Processing helix  chain 'C' and resid 310 through 318
    Processing helix  chain 'C' and resid 319 through 339
      removed outlier: 3.679A  pdb=" N   LEU C 323 " --> pdb=" O   ASP C 319 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   GLY C 327 " --> pdb=" O   LEU C 323 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 356
      removed outlier: 5.003A  pdb=" N   ASP C 351 " --> pdb=" O   ASN C 347 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   MET C 352 " --> pdb=" O   ALA C 348 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   MET C 356 " --> pdb=" O   MET C 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 357 through 373
    Processing helix  chain 'C' and resid 377 through 392
      Proline residue:  C 387  - end of helix
    Processing helix  chain 'C' and resid 401 through 413
      removed outlier: 3.754A  pdb=" N   SER C 412 " --> pdb=" O   ALA C 408 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 417 through 420
    Processing helix  chain 'C' and resid 421 through 429
    Processing helix  chain 'C' and resid 434 through 460

    490 hydrogen bonds defined for protein.
    1464 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.98

  Time building geometry restraints manager: 4.13 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6930
        1.03 -     1.22: 6
        1.22 -     1.42: 2757
        1.42 -     1.61: 3977
        1.61 -     1.80: 98
  Bond restraints: 13768
  Sorted by residual:
  bond pdb=" CG  LEU A 197 "
       pdb=" CD1 LEU A 197 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.33e+00
  bond pdb=" CG  LEU C 197 "
       pdb=" CD1 LEU C 197 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.33e+00
  bond pdb=" CG  LEU A 301 "
       pdb=" CD2 LEU A 301 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.20e+00
  bond pdb=" CG  LEU C 301 "
       pdb=" CD2 LEU C 301 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.19e+00
  bond pdb=" CG1 ILE A  71 "
       pdb=" CD1 ILE A  71 "
    ideal  model  delta    sigma   weight residual
    1.513  1.471  0.042 3.90e-02 6.57e+02 1.14e+00
  ... (remaining 13763 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.00: 22766
        1.00 -     2.00: 2106
        2.00 -     3.00: 106
        3.00 -     4.00: 34
        4.00 -     5.00: 12
  Bond angle restraints: 25024
  Sorted by residual:
  angle pdb=" N   VAL A 401 "
        pdb=" CA  VAL A 401 "
        pdb=" C   VAL A 401 "
      ideal   model   delta    sigma   weight residual
     112.96  109.12    3.84 1.00e+00 1.00e+00 1.47e+01
  angle pdb=" N   VAL C 401 "
        pdb=" CA  VAL C 401 "
        pdb=" C   VAL C 401 "
      ideal   model   delta    sigma   weight residual
     112.96  109.14    3.82 1.00e+00 1.00e+00 1.46e+01
  angle pdb=" CA  VAL A 401 "
        pdb=" C   VAL A 401 "
        pdb=" N   LEU A 402 "
      ideal   model   delta    sigma   weight residual
     118.65  115.98    2.67 1.07e+00 8.73e-01 6.23e+00
  angle pdb=" CA  VAL C 401 "
        pdb=" C   VAL C 401 "
        pdb=" N   LEU C 402 "
      ideal   model   delta    sigma   weight residual
     118.65  116.02    2.63 1.07e+00 8.73e-01 6.04e+00
  angle pdb=" CG  LYS A 259 "
        pdb=" CD  LYS A 259 "
        pdb=" CE  LYS A 259 "
      ideal   model   delta    sigma   weight residual
     111.30  116.30   -5.00 2.30e+00 1.89e-01 4.72e+00
  ... (remaining 25019 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 5567
       17.32 -    34.63: 569
       34.63 -    51.95: 214
       51.95 -    69.26: 87
       69.26 -    86.58: 23
  Dihedral angle restraints: 6460
    sinusoidal: 3384
      harmonic: 3076
  Sorted by residual:
  dihedral pdb=" CA  PHE C  83 "
           pdb=" C   PHE C  83 "
           pdb=" N   GLU C  84 "
           pdb=" CA  GLU C  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.03   17.97     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  PHE A  83 "
           pdb=" C   PHE A  83 "
           pdb=" N   GLU A  84 "
           pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.06   17.94     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  PHE C  80 "
           pdb=" C   PHE C  80 "
           pdb=" N   GLY C  81 "
           pdb=" CA  GLY C  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.11   15.89     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 6457 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 575
       0.024 -    0.048: 302
       0.048 -    0.072: 209
       0.072 -    0.097: 59
       0.097 -    0.121: 13
  Chirality restraints: 1158
  Sorted by residual:
  chirality pdb=" CA  PRO C 418 "
            pdb=" N   PRO C 418 "
            pdb=" C   PRO C 418 "
            pdb=" CB  PRO C 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.64e-01
  chirality pdb=" CA  PRO A 418 "
            pdb=" N   PRO A 418 "
            pdb=" C   PRO A 418 "
            pdb=" CB  PRO A 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.60e-01
  chirality pdb=" CA  ILE C 433 "
            pdb=" N   ILE C 433 "
            pdb=" C   ILE C 433 "
            pdb=" CB  ILE C 433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.21e-01
  ... (remaining 1155 not shown)

  Planarity restraints: 1986
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 421 "   -0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO A 422 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 422 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 422 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 421 "    0.025 5.00e-02 4.00e+02   3.72e-02 2.22e+00
        pdb=" N   PRO C 422 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO C 422 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 422 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 159 "   -0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO C 160 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO C 160 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 160 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1983 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 729
        2.16 -     2.77: 27577
        2.77 -     3.38: 39437
        3.38 -     3.99: 50104
        3.99 -     4.60: 80706
  Nonbonded interactions: 198553
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 184 "
            pdb=" HG  SER A 188 "
     model   vdw
     1.555 2.450
  nonbonded pdb=" O   GLY C 184 "
            pdb=" HG  SER C 188 "
     model   vdw
     1.575 2.450
  nonbonded pdb=" O   VAL C  57 "
            pdb=" HG1 THR C  61 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" O   PRO C 387 "
            pdb=" HG1 THR C 391 "
     model   vdw
     1.611 2.450
  nonbonded pdb=" O   ILE C 267 "
            pdb=" HG1 THR C 271 "
     model   vdw
     1.614 2.450
  ... (remaining 198548 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             232.370
  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:             0.250
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     32.160
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  268.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
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   0.042   6832  Z= 0.310
  Angle     :  0.603   4.997   9318  Z= 0.341
  Chirality :  0.039   0.121   1158
  Planarity :  0.004   0.037   1128
  Dihedral  : 15.887  84.129   2292
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 14.96 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.62 (0.23), residues: 886
  helix: -1.65 (0.16), residues: 696
  sheet:  None (None), residues: 0
  loop : -4.72 (0.31), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 311 
 HIS   0.003   0.001   HIS C 432 
 PHE   0.014   0.001   PHE C  98 
 TYR   0.008   0.001   TYR C  36 
 ARG   0.001   0.000   ARG C 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13435 (  490)
  hydrogen bonds       : angle       5.82696 ( 1464)
  covalent geometry    : bond        0.00763 ( 6832)
  covalent geometry    : angle       0.60286 ( 9318)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Evaluate side-chains
  194 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 150
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6681 (ptpp)
REVERT: A  216 ASP cc_start: 0.7898 (t0) cc_final: 0.7648 (t0)
REVERT: C  173 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6628 (ptpp)
REVERT: C  216 ASP cc_start: 0.7867 (t0) cc_final: 0.7650 (t0)
  outliers start: 44
  outliers final: 34
  residues processed: 183
  average time/residue: 0.4031
  time to fit residues: 98.6323
Evaluate side-chains
  164 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 128
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain C residue   50 SER
Chi-restraints excluded: chain C residue   72 LEU
Chi-restraints excluded: chain C residue  100 PHE
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  177 THR
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  200 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain C residue  317 THR
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  421 THR
Chi-restraints excluded: chain C residue  432 HIS
Chi-restraints excluded: chain C residue  436 SER
Chi-restraints excluded: chain C residue  454 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
C 245 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.128366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.103381 restraints weight = 26917.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 2.35
r_work: 0.3052 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6832  Z= 0.154
  Angle     :  0.577   4.955   9318  Z= 0.306
  Chirality :  0.035   0.132   1158
  Planarity :  0.004   0.035   1128
  Dihedral  :  9.051  59.067    960
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 17.66 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.27), residues: 886
  helix: -0.03 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -4.51 (0.36), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 311 
 HIS   0.003   0.001   HIS C 310 
 PHE   0.014   0.001   PHE A 277 
 TYR   0.007   0.001   TYR A  36 
 ARG   0.001   0.000   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04197 (  490)
  hydrogen bonds       : angle       4.33442 ( 1464)
  covalent geometry    : bond        0.00331 ( 6832)
  covalent geometry    : angle       0.57735 ( 9318)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Evaluate side-chains
  157 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7048 (ptpp)
REVERT: A  216 ASP cc_start: 0.8580 (t0) cc_final: 0.8377 (m-30)
REVERT: A  439 MET cc_start: 0.7920 (mtm) cc_final: 0.7604 (mtt)
REVERT: C  173 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.6975 (ptpp)
REVERT: C  216 ASP cc_start: 0.8593 (t0) cc_final: 0.8367 (t0)
  outliers start: 25
  outliers final: 21
  residues processed: 151
  average time/residue: 0.4135
  time to fit residues: 89.3010
Evaluate side-chains
  150 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain C residue   50 SER
Chi-restraints excluded: chain C residue  100 PHE
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  421 THR
Chi-restraints excluded: chain C residue  436 SER
Chi-restraints excluded: chain C residue  454 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0050
   chunk 0 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.6002

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

Flipped N/Q/H residues before XYZ refinement:
A 334 ASN
C 334 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.120344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.095815 restraints weight = 27945.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 2.31
r_work: 0.2926 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2794 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6832  Z= 0.188
  Angle     :  0.556   6.782   9318  Z= 0.293
  Chirality :  0.035   0.126   1158
  Planarity :  0.004   0.034   1128
  Dihedral  :  8.354  59.855    940
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 18.23 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.29), residues: 886
  helix:  0.62 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -4.29 (0.37), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 311 
 HIS   0.007   0.001   HIS C  19 
 PHE   0.019   0.001   PHE C  54 
 TYR   0.006   0.001   TYR C  36 
 ARG   0.001   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04013 (  490)
  hydrogen bonds       : angle       4.24966 ( 1464)
  covalent geometry    : bond        0.00424 ( 6832)
  covalent geometry    : angle       0.55650 ( 9318)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Evaluate side-chains
  169 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 VAL cc_start: 0.9303 (m) cc_final: 0.9059 (p)
REVERT: A  307 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8136 (mtm110)
REVERT: A  439 MET cc_start: 0.7966 (mtm) cc_final: 0.7646 (mtt)
REVERT: C   19 HIS cc_start: 0.8144 (t70) cc_final: 0.7850 (t-90)
REVERT: C  173 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7002 (ptpp)
REVERT: C  210 VAL cc_start: 0.9307 (m) cc_final: 0.9086 (p)
  outliers start: 30
  outliers final: 26
  residues processed: 161
  average time/residue: 0.3870
  time to fit residues: 85.3545
Evaluate side-chains
  168 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 140
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  307 ARG
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain C residue   50 SER
Chi-restraints excluded: chain C residue  100 PHE
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  200 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  421 THR
Chi-restraints excluded: chain C residue  432 HIS
Chi-restraints excluded: chain C residue  436 SER
Chi-restraints excluded: chain C residue  454 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 79 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:
A 113 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.119809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.094920 restraints weight = 27973.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 2.32
r_work: 0.2931 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6832  Z= 0.141
  Angle     :  0.527   5.204   9318  Z= 0.276
  Chirality :  0.034   0.124   1158
  Planarity :  0.003   0.034   1128
  Dihedral  :  7.982  58.854    936
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.23 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.29), residues: 886
  helix:  0.91 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -4.18 (0.38), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 311 
 HIS   0.003   0.000   HIS C 355 
 PHE   0.026   0.001   PHE C 139 
 TYR   0.005   0.001   TYR C  36 
 ARG   0.001   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03706 (  490)
  hydrogen bonds       : angle       4.07477 ( 1464)
  covalent geometry    : bond        0.00312 ( 6832)
  covalent geometry    : angle       0.52678 ( 9318)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Evaluate side-chains
  171 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7048 (ptpp)
REVERT: A  210 VAL cc_start: 0.9247 (m) cc_final: 0.9033 (p)
  outliers start: 28
  outliers final: 24
  residues processed: 161
  average time/residue: 0.3164
  time to fit residues: 73.5147
Evaluate side-chains
  165 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain C residue   50 SER
Chi-restraints excluded: chain C residue  100 PHE
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  157 MET
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  421 THR
Chi-restraints excluded: chain C residue  432 HIS
Chi-restraints excluded: chain C residue  436 SER
Chi-restraints excluded: chain C residue  454 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 12 optimal weight:    0.4980
   chunk 48 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.119812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.094921 restraints weight = 28295.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 2.31
r_work: 0.2925 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2802 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6832  Z= 0.145
  Angle     :  0.532   4.871   9318  Z= 0.277
  Chirality :  0.034   0.128   1158
  Planarity :  0.003   0.035   1128
  Dihedral  :  7.338  57.126    930
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 17.38 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.29), residues: 886
  helix:  1.20 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -4.12 (0.37), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 311 
 HIS   0.003   0.000   HIS C 355 
 PHE   0.028   0.001   PHE A 139 
 TYR   0.005   0.001   TYR C  36 
 ARG   0.001   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03644 (  490)
  hydrogen bonds       : angle       4.04448 ( 1464)
  covalent geometry    : bond        0.00325 ( 6832)
  covalent geometry    : angle       0.53175 ( 9318)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Evaluate side-chains
  175 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 140
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7022 (ptpp)
REVERT: A  216 ASP cc_start: 0.8732 (t0) cc_final: 0.8363 (m-30)
REVERT: C  173 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7003 (ptpp)
  outliers start: 35
  outliers final: 26
  residues processed: 161
  average time/residue: 0.3210
  time to fit residues: 74.0200
Evaluate side-chains
  165 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain C residue  100 PHE
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  200 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  421 THR
Chi-restraints excluded: chain C residue  432 HIS
Chi-restraints excluded: chain C residue  436 SER
Chi-restraints excluded: chain C residue  454 THR
Chi-restraints excluded: chain C residue  459 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 84 optimal weight:    0.4980
   chunk 65 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.118052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.093275 restraints weight = 28809.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 2.33
r_work: 0.2875 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.3454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6832  Z= 0.150
  Angle     :  0.534   5.834   9318  Z= 0.278
  Chirality :  0.035   0.159   1158
  Planarity :  0.003   0.034   1128
  Dihedral  :  6.858  55.504    927
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 18.38 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.29), residues: 886
  helix:  1.37 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -4.08 (0.37), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 311 
 HIS   0.004   0.000   HIS C 355 
 PHE   0.013   0.001   PHE A 139 
 TYR   0.006   0.001   TYR C  36 
 ARG   0.001   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03620 (  490)
  hydrogen bonds       : angle       4.04623 ( 1464)
  covalent geometry    : bond        0.00336 ( 6832)
  covalent geometry    : angle       0.53388 ( 9318)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Evaluate side-chains
  167 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7082 (ptpp)
REVERT: C  173 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.6993 (ptpp)
  outliers start: 30
  outliers final: 24
  residues processed: 152
  average time/residue: 0.3331
  time to fit residues: 72.4070
Evaluate side-chains
  161 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain C residue  100 PHE
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  157 MET
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  200 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  421 THR
Chi-restraints excluded: chain C residue  432 HIS
Chi-restraints excluded: chain C residue  436 SER
Chi-restraints excluded: chain C residue  454 THR
Chi-restraints excluded: chain C residue  459 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.119290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.094544 restraints weight = 28433.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 2.31
r_work: 0.2920 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.3600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6832  Z= 0.126
  Angle     :  0.521   5.333   9318  Z= 0.269
  Chirality :  0.034   0.165   1158
  Planarity :  0.003   0.035   1128
  Dihedral  :  6.405  54.142    926
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 19.23 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.30), residues: 886
  helix:  1.50 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -3.96 (0.38), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 311 
 HIS   0.004   0.000   HIS C 355 
 PHE   0.012   0.001   PHE A 139 
 TYR   0.005   0.001   TYR A 178 
 ARG   0.001   0.000   ARG C 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03492 (  490)
  hydrogen bonds       : angle       3.97533 ( 1464)
  covalent geometry    : bond        0.00283 ( 6832)
  covalent geometry    : angle       0.52060 ( 9318)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Evaluate side-chains
  168 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.6967 (ptpp)
REVERT: C  173 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.6954 (ptpp)
  outliers start: 27
  outliers final: 22
  residues processed: 154
  average time/residue: 0.3638
  time to fit residues: 79.5037
Evaluate side-chains
  160 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain C residue  100 PHE
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  157 MET
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  200 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  421 THR
Chi-restraints excluded: chain C residue  432 HIS
Chi-restraints excluded: chain C residue  436 SER
Chi-restraints excluded: chain C residue  454 THR
Chi-restraints excluded: chain C residue  459 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    0.3980
   chunk 21 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.117107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.092210 restraints weight = 28863.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 2.30
r_work: 0.2855 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.3759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6832  Z= 0.149
  Angle     :  0.527   4.887   9318  Z= 0.274
  Chirality :  0.035   0.182   1158
  Planarity :  0.003   0.035   1128
  Dihedral  :  6.162  52.767    925
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.37 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.30), residues: 886
  helix:  1.56 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -3.88 (0.38), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 311 
 HIS   0.004   0.000   HIS C 355 
 PHE   0.012   0.001   PHE C  98 
 TYR   0.005   0.001   TYR C  36 
 ARG   0.001   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03542 (  490)
  hydrogen bonds       : angle       3.99929 ( 1464)
  covalent geometry    : bond        0.00335 ( 6832)
  covalent geometry    : angle       0.52690 ( 9318)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Evaluate side-chains
  167 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 HIS cc_start: 0.8196 (t-90) cc_final: 0.7957 (t-90)
REVERT: A  173 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7065 (ptpp)
REVERT: A  307 ARG cc_start: 0.8469 (tpt170) cc_final: 0.8081 (mtm110)
REVERT: C  173 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7068 (ptpp)
  outliers start: 26
  outliers final: 23
  residues processed: 153
  average time/residue: 0.3232
  time to fit residues: 70.2586
Evaluate side-chains
  164 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain C residue  100 PHE
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  157 MET
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  200 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  364 VAL
Chi-restraints excluded: chain C residue  421 THR
Chi-restraints excluded: chain C residue  432 HIS
Chi-restraints excluded: chain C residue  436 SER
Chi-restraints excluded: chain C residue  454 THR
Chi-restraints excluded: chain C residue  459 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 59 optimal weight:    8.9990
   chunk 55 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.117678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.092345 restraints weight = 28205.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.2891 rms_B_bonded: 2.29
r_work: 0.2768 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2640 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.3872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6832  Z= 0.124
  Angle     :  0.518   4.867   9318  Z= 0.268
  Chirality :  0.035   0.198   1158
  Planarity :  0.003   0.035   1128
  Dihedral  :  5.994  52.045    925
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 19.66 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.30), residues: 886
  helix:  1.65 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -3.66 (0.40), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 311 
 HIS   0.004   0.000   HIS C 355 
 PHE   0.008   0.001   PHE A  98 
 TYR   0.004   0.001   TYR C 178 
 ARG   0.001   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03431 (  490)
  hydrogen bonds       : angle       3.92872 ( 1464)
  covalent geometry    : bond        0.00276 ( 6832)
  covalent geometry    : angle       0.51803 ( 9318)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Evaluate side-chains
  165 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 HIS cc_start: 0.8189 (t-90) cc_final: 0.7973 (t-90)
REVERT: A  173 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7116 (ptpp)
REVERT: A  307 ARG cc_start: 0.8450 (tpt170) cc_final: 0.8034 (mtm110)
REVERT: C  173 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7060 (ptpp)
  outliers start: 22
  outliers final: 20
  residues processed: 153
  average time/residue: 0.3500
  time to fit residues: 75.7561
Evaluate side-chains
  163 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain C residue  100 PHE
Chi-restraints excluded: chain C residue  157 MET
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  200 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  364 VAL
Chi-restraints excluded: chain C residue  421 THR
Chi-restraints excluded: chain C residue  432 HIS
Chi-restraints excluded: chain C residue  454 THR
Chi-restraints excluded: chain C residue  459 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.117843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.092313 restraints weight = 28402.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 2.31
r_work: 0.2993 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6832  Z= 0.138
  Angle     :  0.525   5.012   9318  Z= 0.272
  Chirality :  0.035   0.184   1158
  Planarity :  0.003   0.035   1128
  Dihedral  :  5.766  52.180    923
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 20.23 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.30), residues: 886
  helix:  1.69 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -3.57 (0.40), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 311 
 HIS   0.005   0.001   HIS A 355 
 PHE   0.011   0.001   PHE C  98 
 TYR   0.004   0.001   TYR A 178 
 ARG   0.002   0.000   ARG C 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03463 (  490)
  hydrogen bonds       : angle       3.94506 ( 1464)
  covalent geometry    : bond        0.00311 ( 6832)
  covalent geometry    : angle       0.52528 ( 9318)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
Evaluate side-chains
  161 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7008 (ptpp)
REVERT: A  307 ARG cc_start: 0.8432 (tpt170) cc_final: 0.8157 (mtm110)
REVERT: A  439 MET cc_start: 0.7895 (mtm) cc_final: 0.7523 (mtt)
REVERT: C  173 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.6956 (ptpp)
  outliers start: 20
  outliers final: 15
  residues processed: 152
  average time/residue: 0.4833
  time to fit residues: 108.3458
Evaluate side-chains
  155 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain C residue  157 MET
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  200 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  364 VAL
Chi-restraints excluded: chain C residue  421 THR
Chi-restraints excluded: chain C residue  432 HIS
Chi-restraints excluded: chain C residue  459 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 68 optimal weight:    0.3980
   chunk 34 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.118852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.092634 restraints weight = 28285.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 2.37
r_work: 0.2826 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6832  Z= 0.116
  Angle     :  0.513   5.000   9318  Z= 0.264
  Chirality :  0.034   0.172   1158
  Planarity :  0.003   0.035   1128
  Dihedral  :  5.082  52.178    917
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 21.08 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.30), residues: 886
  helix:  1.73 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -3.47 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 311 
 HIS   0.004   0.001   HIS A 355 
 PHE   0.007   0.001   PHE A  98 
 TYR   0.003   0.001   TYR C 178 
 ARG   0.002   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03347 (  490)
  hydrogen bonds       : angle       3.86988 ( 1464)
  covalent geometry    : bond        0.00259 ( 6832)
  covalent geometry    : angle       0.51264 ( 9318)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10588.89 seconds
wall clock time: 190 minutes 3.74 seconds (11403.74 seconds total)