Starting phenix.real_space_refine
on Tue Feb 11 14:13:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6b19_7031/02_2025/6b19_7031.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6b19_7031/02_2025/6b19_7031.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6b19_7031/02_2025/6b19_7031.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6b19_7031/02_2025/6b19_7031.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6b19_7031/02_2025/6b19_7031.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6b19_7031/02_2025/6b19_7031.cif"
  }
  resolution = 4.5
  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=   0.001 sd=   0.006
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
     P      37      5.49       5
     C    3032      2.51       5
     N    1054      2.21       5
     O    1167      1.98       5
     H     409      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5699
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 508, 2512
          Classifications: {'peptide': 508}
          Incomplete info: {'truncation_to_alanine': 456}
          Link IDs: {'CIS': 1, 'PTRANS': 33, 'TRANS': 473}
          Chain breaks: 11
          Unresolved chain link angles: 33
          Unresolved non-hydrogen bonds: 1751
          Unresolved non-hydrogen angles: 2259
          Unresolved non-hydrogen dihedrals: 1501
          Unresolved non-hydrogen chiralities: 154
          Planarities with less than four sites: {'GLN:plan1': 34, 'HIS:plan': 8, 'TYR:plan': 22, 'ASN:plan1': 18, 'TRP:plan': 17, 'ASP:plan': 21, 'PHE:plan': 12, 'GLU:plan': 42, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 915
    Chain: "B"
      Number of atoms: 1974
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 1974
          Classifications: {'peptide': 399}
          Incomplete info: {'truncation_to_alanine': 363}
          Link IDs: {'PTRANS': 28, 'TRANS': 370}
          Chain breaks: 7
          Unresolved chain link angles: 28
          Unresolved non-hydrogen bonds: 1417
          Unresolved non-hydrogen angles: 1829
          Unresolved non-hydrogen dihedrals: 1227
          Unresolved non-hydrogen chiralities: 120
          Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 6, 'TYR:plan': 16, 'ASN:plan1': 12, 'TRP:plan': 16, 'ASP:plan': 18, 'PHE:plan': 11, 'GLU:plan': 35, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 743
    Chain: "C"
      Number of atoms: 612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 612
          Classifications: {'RNA': 19}
          Modifications used: {'5*END': 1, 'rna3p_pur': 11, 'rna3p_pyr': 7}
          Link IDs: {'rna3p': 18}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 601
          Classifications: {'DNA': 2, 'RNA': 17}
          Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 11}
          Link IDs: {'rna3p': 18}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.07, per 1000 atoms: 0.71
  Number of scatterers: 5699
  At special positions: 0
  Unit cell: (96, 110, 91, 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)
     P      37     15.00
     O    1167      8.00
     N    1054      7.00
     C    3032      6.00
     H     409      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: 1.94
  Conformation dependent library (CDL) restraints added in 984.3 milliseconds
  

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1716

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      37.3% alpha, 5.4% beta
      19 base pairs and 16 stacking pairs defined.
    Time for finding SS restraints: 2.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 44
      removed outlier: 4.276A  pdb=" N   THR A  39 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 83
    Processing helix  chain 'A' and resid 155 through 175
      removed outlier: 3.617A  pdb=" N   ILE A 159 " --> pdb=" O   GLY A 155 " (cutoff:3.500A)
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 196 through 211
      removed outlier: 3.633A  pdb=" N   LYS A 201 " --> pdb=" O   GLN A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 268
    Processing helix  chain 'A' and resid 269 through 271
      No H-bonds generated for 'chain 'A' and resid 269 through 271'
    Processing helix  chain 'A' and resid 276 through 283
      removed outlier: 4.006A  pdb=" N   LEU A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 312
      removed outlier: 3.520A  pdb=" N   LEU A 310 " --> pdb=" O   ASN A 306 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LYS A 311 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLU A 312 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 383
    Processing helix  chain 'A' and resid 394 through 403
    Processing helix  chain 'A' and resid 473 through 489
      removed outlier: 3.699A  pdb=" N   ASP A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 508
      removed outlier: 3.946A  pdb=" N   LEU A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA A 508 " --> pdb=" O   GLY A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 528
    Processing helix  chain 'A' and resid 545 through 550
    Processing helix  chain 'B' and resid 28 through 45
      removed outlier: 3.680A  pdb=" N   VAL B  35 " --> pdb=" O   ILE B  31 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   GLU B  36 " --> pdb=" O   LYS B  32 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ILE B  37 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 84
    Processing helix  chain 'B' and resid 84 through 92
      removed outlier: 4.035A  pdb=" N   TRP B  88 " --> pdb=" O   THR B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 118
    Processing helix  chain 'B' and resid 122 through 126
      removed outlier: 4.003A  pdb=" N   LYS B 126 " --> pdb=" O   ASP B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
    Processing helix  chain 'B' and resid 154 through 160
    Processing helix  chain 'B' and resid 160 through 175
      Proline residue:  B 170  - end of helix
    Processing helix  chain 'B' and resid 194 through 212
    Processing helix  chain 'B' and resid 253 through 268
    Processing helix  chain 'B' and resid 278 through 283
    Processing helix  chain 'B' and resid 296 through 312
    Processing helix  chain 'B' and resid 363 through 384
    Processing helix  chain 'B' and resid 394 through 402
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48
    Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 180
      removed outlier: 3.545A  pdb=" N   VAL A 179 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 353
      removed outlier: 4.936A  pdb=" N   GLN A 336 " --> pdb=" O   GLN A 332 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLU A 328 " --> pdb=" O   GLN A 340 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   ILE A 329 " --> pdb=" O   LYS A 390 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   PHE A 389 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 441 through 443
    Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 493
    Processing sheet with id=AA6, first strand: chain 'B' and resid 61 through 63
    Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 183
    Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 330
      removed outlier: 6.634A  pdb=" N   ILE B 341 " --> pdb=" O   LEU B 349 " (cutoff:3.500A)

    246 hydrogen bonds defined for protein.
    690 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      52 hydrogen bonds
      104 hydrogen bond angles
      0 basepair planarities
      19 basepair parallelities
      16 stacking parallelities
  Total time for adding SS restraints: 1.87

  Time building geometry restraints manager: 2.06 seconds

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

  Histogram of bond lengths:
        0.75 -     1.20: 409
        1.20 -     1.64: 5362
        1.64 -     2.09: 0
        2.09 -     2.53: 0
        2.53 -     2.98: 1
  Bond restraints: 5772
  Sorted by residual:
  bond pdb=" C   THR A 286 "
       pdb=" N   LEU A 289 "
    ideal  model  delta    sigma   weight residual
    1.329  2.978 -1.649 1.40e-02 5.10e+03 1.39e+04
  bond pdb=" N6    A C 191 "
       pdb=" H61   A C 191 "
    ideal  model  delta    sigma   weight residual
    0.860  0.751  0.109 2.00e-02 2.50e+03 2.98e+01
  bond pdb=" N6    A C 191 "
       pdb=" H62   A C 191 "
    ideal  model  delta    sigma   weight residual
    0.860  0.925 -0.065 2.00e-02 2.50e+03 1.05e+01
  bond pdb=" C1'   A C 191 "
       pdb=" N9    A C 191 "
    ideal  model  delta    sigma   weight residual
    1.475  1.445  0.030 1.50e-02 4.44e+03 3.93e+00
  bond pdb=" C   ILE B 178 "
       pdb=" N   VAL B 179 "
    ideal  model  delta    sigma   weight residual
    1.328  1.282  0.046 2.53e-02 1.56e+03 3.24e+00
  ... (remaining 5767 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    16.28: 8519
       16.28 -    32.56: 0
       32.56 -    48.84: 1
       48.84 -    65.12: 0
       65.12 -    81.40: 1
  Bond angle restraints: 8521
  Sorted by residual:
  angle pdb=" O   THR A 286 "
        pdb=" C   THR A 286 "
        pdb=" N   LEU A 289 "
      ideal   model   delta    sigma   weight residual
     122.59   41.19   81.40 1.33e+00 5.65e-01 3.75e+03
  angle pdb=" CA  THR A 286 "
        pdb=" C   THR A 286 "
        pdb=" N   LEU A 289 "
      ideal   model   delta    sigma   weight residual
     116.84  152.89  -36.05 1.71e+00 3.42e-01 4.45e+02
  angle pdb=" C   ASN A  54 "
        pdb=" N   PRO A  55 "
        pdb=" CA  PRO A  55 "
      ideal   model   delta    sigma   weight residual
     119.84  128.00   -8.16 1.25e+00 6.40e-01 4.26e+01
  angle pdb=" C   THR A 397 "
        pdb=" N   TRP A 398 "
        pdb=" CA  TRP A 398 "
      ideal   model   delta    sigma   weight residual
     120.29  114.26    6.03 1.42e+00 4.96e-01 1.80e+01
  angle pdb=" C   THR A 286 "
        pdb=" N   LEU A 289 "
        pdb=" CA  LEU A 289 "
      ideal   model   delta    sigma   weight residual
     121.70  114.45    7.25 1.80e+00 3.09e-01 1.62e+01
  ... (remaining 8516 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.31: 3152
       29.31 -    58.62: 71
       58.62 -    87.93: 53
       87.93 -   117.24: 2
      117.24 -   146.55: 2
  Dihedral angle restraints: 3280
    sinusoidal: 677
      harmonic: 2603
  Sorted by residual:
  dihedral pdb=" CA  GLU A 413 "
           pdb=" C   GLU A 413 "
           pdb=" N   TRP A 414 "
           pdb=" CA  TRP A 414 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.37  -19.63     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  ASN B 418 "
           pdb=" C   ASN B 418 "
           pdb=" N   THR B 419 "
           pdb=" CA  THR B 419 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.86  -19.14     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  THR A 286 "
           pdb=" C   THR A 286 "
           pdb=" N   LEU A 289 "
           pdb=" CA  LEU A 289 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   18.13  -18.13     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 3277 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 665
       0.039 -    0.078: 250
       0.078 -    0.118: 106
       0.118 -    0.157: 19
       0.157 -    0.196: 3
  Chirality restraints: 1043
  Sorted by residual:
  chirality pdb=" C3'   G C 181 "
            pdb=" C4'   G C 181 "
            pdb=" O3'   G C 181 "
            pdb=" C2'   G C 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.30   -0.20 2.00e-01 2.50e+01 9.59e-01
  chirality pdb=" CA  THR B 240 "
            pdb=" N   THR B 240 "
            pdb=" C   THR B 240 "
            pdb=" CB  THR B 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.70   -0.18 2.00e-01 2.50e+01 7.74e-01
  chirality pdb=" CA  LEU B 368 "
            pdb=" N   LEU B 368 "
            pdb=" C   LEU B 368 "
            pdb=" CB  LEU B 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.56e-01
  ... (remaining 1040 not shown)

  Planarity restraints: 958
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 286 "   -0.201 2.00e-02 2.50e+03   1.73e-01 2.99e+02
        pdb=" C   THR A 286 "    0.240 2.00e-02 2.50e+03
        pdb=" O   THR A 286 "    0.082 2.00e-02 2.50e+03
        pdb=" N   LEU A 289 "   -0.122 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A  41 "    0.018 2.00e-02 2.50e+03   3.56e-02 1.27e+01
        pdb=" C   MET A  41 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   MET A  41 "    0.023 2.00e-02 2.50e+03
        pdb=" N   GLU A  42 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 296 "   -0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   THR B 296 "    0.059 2.00e-02 2.50e+03
        pdb=" O   THR B 296 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLU B 297 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 955 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.34: 282
        2.34 -     2.91: 4305
        2.91 -     3.47: 8362
        3.47 -     4.04: 11082
        4.04 -     4.60: 14332
  Nonbonded interactions: 38363
  Sorted by model distance:
  nonbonded pdb=" H2'   G D  69 "
            pdb=" H8    G D  70 "
     model   vdw
     1.781 2.270
  nonbonded pdb=" H2'   C D  72 "
            pdb=" H8    G D  73 "
     model   vdw
     1.806 2.270
  nonbonded pdb=" H2'   G C 186 "
            pdb=" H6    C C 187 "
     model   vdw
     1.839 2.270
  nonbonded pdb=" H2'   G D  73 "
            pdb=" H6    C D  74 "
     model   vdw
     1.853 2.270
  nonbonded pdb=" H2'   G C 183 "
            pdb=" H8    G C 184 "
     model   vdw
     1.863 2.270
  ... (remaining 38358 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.690
  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:             0.190
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     19.520
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6326
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      :  0.023   1.649   5363  Z= 1.967
  Angle     :  1.382  81.401   7585  Z= 0.937
  Chirality :  0.048   0.196   1043
  Planarity :  0.008   0.173    925
  Dihedral  : 15.602  74.879   1477
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 16.18
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 19.42 %
    Favored  : 80.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  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: -5.73 (0.22), residues: 865
  helix: -2.49 (0.24), residues: 298
  sheet: -3.46 (0.48), residues: 95
  loop : -5.02 (0.21), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  24 
 PHE   0.000   0.000   PHE A  61 
 TYR   0.000   0.000   TYR A  56 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.586 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0615
  time to fit residues: 1.9728
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    9.9990
   chunk 68 optimal weight:    5.9990
   chunk 38 optimal weight:   30.0000
   chunk 23 optimal weight:    0.0870
   chunk 46 optimal weight:    7.9990
   chunk 36 optimal weight:   20.0000
   chunk 71 optimal weight:    8.9990
   chunk 27 optimal weight:   50.0000
   chunk 43 optimal weight:   40.0000
   chunk 53 optimal weight:   20.0000
   chunk 82 optimal weight:   40.0000
   overall best weight:    6.6166

-------------------------------------------------------------------------------
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 = 0.3397 r_free = 0.3397 target = 0.064000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.057617 restraints weight = 143052.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.058020 restraints weight = 118227.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.058341 restraints weight = 102180.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6144
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5363  Z= 0.237
  Angle     :  0.677   4.706   7585  Z= 0.383
  Chirality :  0.043   0.204   1043
  Planarity :  0.003   0.018    925
  Dihedral  : 15.784  74.692   1477
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 21.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.18 %
    Favored  : 79.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.52 (0.25), residues: 867
  helix: -0.86 (0.28), residues: 320
  sheet: -3.68 (0.52), residues: 80
  loop : -4.70 (0.22), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  24 
 PHE   0.000   0.000   PHE A  61 
 TYR   0.000   0.000   TYR A  56 

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.604 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0582
  time to fit residues: 1.9708
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 78 optimal weight:   40.0000
   chunk 79 optimal weight:    6.9990
   chunk 87 optimal weight:   30.0000
   chunk 69 optimal weight:    6.9990
   chunk 86 optimal weight:   40.0000
   chunk 60 optimal weight:    2.9990
   chunk 67 optimal weight:   20.0000
   chunk 84 optimal weight:    8.9990
   chunk 85 optimal weight:   10.0000
   chunk 89 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    7.1990

-------------------------------------------------------------------------------
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 = 0.3363 r_free = 0.3363 target = 0.061936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.055784 restraints weight = 140263.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.056211 restraints weight = 113615.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.056475 restraints weight = 97039.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6208
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5363  Z= 0.245
  Angle     :  0.690   6.675   7585  Z= 0.387
  Chirality :  0.044   0.201   1043
  Planarity :  0.003   0.015    925
  Dihedral  : 16.020  74.561   1477
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 24.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.11 %
    Favored  : 78.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.16 (0.26), residues: 867
  helix: -0.37 (0.28), residues: 321
  sheet: -2.81 (0.64), residues: 56
  loop : -4.76 (0.22), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  24 
 PHE   0.000   0.000   PHE A  61 
 TYR   0.000   0.000   TYR A  56 

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.627 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0558
  time to fit residues: 1.9958
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 48 optimal weight:   30.0000
   chunk 51 optimal weight:    0.0010
   chunk 45 optimal weight:    7.9990
   chunk 30 optimal weight:    9.9990
   chunk 58 optimal weight:   10.0000
   chunk 19 optimal weight:   50.0000
   chunk 41 optimal weight:   30.0000
   chunk 13 optimal weight:    9.9990
   chunk 89 optimal weight:   10.0000
   chunk 83 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   overall best weight:    7.5996

-------------------------------------------------------------------------------
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 = 0.3349 r_free = 0.3349 target = 0.061187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.055143 restraints weight = 144131.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.055560 restraints weight = 117662.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.055862 restraints weight = 100135.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6236
moved from start:          0.5080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   5363  Z= 0.242
  Angle     :  0.703   7.077   7585  Z= 0.396
  Chirality :  0.044   0.191   1043
  Planarity :  0.003   0.015    925
  Dihedral  : 16.487  75.013   1477
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 23.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 22.84 %
    Favored  : 77.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.10 (0.26), residues: 867
  helix: -0.32 (0.29), residues: 319
  sheet: -3.23 (0.55), residues: 71
  loop : -4.65 (0.23), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  24 
 PHE   0.000   0.000   PHE A  61 
 TYR   0.000   0.000   TYR A  56 

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.587 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0624
  time to fit residues: 2.0467
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 50 optimal weight:   40.0000
   chunk 57 optimal weight:   30.0000
   chunk 46 optimal weight:   20.0000
   chunk 44 optimal weight:   30.0000
   chunk 52 optimal weight:   30.0000
   chunk 19 optimal weight:   50.0000
   chunk 11 optimal weight:   40.0000
   chunk 39 optimal weight:    0.8980
   chunk 83 optimal weight:   30.0000
   chunk 61 optimal weight:   20.0000
   chunk 75 optimal weight:    7.9990
   overall best weight:   15.7794

-------------------------------------------------------------------------------
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 = 0.3294 r_free = 0.3294 target = 0.059030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.052626 restraints weight = 143344.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.052922 restraints weight = 116990.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.053264 restraints weight = 101852.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6269
moved from start:          0.6696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   5363  Z= 0.456
  Angle     :  1.078   9.463   7585  Z= 0.606
  Chirality :  0.053   0.269   1043
  Planarity :  0.005   0.022    925
  Dihedral  : 18.419  99.173   1477
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 51.44
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 31.14 %
    Favored  : 68.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -5.56 (0.23), residues: 867
  helix: -2.10 (0.25), residues: 291
  sheet: -3.36 (0.65), residues: 54
  loop : -5.04 (0.21), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  24 
 PHE   0.000   0.000   PHE A  61 
 TYR   0.000   0.000   TYR A  56 

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.580 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0570
  time to fit residues: 1.9444
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 25 optimal weight:   40.0000
   chunk 38 optimal weight:   20.0000
   chunk 45 optimal weight:   40.0000
   chunk 74 optimal weight:    4.9990
   chunk 20 optimal weight:   40.0000
   chunk 41 optimal weight:   40.0000
   chunk 85 optimal weight:   10.0000
   chunk 55 optimal weight:   30.0000
   chunk 72 optimal weight:   40.0000
   chunk 23 optimal weight:   20.0000
   chunk 73 optimal weight:    9.9990
   overall best weight:   12.9996

-------------------------------------------------------------------------------
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 = 0.3308 r_free = 0.3308 target = 0.059596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.053281 restraints weight = 144315.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.053659 restraints weight = 117086.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.053960 restraints weight = 100025.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6276
moved from start:          0.7078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   5363  Z= 0.360
  Angle     :  0.910   8.567   7585  Z= 0.512
  Chirality :  0.049   0.212   1043
  Planarity :  0.004   0.017    925
  Dihedral  : 18.269  99.942   1477
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 39.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 31.37 %
    Favored  : 68.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    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: -5.50 (0.24), residues: 867
  helix: -2.02 (0.26), residues: 285
  sheet: -3.94 (0.52), residues: 76
  loop : -4.90 (0.22), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  24 
 PHE   0.000   0.000   PHE A  61 
 TYR   0.000   0.000   TYR A  56 

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.556 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0568
  time to fit residues: 1.8372
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 67 optimal weight:   20.0000
   chunk 87 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0570
   chunk 40 optimal weight:   50.0000
   chunk 6 optimal weight:    9.9990
   chunk 36 optimal weight:   20.0000
   chunk 80 optimal weight:   50.0000
   chunk 82 optimal weight:   50.0000
   chunk 34 optimal weight:    0.3980
   chunk 24 optimal weight:    2.9990
   chunk 4 optimal weight:   20.0000
   overall best weight:    4.0904

-------------------------------------------------------------------------------
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 = 0.3721 r_free = 0.3721 target = 0.075698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.062003 restraints weight = 65652.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.062218 restraints weight = 58076.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.062067 restraints weight = 55498.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.6834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   5363  Z= 0.160
  Angle     :  0.593   5.574   7585  Z= 0.330
  Chirality :  0.043   0.145   1043
  Planarity :  0.002   0.015    925
  Dihedral  : 17.315  94.056   1477
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 19.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.91 %
    Favored  : 78.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.43 (0.26), residues: 867
  helix: -0.69 (0.29), residues: 311
  sheet: -3.35 (0.62), residues: 62
  loop : -4.72 (0.22), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  24 
 PHE   0.000   0.000   PHE A  61 
 TYR   0.000   0.000   TYR A  56 

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.624 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0579
  time to fit residues: 1.9458
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 46 optimal weight:    0.0070
   chunk 25 optimal weight:   50.0000
   chunk 40 optimal weight:   50.0000
   chunk 13 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0970
   chunk 18 optimal weight:   30.0000
   chunk 54 optimal weight:   30.0000
   chunk 63 optimal weight:   50.0000
   chunk 74 optimal weight:   30.0000
   chunk 89 optimal weight:   10.0000
   chunk 70 optimal weight:    8.9990
   overall best weight:    4.8204

-------------------------------------------------------------------------------
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 = 0.3709 r_free = 0.3709 target = 0.075252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.061723 restraints weight = 65014.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.061916 restraints weight = 59686.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.061832 restraints weight = 54716.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6755
moved from start:          0.6971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   5363  Z= 0.178
  Angle     :  0.596   5.463   7585  Z= 0.334
  Chirality :  0.043   0.147   1043
  Planarity :  0.002   0.012    925
  Dihedral  : 17.279  97.703   1477
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 21.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 25.14 %
    Favored  : 74.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.03 (0.27), residues: 867
  helix: -0.13 (0.30), residues: 314
  sheet: -3.37 (0.55), residues: 76
  loop : -4.65 (0.23), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  24 
 PHE   0.000   0.000   PHE A  61 
 TYR   0.000   0.000   TYR A  56 

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.456 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0514
  time to fit residues: 1.6579
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 4 optimal weight:   20.0000
   chunk 24 optimal weight:   10.0000
   chunk 75 optimal weight:   30.0000
   chunk 88 optimal weight:   30.0000
   chunk 40 optimal weight:   50.0000
   chunk 13 optimal weight:   30.0000
   chunk 74 optimal weight:   30.0000
   chunk 20 optimal weight:    9.9990
   chunk 67 optimal weight:   30.0000
   chunk 56 optimal weight:   50.0000
   chunk 32 optimal weight:   20.0000
   overall best weight:   17.9998

-------------------------------------------------------------------------------
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 = 0.3277 r_free = 0.3277 target = 0.058752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.052285 restraints weight = 141403.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.052578 restraints weight = 116859.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.052848 restraints weight = 101456.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6290
moved from start:          0.7935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   5363  Z= 0.478
  Angle     :  1.094   9.409   7585  Z= 0.615
  Chirality :  0.054   0.256   1043
  Planarity :  0.006   0.023    925
  Dihedral  : 18.861 108.121   1477
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 54.73
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 35.06 %
    Favored  : 64.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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: -5.66 (0.23), residues: 867
  helix: -2.04 (0.26), residues: 280
  sheet: -3.63 (0.61), residues: 54
  loop : -5.11 (0.20), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  24 
 PHE   0.000   0.000   PHE A  61 
 TYR   0.000   0.000   TYR A  56 

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.607 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0560
  time to fit residues: 1.9229
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 88 optimal weight:   30.0000
   chunk 46 optimal weight:   20.0000
   chunk 28 optimal weight:   40.0000
   chunk 15 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 42 optimal weight:   50.0000
   chunk 44 optimal weight:   20.0000
   chunk 49 optimal weight:   10.0000
   chunk 27 optimal weight:   50.0000
   chunk 50 optimal weight:   30.0000
   chunk 82 optimal weight:   50.0000
   overall best weight:   15.3998

-------------------------------------------------------------------------------
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 = 0.3288 r_free = 0.3288 target = 0.059136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.052630 restraints weight = 144058.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.052985 restraints weight = 118684.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.053211 restraints weight = 102082.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6290
moved from start:          0.8414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   5363  Z= 0.411
  Angle     :  0.989   8.811   7585  Z= 0.559
  Chirality :  0.051   0.212   1043
  Planarity :  0.005   0.019    925
  Dihedral  : 18.852 104.598   1477
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 46.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 33.79 %
    Favored  : 66.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.60 %

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: -5.91 (0.22), residues: 867
  helix: -2.31 (0.26), residues: 281
  sheet: -4.30 (0.52), residues: 62
  loop : -5.15 (0.20), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  24 
 PHE   0.000   0.000   PHE A  61 
 TYR   0.000   0.000   TYR A  56 

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.557 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0556
  time to fit residues: 1.9378
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 21 optimal weight:   40.0000
   chunk 53 optimal weight:   30.0000
   chunk 86 optimal weight:   30.0000
   chunk 64 optimal weight:   20.0000
   chunk 80 optimal weight:   40.0000
   chunk 90 optimal weight:   10.0000
   chunk 67 optimal weight:   30.0000
   chunk 6 optimal weight:   30.0000
   chunk 27 optimal weight:   30.0000
   chunk 45 optimal weight:   30.0000
   chunk 76 optimal weight:    0.4980
   overall best weight:   18.0996

-------------------------------------------------------------------------------
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 = 0.3263 r_free = 0.3263 target = 0.058569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.052085 restraints weight = 141224.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.052441 restraints weight = 116130.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.052706 restraints weight = 100473.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6320
moved from start:          0.8960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   5363  Z= 0.495
  Angle     :  1.132   9.525   7585  Z= 0.636
  Chirality :  0.054   0.243   1043
  Planarity :  0.006   0.023    925
  Dihedral  : 19.433 109.043   1477
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 60.65
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 38.75 %
    Favored  : 61.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.72 %

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: -6.28 (0.22), residues: 867
  helix: -2.72 (0.25), residues: 277
  sheet: -4.75 (0.48), residues: 58
  loop : -5.28 (0.20), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  24 
 PHE   0.000   0.000   PHE A  61 
 TYR   0.000   0.000   TYR A  56 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1788.88 seconds
wall clock time: 32 minutes 21.91 seconds (1941.91 seconds total)