Starting phenix.real_space_refine
on Tue Mar  3 12:14:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wk8_32562/03_2026/7wk8_32562.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wk8_32562/03_2026/7wk8_32562.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wk8_32562/03_2026/7wk8_32562.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wk8_32562/03_2026/7wk8_32562.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wk8_32562/03_2026/7wk8_32562.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wk8_32562/03_2026/7wk8_32562.cif"
  }
  resolution = 3.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2512      2.51       5
     N     671      2.21       5
     O     783      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3982
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1662
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201}
    Chain: "D"
      Number of atoms: 1656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1656
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201}
    Chain: "B"
      Number of atoms: 150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 150
          Classifications: {'peptide': 18}
          Link IDs: {'PTRANS': 2, 'TRANS': 15}
    Chain: "A"
      Number of atoms: 514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 514
          Classifications: {'peptide': 66}
          Link IDs: {'PTRANS': 3, 'TRANS': 62}
  Time building chain proxies: 0.99, per 1000 atoms: 0.25
  Number of scatterers: 3982
  At special positions: 0
  Unit cell: (96.184, 95.091, 61.208, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O     783      8.00
     N     671      7.00
     C    2512      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 147 " - pdb=" SG  CYS C 202 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 138 " - pdb=" SG  CYS D 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 162.7 milliseconds
  

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  970

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 12 sheets defined
      3.3% alpha, 43.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'C' and resid 87 through 91
    Processing helix  chain 'D' and resid 127 through 132
      removed outlier: 4.250A  pdb=" N   SER D 131 " --> pdb=" O   GLU D 127 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLY D 132 " --> pdb=" O   GLN D 128 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 127 through 132'
    Processing helix  chain 'D' and resid 187 through 192
      removed outlier: 3.977A  pdb=" N   ARG D 192 " --> pdb=" O   ASP D 188 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5
      removed outlier: 3.571A  pdb=" N   GLN C   3 " --> pdb=" O   SER C  25 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   SER C  25 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   VAL C  18 " --> pdb=" O   LEU C  83 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LEU C  83 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   MET C  81 " --> pdb=" O   LEU C  20 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 9 through 12
      removed outlier: 3.570A  pdb=" N   VAL C  12 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA C  92 " --> pdb=" O   VAL C 116 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   MET C  34 " --> pdb=" O   MET C  50 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   MET C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   TRP C  36 " --> pdb=" O   ILE C  48 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG C  40 " --> pdb=" O   GLY C  44 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 9 through 12
      removed outlier: 3.570A  pdb=" N   VAL C  12 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA C  92 " --> pdb=" O   VAL C 116 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ARG C  98 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 127 through 131
      removed outlier: 3.775A  pdb=" N   GLY C 146 " --> pdb=" O   LEU C 131 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   TYR C 182 " --> pdb=" O   GLY C 151 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161
    Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 7
      removed outlier: 3.584A  pdb=" N   SER D  22 " --> pdb=" O   SER D   7 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE D  21 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   CYS D  23 " --> pdb=" O   PHE D  75 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR D  76 " --> pdb=" O   SER D  69 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.580A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 109 " (cutoff:3.500A)
      removed outlier: 7.565A  pdb=" N   TRP D  39 " --> pdb=" O   LEU D  51 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU D  51 " --> pdb=" O   TRP D  39 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.580A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 109 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   HIS D  94 " --> pdb=" O   ALA D 101 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ALA D 101 " --> pdb=" O   HIS D  94 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 31
    Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 122
      removed outlier: 3.741A  pdb=" N   VAL D 137 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   TYR D 177 " --> pdb=" O   ASN D 142 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   SER D 180 " --> pdb=" O   SER D 166 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER D 166 " --> pdb=" O   SER D 180 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 157 through 158
      removed outlier: 3.897A  pdb=" N   TYR D 196 " --> pdb=" O   PHE D 213 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE D 213 " --> pdb=" O   TYR D 196 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 325 through 328
      removed outlier: 3.538A  pdb=" N   GLY A 550 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   ASP A 574 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ALA A 575 " --> pdb=" O   GLY A 566 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY A 566 " --> pdb=" O   ALA A 575 " (cutoff:3.500A)

    128 hydrogen bonds defined for protein.
    315 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.45

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1262
        1.35 -     1.46: 998
        1.46 -     1.58: 1799
        1.58 -     1.70: 0
        1.70 -     1.82: 22
  Bond restraints: 4081
  Sorted by residual:
  bond pdb=" N   LEU C 184 "
       pdb=" CA  LEU C 184 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.27e-02 6.20e+03 8.18e+00
  bond pdb=" N   THR C 183 "
       pdb=" CA  THR C 183 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.26e-02 6.30e+03 7.73e+00
  bond pdb=" C   GLU D 109 "
       pdb=" N   ILE D 110 "
    ideal  model  delta    sigma   weight residual
    1.329  1.362 -0.033 1.32e-02 5.74e+03 6.18e+00
  bond pdb=" N   SER C 119 "
       pdb=" CA  SER C 119 "
    ideal  model  delta    sigma   weight residual
    1.455  1.479 -0.024 1.18e-02 7.18e+03 4.02e+00
  bond pdb=" N   SER C 185 "
       pdb=" CA  SER C 185 "
    ideal  model  delta    sigma   weight residual
    1.464  1.487 -0.024 1.25e-02 6.40e+03 3.57e+00
  ... (remaining 4076 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 5406
        2.05 -     4.11: 118
        4.11 -     6.16: 28
        6.16 -     8.21: 2
        8.21 -    10.27: 3
  Bond angle restraints: 5557
  Sorted by residual:
  angle pdb=" C   SER C 179 "
        pdb=" N   ASP C 180 "
        pdb=" CA  ASP C 180 "
      ideal   model   delta    sigma   weight residual
     122.07  127.27   -5.20 1.43e+00 4.89e-01 1.32e+01
  angle pdb=" C   ALA C 137 "
        pdb=" N   GLN C 138 "
        pdb=" CA  GLN C 138 "
      ideal   model   delta    sigma   weight residual
     122.07  127.19   -5.12 1.43e+00 4.89e-01 1.28e+01
  angle pdb=" C   ILE D 154 "
        pdb=" N   ASP D 155 "
        pdb=" CA  ASP D 155 "
      ideal   model   delta    sigma   weight residual
     122.19  127.23   -5.04 1.41e+00 5.03e-01 1.28e+01
  angle pdb=" C   ASP D 174 "
        pdb=" N   SER D 175 "
        pdb=" CA  SER D 175 "
      ideal   model   delta    sigma   weight residual
     122.19  127.16   -4.97 1.41e+00 5.03e-01 1.24e+01
  angle pdb=" C   ASN C 162 "
        pdb=" N   SER C 163 "
        pdb=" CA  SER C 163 "
      ideal   model   delta    sigma   weight residual
     122.34  127.21   -4.87 1.39e+00 5.18e-01 1.23e+01
  ... (remaining 5552 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.81: 2296
       11.81 -    23.62: 110
       23.62 -    35.43: 33
       35.43 -    47.24: 17
       47.24 -    59.05: 1
  Dihedral angle restraints: 2457
    sinusoidal: 955
      harmonic: 1502
  Sorted by residual:
  dihedral pdb=" CA  TRP C 195 "
           pdb=" C   TRP C 195 "
           pdb=" N   PRO C 196 "
           pdb=" CA  PRO C 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.14   18.86     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  TYR C 101 "
           pdb=" C   TYR C 101 "
           pdb=" N   ASP C 102 "
           pdb=" CA  ASP C 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.84   18.16     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  LYS A 535 "
           pdb=" C   LYS A 535 "
           pdb=" N   ASN A 536 "
           pdb=" CA  ASN A 536 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.20  -16.80     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 2454 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 532
       0.066 -    0.132: 79
       0.132 -    0.199: 10
       0.199 -    0.265: 2
       0.265 -    0.331: 2
  Chirality restraints: 625
  Sorted by residual:
  chirality pdb=" CB  ILE D 121 "
            pdb=" CA  ILE D 121 "
            pdb=" CG1 ILE D 121 "
            pdb=" CG2 ILE D 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CB  VAL C 188 "
            pdb=" CA  VAL C 188 "
            pdb=" CG1 VAL C 188 "
            pdb=" CG2 VAL C 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.73e+00
  chirality pdb=" CB  VAL C 204 "
            pdb=" CA  VAL C 204 "
            pdb=" CG1 VAL C 204 "
            pdb=" CG2 VAL C 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.74e+00
  ... (remaining 622 not shown)

  Planarity restraints: 712
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 118 "    0.020 2.00e-02 2.50e+03   4.11e-02 1.69e+01
        pdb=" C   VAL C 118 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   VAL C 118 "    0.027 2.00e-02 2.50e+03
        pdb=" N   SER C 119 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C 195 "    0.047 5.00e-02 4.00e+02   7.01e-02 7.86e+00
        pdb=" N   PRO C 196 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO C 196 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C 196 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 204 "    0.012 2.00e-02 2.50e+03   2.37e-02 5.60e+00
        pdb=" C   VAL C 204 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   VAL C 204 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ALA C 205 "    0.014 2.00e-02 2.50e+03
  ... (remaining 709 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 749
        2.79 -     3.32: 3126
        3.32 -     3.84: 6244
        3.84 -     4.37: 6603
        4.37 -     4.90: 11958
  Nonbonded interactions: 28680
  Sorted by model distance:
  nonbonded pdb=" OG  SER D  22 "
            pdb=" OD1 ASP D  74 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OD1 ASN C  61 "
            pdb=" N   GLN C  62 "
     model   vdw
     2.374 3.120
  nonbonded pdb=" O   PRO C   7 "
            pdb=" OG1 THR C 114 "
     model   vdw
     2.393 3.040
  nonbonded pdb=" OG  SER D 205 "
            pdb=" O   SER D 207 "
     model   vdw
     2.396 3.040
  nonbonded pdb=" O   ALA C 105 "
            pdb=" OG  SER D  95 "
     model   vdw
     2.403 3.040
  ... (remaining 28675 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:             1.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     5.330
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
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      :  0.004   0.054   4086  Z= 0.210
  Angle     :  0.743  10.268   5567  Z= 0.419
  Chirality :  0.054   0.331    625
  Planarity :  0.006   0.070    712
  Dihedral  :  8.507  59.046   1472
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.94 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.22 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.34 (0.31), residues: 508
  helix: -4.97 (0.38), residues: 8
  sheet: -0.12 (0.30), residues: 220
  loop : -1.41 (0.30), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  65 
 TYR   0.014   0.001   TYR C 103 
 PHE   0.021   0.002   PHE D 143 
 TRP   0.024   0.002   TRP D  39 
 HIS   0.002   0.001   HIS D 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 4081)
  covalent geometry    : angle       0.74282 ( 5557)
  SS BOND              : bond        0.00153 (    5)
  SS BOND              : angle       0.98373 (   10)
  hydrogen bonds       : bond        0.23575 (  121)
  hydrogen bonds       : angle       8.54891 (  315)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.098 
Fit side-chains
REVERT: C   38 LYS cc_start: 0.8215 (tttt) cc_final: 0.8007 (tttt)
REVERT: C   61 ASN cc_start: 0.8783 (t0) cc_final: 0.8576 (t0)
REVERT: C   63 LYS cc_start: 0.8882 (tttt) cc_final: 0.8569 (ttpp)
REVERT: C   88 SER cc_start: 0.8757 (p) cc_final: 0.8480 (p)
REVERT: C   91 SER cc_start: 0.8041 (m) cc_final: 0.7726 (p)
REVERT: C  114 THR cc_start: 0.7706 (m) cc_final: 0.7418 (p)
REVERT: C  144 THR cc_start: 0.8047 (m) cc_final: 0.7792 (m)
REVERT: C  172 THR cc_start: 0.8640 (m) cc_final: 0.8403 (p)
REVERT: C  193 SER cc_start: 0.7975 (p) cc_final: 0.7677 (p)
REVERT: D   37 MET cc_start: 0.7757 (tpp) cc_final: 0.6524 (tpp)
REVERT: D   86 ASP cc_start: 0.8104 (m-30) cc_final: 0.7819 (m-30)
REVERT: D  215 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8179 (ttp80)
  outliers start: 1
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0661
  time to fit residues: 7.8858
Evaluate side-chains
  81 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0970
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0570
   chunk 19 optimal weight:    0.0050
   chunk 30 optimal weight:    0.4980
   chunk 22 optimal weight:    0.2980
   overall best weight:    0.1910

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

Flipped N/Q/H residues before XYZ refinement:
C 112 GLN
C 178 GLN
D   6 GLN
B 331 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.101725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.090159 restraints weight = 7244.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.092408 restraints weight = 4067.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.093858 restraints weight = 2702.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.094914 restraints weight = 1998.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.095673 restraints weight = 1584.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4086  Z= 0.118
  Angle     :  0.522   5.058   5567  Z= 0.269
  Chirality :  0.043   0.160    625
  Planarity :  0.004   0.041    712
  Dihedral  :  4.018  24.180    551
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.77 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  5.10 %
    Favored  : 93.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.33), residues: 508
  helix: -3.90 (0.93), residues: 8
  sheet:  0.46 (0.33), residues: 204
  loop : -0.82 (0.31), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 567 
 TYR   0.013   0.001   TYR D  53 
 PHE   0.009   0.001   PHE C 153 
 TRP   0.021   0.002   TRP D  39 
 HIS   0.004   0.001   HIS D 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 4081)
  covalent geometry    : angle       0.52105 ( 5557)
  SS BOND              : bond        0.00480 (    5)
  SS BOND              : angle       0.99099 (   10)
  hydrogen bonds       : bond        0.03261 (  121)
  hydrogen bonds       : angle       6.45620 (  315)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.150 
Fit side-chains
REVERT: C   38 LYS cc_start: 0.8490 (tttt) cc_final: 0.8256 (tttt)
REVERT: C   63 LYS cc_start: 0.8782 (tttt) cc_final: 0.8541 (ttpp)
REVERT: C   91 SER cc_start: 0.8358 (m) cc_final: 0.7949 (p)
REVERT: C  115 LEU cc_start: 0.8247 (tp) cc_final: 0.7953 (tt)
REVERT: C  193 SER cc_start: 0.8233 (p) cc_final: 0.8011 (p)
REVERT: D   37 MET cc_start: 0.7771 (tpp) cc_final: 0.6273 (tpp)
REVERT: D   86 ASP cc_start: 0.8229 (m-30) cc_final: 0.7849 (m-30)
REVERT: D  179 MET cc_start: 0.7562 (ptm) cc_final: 0.7261 (ptp)
REVERT: D  215 ARG cc_start: 0.8511 (ttp80) cc_final: 0.8142 (ttp80)
REVERT: B  325 SER cc_start: 0.8368 (t) cc_final: 0.8105 (p)
  outliers start: 6
  outliers final: 3
  residues processed: 90
  average time/residue: 0.0688
  time to fit residues: 7.7379
Evaluate side-chains
  84 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain B residue  332 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 47 optimal weight:    0.2980
   chunk 29 optimal weight:    0.6980
   chunk 45 optimal weight:    0.4980
   chunk 16 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0570
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
C 112 GLN
D   6 GLN
D  42 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.093713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.082370 restraints weight = 7252.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.084424 restraints weight = 4176.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.085715 restraints weight = 2812.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.086707 restraints weight = 2111.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.087410 restraints weight = 1697.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   4086  Z= 0.222
  Angle     :  0.613   7.557   5567  Z= 0.316
  Chirality :  0.045   0.140    625
  Planarity :  0.004   0.041    712
  Dihedral  :  4.473  24.116    551
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.36 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  6.87 %
    Favored  : 91.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.35), residues: 508
  helix: -2.55 (1.62), residues: 8
  sheet:  0.83 (0.34), residues: 213
  loop : -0.71 (0.33), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 567 
 TYR   0.015   0.002   TYR C  80 
 PHE   0.013   0.002   PHE C 153 
 TRP   0.017   0.002   TRP D  39 
 HIS   0.006   0.002   HIS D 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 4081)
  covalent geometry    : angle       0.61264 ( 5557)
  SS BOND              : bond        0.00481 (    5)
  SS BOND              : angle       0.90524 (   10)
  hydrogen bonds       : bond        0.04294 (  121)
  hydrogen bonds       : angle       6.58755 (  315)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.143 
Fit side-chains
REVERT: C   38 LYS cc_start: 0.8626 (tttt) cc_final: 0.8400 (tttt)
REVERT: C   61 ASN cc_start: 0.8875 (t0) cc_final: 0.8607 (t0)
REVERT: C   63 LYS cc_start: 0.8837 (tttt) cc_final: 0.8521 (ttpp)
REVERT: C   91 SER cc_start: 0.8507 (m) cc_final: 0.8081 (p)
REVERT: C  204 VAL cc_start: 0.8230 (p) cc_final: 0.7876 (m)
REVERT: C  215 LYS cc_start: 0.7339 (mmmt) cc_final: 0.6412 (mmmt)
REVERT: D   29 VAL cc_start: 0.8361 (m) cc_final: 0.8053 (p)
REVERT: D   37 MET cc_start: 0.7806 (tpp) cc_final: 0.7437 (mmm)
REVERT: D   54 LEU cc_start: 0.8771 (mp) cc_final: 0.8555 (mt)
REVERT: D   74 ASP cc_start: 0.8126 (m-30) cc_final: 0.7849 (m-30)
REVERT: D   86 ASP cc_start: 0.8280 (m-30) cc_final: 0.7912 (m-30)
REVERT: D  215 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8291 (ttp80)
  outliers start: 7
  outliers final: 6
  residues processed: 87
  average time/residue: 0.0725
  time to fit residues: 7.8902
Evaluate side-chains
  88 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  204 THR
Chi-restraints excluded: chain B residue  332 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0670
   chunk 15 optimal weight:    0.0970
   chunk 22 optimal weight:    0.2980
   chunk 20 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.3316

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

Flipped N/Q/H residues before XYZ refinement:
D  93 HIS
A 532 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.092590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.081329 restraints weight = 7219.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.083394 restraints weight = 4145.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.084713 restraints weight = 2789.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.085653 restraints weight = 2082.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.086384 restraints weight = 1673.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   4086  Z= 0.163
  Angle     :  0.549   5.443   5567  Z= 0.279
  Chirality :  0.043   0.135    625
  Planarity :  0.003   0.031    712
  Dihedral  :  4.280  24.393    551
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.97 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  :  9.09 %
    Favored  : 88.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.35), residues: 508
  helix: -2.20 (1.81), residues: 8
  sheet:  1.02 (0.35), residues: 206
  loop : -0.60 (0.34), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 567 
 TYR   0.009   0.001   TYR C  80 
 PHE   0.009   0.001   PHE C 153 
 TRP   0.019   0.002   TRP D  39 
 HIS   0.003   0.001   HIS D 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 4081)
  covalent geometry    : angle       0.54903 ( 5557)
  SS BOND              : bond        0.00309 (    5)
  SS BOND              : angle       0.71848 (   10)
  hydrogen bonds       : bond        0.03401 (  121)
  hydrogen bonds       : angle       6.39079 (  315)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.154 
Fit side-chains
REVERT: C   91 SER cc_start: 0.8573 (m) cc_final: 0.8141 (p)
REVERT: C  204 VAL cc_start: 0.8235 (p) cc_final: 0.7975 (m)
REVERT: C  215 LYS cc_start: 0.7307 (mmmt) cc_final: 0.6441 (mmmt)
REVERT: D    1 ASP cc_start: 0.8442 (p0) cc_final: 0.8115 (p0)
REVERT: D   32 SER cc_start: 0.8681 (m) cc_final: 0.8359 (p)
REVERT: D   37 MET cc_start: 0.7721 (tpp) cc_final: 0.7110 (tmm)
REVERT: D   86 ASP cc_start: 0.8299 (m-30) cc_final: 0.7954 (m-30)
REVERT: D  152 TRP cc_start: 0.8824 (m100) cc_final: 0.8159 (m100)
REVERT: D  215 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8318 (ttp80)
  outliers start: 11
  outliers final: 10
  residues processed: 84
  average time/residue: 0.0653
  time to fit residues: 6.8014
Evaluate side-chains
  87 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain A residue  571 ASP
Chi-restraints excluded: chain A residue  592 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 44 optimal weight:    0.3980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
D   6 GLN
A 532 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.089093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.077958 restraints weight = 7247.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.079913 restraints weight = 4108.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.081215 restraints weight = 2776.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.082172 restraints weight = 2077.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.082855 restraints weight = 1668.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.3475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075   4086  Z= 0.283
  Angle     :  0.658   5.957   5567  Z= 0.342
  Chirality :  0.045   0.149    625
  Planarity :  0.004   0.032    712
  Dihedral  :  4.761  22.194    551
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.15 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  :  9.76 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.35), residues: 508
  helix: -2.06 (1.85), residues: 8
  sheet:  0.99 (0.35), residues: 211
  loop : -0.76 (0.33), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 215 
 TYR   0.014   0.002   TYR C  80 
 PHE   0.016   0.002   PHE C 153 
 TRP   0.013   0.002   TRP C 106 
 HIS   0.007   0.002   HIS D  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00646 ( 4081)
  covalent geometry    : angle       0.65755 ( 5557)
  SS BOND              : bond        0.00493 (    5)
  SS BOND              : angle       1.04345 (   10)
  hydrogen bonds       : bond        0.04451 (  121)
  hydrogen bonds       : angle       6.96000 (  315)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.105 
Fit side-chains
REVERT: C   61 ASN cc_start: 0.8837 (t0) cc_final: 0.8627 (t0)
REVERT: C   91 SER cc_start: 0.8633 (m) cc_final: 0.8166 (p)
REVERT: C  204 VAL cc_start: 0.8415 (p) cc_final: 0.8128 (m)
REVERT: C  215 LYS cc_start: 0.7495 (mmmt) cc_final: 0.6613 (mmmt)
REVERT: D   32 SER cc_start: 0.8787 (m) cc_final: 0.8438 (p)
REVERT: D   37 MET cc_start: 0.7725 (tpp) cc_final: 0.7457 (mmm)
REVERT: D   86 ASP cc_start: 0.8328 (m-30) cc_final: 0.7987 (m-30)
REVERT: D  215 ARG cc_start: 0.8680 (ttp80) cc_final: 0.8334 (ttp80)
  outliers start: 11
  outliers final: 10
  residues processed: 78
  average time/residue: 0.0710
  time to fit residues: 6.9126
Evaluate side-chains
  81 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain D residue   62 VAL
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain A residue  571 ASP
Chi-restraints excluded: chain A residue  592 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0970
   chunk 20 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 33 optimal weight:    0.2980
   chunk 47 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0670
   overall best weight:    0.3516

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

Flipped N/Q/H residues before XYZ refinement:
D   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.089624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.078481 restraints weight = 7498.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.080457 restraints weight = 4187.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.081811 restraints weight = 2805.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.082713 restraints weight = 2086.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.083415 restraints weight = 1682.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.3524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   4086  Z= 0.177
  Angle     :  0.578   6.303   5567  Z= 0.296
  Chirality :  0.043   0.140    625
  Planarity :  0.004   0.030    712
  Dihedral  :  4.488  22.848    551
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.95 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.64 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.35), residues: 508
  helix: -1.75 (1.98), residues: 8
  sheet:  1.07 (0.35), residues: 208
  loop : -0.73 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 328 
 TYR   0.009   0.001   TYR C  80 
 PHE   0.010   0.001   PHE C 153 
 TRP   0.014   0.001   TRP D  39 
 HIS   0.004   0.001   HIS D 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 4081)
  covalent geometry    : angle       0.57394 ( 5557)
  SS BOND              : bond        0.00417 (    5)
  SS BOND              : angle       1.62341 (   10)
  hydrogen bonds       : bond        0.03629 (  121)
  hydrogen bonds       : angle       6.79843 (  315)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.133 
Fit side-chains
REVERT: C   91 SER cc_start: 0.8635 (m) cc_final: 0.8151 (p)
REVERT: C  204 VAL cc_start: 0.8398 (p) cc_final: 0.8069 (m)
REVERT: C  215 LYS cc_start: 0.7392 (mmmt) cc_final: 0.6587 (mmmt)
REVERT: D    1 ASP cc_start: 0.8438 (p0) cc_final: 0.8219 (p0)
REVERT: D   32 SER cc_start: 0.8807 (m) cc_final: 0.8455 (p)
REVERT: D   37 MET cc_start: 0.7674 (tpp) cc_final: 0.7387 (mmm)
REVERT: D   86 ASP cc_start: 0.8337 (m-30) cc_final: 0.7960 (m-30)
REVERT: D  102 PHE cc_start: 0.8734 (m-10) cc_final: 0.8519 (m-80)
REVERT: D  152 TRP cc_start: 0.8834 (m100) cc_final: 0.8104 (m100)
REVERT: D  215 ARG cc_start: 0.8674 (ttp80) cc_final: 0.8317 (ttp80)
  outliers start: 9
  outliers final: 8
  residues processed: 78
  average time/residue: 0.0656
  time to fit residues: 6.3319
Evaluate side-chains
  78 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain A residue  571 ASP
Chi-restraints excluded: chain A residue  592 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 36 optimal weight:    0.4980
   chunk 47 optimal weight:    0.8980
   chunk 25 optimal weight:    0.3980
   chunk 42 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
D   6 GLN
D  93 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.087904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.076821 restraints weight = 7560.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.078766 restraints weight = 4229.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.080116 restraints weight = 2836.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.081073 restraints weight = 2117.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.081752 restraints weight = 1696.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.3722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067   4086  Z= 0.257
  Angle     :  0.628   5.748   5567  Z= 0.326
  Chirality :  0.045   0.148    625
  Planarity :  0.004   0.034    712
  Dihedral  :  4.678  21.599    551
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.35 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.42 %
    Favored  : 87.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.35), residues: 508
  helix: -1.84 (1.95), residues: 8
  sheet:  1.05 (0.35), residues: 208
  loop : -0.88 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 192 
 TYR   0.012   0.002   TYR C  80 
 PHE   0.014   0.002   PHE C 153 
 TRP   0.012   0.002   TRP C 106 
 HIS   0.006   0.002   HIS D  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 ( 4081)
  covalent geometry    : angle       0.62517 ( 5557)
  SS BOND              : bond        0.00435 (    5)
  SS BOND              : angle       1.60083 (   10)
  hydrogen bonds       : bond        0.04218 (  121)
  hydrogen bonds       : angle       7.02535 (  315)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.148 
Fit side-chains
REVERT: C   91 SER cc_start: 0.8727 (m) cc_final: 0.8222 (p)
REVERT: C  204 VAL cc_start: 0.8454 (p) cc_final: 0.8134 (m)
REVERT: C  215 LYS cc_start: 0.7416 (mmmt) cc_final: 0.6609 (mmmt)
REVERT: D   32 SER cc_start: 0.8827 (m) cc_final: 0.8482 (p)
REVERT: D   37 MET cc_start: 0.7669 (tpp) cc_final: 0.7419 (mmm)
REVERT: D   86 ASP cc_start: 0.8345 (m-30) cc_final: 0.7985 (m-30)
REVERT: D  102 PHE cc_start: 0.8695 (m-10) cc_final: 0.8467 (m-80)
REVERT: D  152 TRP cc_start: 0.8840 (m100) cc_final: 0.8121 (m100)
REVERT: D  215 ARG cc_start: 0.8685 (ttp80) cc_final: 0.8319 (ttp80)
  outliers start: 9
  outliers final: 9
  residues processed: 78
  average time/residue: 0.0692
  time to fit residues: 6.8179
Evaluate side-chains
  81 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain A residue  571 ASP
Chi-restraints excluded: chain A residue  592 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0970
   chunk 21 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 12 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.2953 r_free = 0.2953 target = 0.087970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.076897 restraints weight = 7367.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.078840 restraints weight = 4193.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.080216 restraints weight = 2813.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.081142 restraints weight = 2096.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.081859 restraints weight = 1680.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.3821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   4086  Z= 0.246
  Angle     :  0.622   6.787   5567  Z= 0.322
  Chirality :  0.045   0.216    625
  Planarity :  0.004   0.041    712
  Dihedral  :  4.685  21.779    551
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.15 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 11.09 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.35), residues: 508
  helix: -1.79 (2.01), residues: 8
  sheet:  1.00 (0.35), residues: 208
  loop : -0.96 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 328 
 TYR   0.013   0.002   TYR C  80 
 PHE   0.013   0.002   PHE C 153 
 TRP   0.012   0.002   TRP C 106 
 HIS   0.006   0.002   HIS D  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 4081)
  covalent geometry    : angle       0.61986 ( 5557)
  SS BOND              : bond        0.00388 (    5)
  SS BOND              : angle       1.36939 (   10)
  hydrogen bonds       : bond        0.04088 (  121)
  hydrogen bonds       : angle       7.05157 (  315)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.149 
Fit side-chains
REVERT: C   91 SER cc_start: 0.8732 (m) cc_final: 0.8238 (p)
REVERT: C  204 VAL cc_start: 0.8462 (p) cc_final: 0.8141 (m)
REVERT: C  215 LYS cc_start: 0.7413 (mmmt) cc_final: 0.6613 (mmmt)
REVERT: D   32 SER cc_start: 0.8806 (m) cc_final: 0.8482 (p)
REVERT: D   37 MET cc_start: 0.7654 (tpp) cc_final: 0.7423 (mmm)
REVERT: D   86 ASP cc_start: 0.8347 (m-30) cc_final: 0.7990 (m-30)
REVERT: D  152 TRP cc_start: 0.8836 (m100) cc_final: 0.8115 (m100)
REVERT: D  215 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8321 (ttp80)
  outliers start: 10
  outliers final: 8
  residues processed: 79
  average time/residue: 0.0685
  time to fit residues: 6.8047
Evaluate side-chains
  80 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain A residue  592 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 25 optimal weight:    0.4980
   chunk 35 optimal weight:    0.0980
   chunk 47 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 29 optimal weight:    0.2980
   chunk 39 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0970
   chunk 17 optimal weight:    0.0870
   chunk 33 optimal weight:    0.2980
   overall best weight:    0.1756

-------------------------------------------------------------------------------
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 = 0.2993 r_free = 0.2993 target = 0.090297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.079050 restraints weight = 7398.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.081047 restraints weight = 4174.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.082442 restraints weight = 2794.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.083416 restraints weight = 2075.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.084106 restraints weight = 1658.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.3729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4086  Z= 0.112
  Angle     :  0.533   6.775   5567  Z= 0.270
  Chirality :  0.043   0.171    625
  Planarity :  0.004   0.036    712
  Dihedral  :  4.289  24.864    551
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.95 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 11.09 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.37), residues: 508
  helix: -1.30 (2.15), residues: 8
  sheet:  0.99 (0.34), residues: 220
  loop : -0.66 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 328 
 TYR   0.009   0.001   TYR D  53 
 PHE   0.005   0.001   PHE A 565 
 TRP   0.014   0.001   TRP D  39 
 HIS   0.002   0.001   HIS D 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 4081)
  covalent geometry    : angle       0.53117 ( 5557)
  SS BOND              : bond        0.00297 (    5)
  SS BOND              : angle       1.03730 (   10)
  hydrogen bonds       : bond        0.03038 (  121)
  hydrogen bonds       : angle       6.52059 (  315)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.148 
Fit side-chains
REVERT: C   91 SER cc_start: 0.8705 (m) cc_final: 0.8232 (p)
REVERT: C  204 VAL cc_start: 0.8390 (p) cc_final: 0.8078 (m)
REVERT: C  215 LYS cc_start: 0.7313 (mmmt) cc_final: 0.6511 (mmmt)
REVERT: D   32 SER cc_start: 0.8816 (m) cc_final: 0.8441 (p)
REVERT: D   37 MET cc_start: 0.7624 (tpp) cc_final: 0.7347 (mmm)
REVERT: D   86 ASP cc_start: 0.8359 (m-30) cc_final: 0.7991 (m-30)
REVERT: D  152 TRP cc_start: 0.8809 (m100) cc_final: 0.8223 (m100)
REVERT: D  215 ARG cc_start: 0.8690 (ttp80) cc_final: 0.8333 (ttp80)
REVERT: A  584 ILE cc_start: 0.8308 (mm) cc_final: 0.8090 (mm)
  outliers start: 9
  outliers final: 7
  residues processed: 82
  average time/residue: 0.0733
  time to fit residues: 7.4745
Evaluate side-chains
  83 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  188 ASP
Chi-restraints excluded: chain A residue  592 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 12 optimal weight:    0.3980
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0020
   chunk 15 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0470
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.4286

-------------------------------------------------------------------------------
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 = 0.2959 r_free = 0.2959 target = 0.088591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.077309 restraints weight = 7351.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.079332 restraints weight = 4216.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.080625 restraints weight = 2841.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.081548 restraints weight = 2131.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.082248 restraints weight = 1722.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.3848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   4086  Z= 0.211
  Angle     :  0.599   6.882   5567  Z= 0.307
  Chirality :  0.045   0.226    625
  Planarity :  0.004   0.044    712
  Dihedral  :  4.465  22.278    551
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.74 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 11.97 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.36), residues: 508
  helix: -1.44 (2.07), residues: 8
  sheet:  0.94 (0.34), residues: 221
  loop : -0.73 (0.36), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 328 
 TYR   0.010   0.002   TYR C 182 
 PHE   0.011   0.002   PHE A 565 
 TRP   0.010   0.001   TRP C 106 
 HIS   0.005   0.001   HIS D  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 4081)
  covalent geometry    : angle       0.59749 ( 5557)
  SS BOND              : bond        0.00342 (    5)
  SS BOND              : angle       1.26050 (   10)
  hydrogen bonds       : bond        0.03779 (  121)
  hydrogen bonds       : angle       6.68530 (  315)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.128 
Fit side-chains
REVERT: C   91 SER cc_start: 0.8671 (m) cc_final: 0.8197 (p)
REVERT: C  204 VAL cc_start: 0.8434 (p) cc_final: 0.8117 (m)
REVERT: C  215 LYS cc_start: 0.7390 (mmmt) cc_final: 0.6599 (mmmt)
REVERT: D   32 SER cc_start: 0.8824 (m) cc_final: 0.8453 (p)
REVERT: D   37 MET cc_start: 0.7668 (tpp) cc_final: 0.7426 (mmm)
REVERT: D   86 ASP cc_start: 0.8367 (m-30) cc_final: 0.8018 (m-30)
REVERT: D  152 TRP cc_start: 0.8832 (m100) cc_final: 0.8179 (m100)
REVERT: D  215 ARG cc_start: 0.8684 (ttp80) cc_final: 0.8320 (ttp80)
  outliers start: 7
  outliers final: 7
  residues processed: 81
  average time/residue: 0.0665
  time to fit residues: 6.7453
Evaluate side-chains
  82 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  188 ASP
Chi-restraints excluded: chain A residue  592 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 19 optimal weight:    0.2980
   chunk 41 optimal weight:    0.4980
   chunk 38 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 44 optimal weight:    0.3980
   chunk 35 optimal weight:    0.0770
   chunk 23 optimal weight:    0.0980
   chunk 10 optimal weight:    0.9980
   chunk 1 optimal weight:    0.1980
   chunk 28 optimal weight:    0.0980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.1538

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

Flipped N/Q/H residues before XYZ refinement:
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.090942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.079929 restraints weight = 7331.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.081877 restraints weight = 4108.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.083215 restraints weight = 2753.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.084202 restraints weight = 2055.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.084916 restraints weight = 1638.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.3788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4086  Z= 0.104
  Angle     :  0.529   6.667   5567  Z= 0.267
  Chirality :  0.043   0.164    625
  Planarity :  0.004   0.040    712
  Dihedral  :  4.219  25.228    551
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.95 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 12.20 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.37), residues: 508
  helix: -0.91 (2.28), residues: 8
  sheet:  1.03 (0.34), residues: 220
  loop : -0.61 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  40 
 TYR   0.009   0.001   TYR D  53 
 PHE   0.006   0.001   PHE D 102 
 TRP   0.014   0.001   TRP D  39 
 HIS   0.002   0.001   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 4081)
  covalent geometry    : angle       0.52831 ( 5557)
  SS BOND              : bond        0.00279 (    5)
  SS BOND              : angle       0.96614 (   10)
  hydrogen bonds       : bond        0.02947 (  121)
  hydrogen bonds       : angle       6.27893 (  315)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 871.32 seconds
wall clock time: 15 minutes 38.53 seconds (938.53 seconds total)