Starting phenix.real_space_refine
on Sat May 10 01:02:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqo_45817/05_2025/9cqo_45817.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqo_45817/05_2025/9cqo_45817.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqo_45817/05_2025/9cqo_45817.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqo_45817/05_2025/9cqo_45817.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqo_45817/05_2025/9cqo_45817.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqo_45817/05_2025/9cqo_45817.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.018
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
     Fe      4      7.16       5
     S      12      5.16       5
     C    2900      2.51       5
     N     760      2.21       5
     O     794      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4470
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "C"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.31, per 1000 atoms: 0.96
  Number of scatterers: 4470
  At special positions: 0
  Unit cell: (76.44, 72.765, 66.15, 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)
     Fe      4     26.01
     S      12     16.00
     O     794      8.00
     N     760      7.00
     C    2900      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.36
  Conformation dependent library (CDL) restraints added in 539.1 milliseconds
  

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1052

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 0 sheets defined
      89.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 80 through 89
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 3.607A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 138
    Processing helix  chain 'B' and resid 4 through 17
      removed outlier: 3.766A  pdb=" N   LYS B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 4.182A  pdb=" N   GLY B  25 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 46
      removed outlier: 4.057A  pdb=" N   GLU B  43 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 5.392A  pdb=" N   SER B  44 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLY B  46 " --> pdb=" O   GLU B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 56
    Processing helix  chain 'B' and resid 57 through 76
    Processing helix  chain 'B' and resid 77 through 79
      No H-bonds generated for 'chain 'B' and resid 77 through 79'
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 85 through 95
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 4.015A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 122
      No H-bonds generated for 'chain 'B' and resid 120 through 122'
    Processing helix  chain 'B' and resid 123 through 143
    Processing helix  chain 'C' and resid 3 through 18
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 75 through 80
    Processing helix  chain 'C' and resid 80 through 90
    Processing helix  chain 'C' and resid 94 through 113
      removed outlier: 3.690A  pdb=" N   PHE C  98 " --> pdb=" O   ASP C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 137
    Processing helix  chain 'D' and resid 4 through 17
      removed outlier: 3.657A  pdb=" N   LYS D  17 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 35
      removed outlier: 3.905A  pdb=" N   GLY D  25 " --> pdb=" O   ASP D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 41
    Processing helix  chain 'D' and resid 42 through 46
      removed outlier: 3.568A  pdb=" N   GLY D  46 " --> pdb=" O   GLU D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 56
    Processing helix  chain 'D' and resid 57 through 76
    Processing helix  chain 'D' and resid 77 through 79
      No H-bonds generated for 'chain 'D' and resid 77 through 79'
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 85 through 95
    Processing helix  chain 'D' and resid 99 through 119
      removed outlier: 3.990A  pdb=" N   PHE D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ARG D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 122
      No H-bonds generated for 'chain 'D' and resid 120 through 122'
    Processing helix  chain 'D' and resid 123 through 143

    343 hydrogen bonds defined for protein.
    978 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.12

  Time building geometry restraints manager: 1.56 seconds

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

  Histogram of bond lengths:
        1.21 -     1.38: 1647
        1.38 -     1.55: 2921
        1.55 -     1.72: 8
        1.72 -     1.89: 18
        1.89 -     2.06: 16
  Bond restraints: 4610
  Sorted by residual:
  bond pdb=" N   PHE D  42 "
       pdb=" CA  PHE D  42 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.18e-02 7.18e+03 1.03e+01
  bond pdb=" N   GLU D  43 "
       pdb=" CA  GLU D  43 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.21e-02 6.83e+03 9.34e+00
  bond pdb=" N   VAL D  11 "
       pdb=" CA  VAL D  11 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.17e-02 7.31e+03 8.83e+00
  bond pdb=" N   HIS C  89 "
       pdb=" CA  HIS C  89 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.23e-02 6.61e+03 8.15e+00
  bond pdb=" N   VAL B 133 "
       pdb=" CA  VAL B 133 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.10e+00
  ... (remaining 4605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 5772
        1.22 -     2.43: 338
        2.43 -     3.65: 161
        3.65 -     4.87: 43
        4.87 -     6.09: 16
  Bond angle restraints: 6330
  Sorted by residual:
  angle pdb=" N   HIS C  89 "
        pdb=" CA  HIS C  89 "
        pdb=" C   HIS C  89 "
      ideal   model   delta    sigma   weight residual
     111.36  116.19   -4.83 1.09e+00 8.42e-01 1.96e+01
  angle pdb=" O   LEU A 113 "
        pdb=" C   LEU A 113 "
        pdb=" N   PRO A 114 "
      ideal   model   delta    sigma   weight residual
     121.37  117.45    3.92 9.00e-01 1.23e+00 1.90e+01
  angle pdb=" O   LEU C 113 "
        pdb=" C   LEU C 113 "
        pdb=" N   PRO C 114 "
      ideal   model   delta    sigma   weight residual
     121.37  117.52    3.85 9.00e-01 1.23e+00 1.83e+01
  angle pdb=" CA  HIS C  87 "
        pdb=" C   HIS C  87 "
        pdb=" O   HIS C  87 "
      ideal   model   delta    sigma   weight residual
     120.82  116.46    4.36 1.05e+00 9.07e-01 1.72e+01
  angle pdb=" CA  THR C 118 "
        pdb=" C   THR C 118 "
        pdb=" N   PRO C 119 "
      ideal   model   delta    sigma   weight residual
     117.48  122.07   -4.59 1.15e+00 7.56e-01 1.59e+01
  ... (remaining 6325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 2368
       17.73 -    35.46: 166
       35.46 -    53.19: 56
       53.19 -    70.93: 15
       70.93 -    88.66: 9
  Dihedral angle restraints: 2614
    sinusoidal: 990
      harmonic: 1624
  Sorted by residual:
  dihedral pdb=" C2D HEM B 201 "
           pdb=" C3D HEM B 201 "
           pdb=" CAD HEM B 201 "
           pdb=" CBD HEM B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.00  -83.44   83.44     2      2.00e+01 2.50e-03 1.18e+01
  dihedral pdb=" C2D HEM D 201 "
           pdb=" C3D HEM D 201 "
           pdb=" CAD HEM D 201 "
           pdb=" CBD HEM D 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -75.84   75.84     2      2.00e+01 2.50e-03 1.13e+01
  dihedral pdb=" C2D HEM C 201 "
           pdb=" C3D HEM C 201 "
           pdb=" CAD HEM C 201 "
           pdb=" CBD HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -107.83  -72.17     2      2.00e+01 2.50e-03 1.09e+01
  ... (remaining 2611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 564
       0.055 -    0.110: 99
       0.110 -    0.164: 20
       0.164 -    0.219: 6
       0.219 -    0.274: 3
  Chirality restraints: 692
  Sorted by residual:
  chirality pdb=" CB  VAL B 134 "
            pdb=" CA  VAL B 134 "
            pdb=" CG1 VAL B 134 "
            pdb=" CG2 VAL B 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" CB  VAL D 134 "
            pdb=" CA  VAL D 134 "
            pdb=" CG1 VAL D 134 "
            pdb=" CG2 VAL D 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  HIS C  89 "
            pdb=" N   HIS C  89 "
            pdb=" C   HIS C  89 "
            pdb=" CB  HIS C  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  ... (remaining 689 not shown)

  Planarity restraints: 790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A   3 "    0.036 5.00e-02 4.00e+02   5.52e-02 4.87e+00
        pdb=" N   PRO A   4 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A   4 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A   4 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 113 "    0.011 2.00e-02 2.50e+03   2.06e-02 4.25e+00
        pdb=" C   LEU A 113 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   LEU A 113 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PRO A 114 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 123 "    0.030 5.00e-02 4.00e+02   4.55e-02 3.31e+00
        pdb=" N   PRO B 124 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 124 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 124 "    0.025 5.00e-02 4.00e+02
  ... (remaining 787 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 599
        2.75 -     3.29: 4268
        3.29 -     3.83: 7836
        3.83 -     4.36: 8979
        4.36 -     4.90: 15757
  Nonbonded interactions: 37439
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A  27 "
            pdb=" NE2 HIS A 112 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" OE1 GLU C  27 "
            pdb=" NE2 HIS C 112 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" OE1 GLU D  26 "
            pdb=" NE2 HIS D 117 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" O   PRO A  77 "
            pdb=" OH  TYR A 140 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   SER A 133 "
            pdb=" OG1 THR A 137 "
     model   vdw
     2.305 3.040
  ... (remaining 37434 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.950
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.320
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  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:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
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      :  0.007   0.225   4614  Z= 0.339
  Angle     :  0.837   6.087   6330  Z= 0.564
  Chirality :  0.050   0.274    692
  Planarity :  0.006   0.055    790
  Dihedral  : 15.651  88.657   1562
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 10.79 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.00 (0.36), residues: 558
  helix:  2.39 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.58 (0.62), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  15 
 HIS   0.005   0.001   HIS C  87 
 PHE   0.013   0.002   PHE D  42 
 TYR   0.006   0.001   TYR B  35 
 ARG   0.008   0.001   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11535 (  343)
  hydrogen bonds       : angle       4.90656 (  978)
  covalent geometry    : bond        0.00512 ( 4610)
  covalent geometry    : angle       0.83665 ( 6330)
  Misc. bond           : bond        0.17153 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LYS cc_start: 0.7942 (tptp) cc_final: 0.7455 (ttmm)
REVERT: A   61 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7676 (mtpt)
REVERT: A   92 ARG cc_start: 0.8636 (mtt-85) cc_final: 0.7604 (mtm-85)
REVERT: B   52 ASP cc_start: 0.8214 (m-30) cc_final: 0.8006 (m-30)
REVERT: B   65 LYS cc_start: 0.8388 (ttmt) cc_final: 0.8160 (tttt)
  outliers start: 13
  outliers final: 4
  residues processed: 58
  average time/residue: 0.2427
  time to fit residues: 17.0068
Evaluate side-chains
  46 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0470
   chunk 23 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.8482

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

Flipped N/Q/H residues before XYZ refinement:
B 131 GLN
C  89 HIS
D  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.155057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.130121 restraints weight = 4198.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.26
r_work: 0.3204 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.114   4614  Z= 0.165
  Angle     :  0.605   5.361   6330  Z= 0.285
  Chirality :  0.041   0.128    692
  Planarity :  0.006   0.048    790
  Dihedral  : 10.228  85.074    624
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  :  9.25 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.80 (0.36), residues: 558
  helix:  2.25 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.54 (0.61), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  14 
 HIS   0.005   0.001   HIS C  87 
 PHE   0.013   0.002   PHE D  85 
 TYR   0.008   0.001   TYR A  42 
 ARG   0.006   0.001   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04168 (  343)
  hydrogen bonds       : angle       4.18022 (  978)
  covalent geometry    : bond        0.00440 ( 4610)
  covalent geometry    : angle       0.60539 ( 6330)
  Misc. bond           : bond        0.10215 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LYS cc_start: 0.7796 (tptp) cc_final: 0.7164 (ttmm)
REVERT: A   61 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7215 (mtpt)
REVERT: A   92 ARG cc_start: 0.8740 (mtt-85) cc_final: 0.7661 (mtm-85)
REVERT: B   65 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7717 (tttm)
REVERT: C   76 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6855 (mtt)
REVERT: D  120 LYS cc_start: 0.7530 (mmtp) cc_final: 0.7129 (mmmt)
  outliers start: 14
  outliers final: 9
  residues processed: 54
  average time/residue: 0.2314
  time to fit residues: 15.2064
Evaluate side-chains
  54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   89 SER
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 22 optimal weight:    0.1980
   chunk 42 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 43 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:
C  89 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.159586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.137209 restraints weight = 4150.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 0.99
r_work: 0.3249 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.119   4614  Z= 0.126
  Angle     :  0.562   5.590   6330  Z= 0.257
  Chirality :  0.038   0.122    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.925  83.477    624
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  :  7.93 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.98 (0.36), residues: 558
  helix:  2.38 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.54 (0.60), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.003   0.001   HIS C  87 
 PHE   0.008   0.001   PHE D  85 
 TYR   0.005   0.001   TYR B  35 
 ARG   0.005   0.001   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03395 (  343)
  hydrogen bonds       : angle       3.96899 (  978)
  covalent geometry    : bond        0.00339 ( 4610)
  covalent geometry    : angle       0.56175 ( 6330)
  Misc. bond           : bond        0.08605 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LYS cc_start: 0.8085 (tptp) cc_final: 0.7596 (ttmm)
REVERT: A   61 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7574 (mtpt)
REVERT: A   76 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6576 (mmt)
REVERT: A   92 ARG cc_start: 0.8701 (mtt-85) cc_final: 0.7845 (mtm-85)
REVERT: B   14 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7794 (tp)
REVERT: B   66 LYS cc_start: 0.8405 (mmmm) cc_final: 0.7832 (mtpt)
REVERT: C   76 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6792 (mtt)
REVERT: D  120 LYS cc_start: 0.7559 (mmtp) cc_final: 0.7233 (mmmt)
  outliers start: 13
  outliers final: 8
  residues processed: 53
  average time/residue: 0.2319
  time to fit residues: 15.0272
Evaluate side-chains
  52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 39 optimal weight:    0.0170
   chunk 36 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0570
   chunk 49 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
C  89 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.160341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.137811 restraints weight = 4167.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.00
r_work: 0.3257 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.137   4614  Z= 0.114
  Angle     :  0.549   5.737   6330  Z= 0.249
  Chirality :  0.037   0.121    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.804  83.491    622
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  :  7.93 %
    Favored  : 88.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.11 (0.36), residues: 558
  helix:  2.50 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.49 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.006   0.001   HIS C  89 
 PHE   0.006   0.001   PHE B 118 
 TYR   0.005   0.001   TYR B  35 
 ARG   0.003   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03187 (  343)
  hydrogen bonds       : angle       3.87935 (  978)
  covalent geometry    : bond        0.00302 ( 4610)
  covalent geometry    : angle       0.54922 ( 6330)
  Misc. bond           : bond        0.08641 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LYS cc_start: 0.8080 (tptp) cc_final: 0.7582 (ttmm)
REVERT: A   61 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7564 (mtpt)
REVERT: A   76 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6504 (mmt)
REVERT: A   92 ARG cc_start: 0.8689 (mtt-85) cc_final: 0.7820 (mtm-85)
REVERT: B   14 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7849 (tp)
REVERT: B   66 LYS cc_start: 0.8352 (mmmm) cc_final: 0.7794 (mtpt)
REVERT: B  120 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7343 (tttt)
REVERT: C   76 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6757 (mtt)
REVERT: D  120 LYS cc_start: 0.7550 (mmtp) cc_final: 0.7215 (mmmt)
  outliers start: 14
  outliers final: 9
  residues processed: 46
  average time/residue: 0.2581
  time to fit residues: 14.4165
Evaluate side-chains
  53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 27 optimal weight:    0.2980
   chunk 45 optimal weight:    0.0980
   chunk 26 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C  89 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.159092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.136681 restraints weight = 4234.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 0.99
r_work: 0.3245 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.136   4614  Z= 0.126
  Angle     :  0.559   6.263   6330  Z= 0.254
  Chirality :  0.038   0.121    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.684  82.821    620
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  :  8.15 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.09 (0.36), residues: 558
  helix:  2.49 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.44 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C  89 
 PHE   0.007   0.001   PHE D  85 
 TYR   0.005   0.001   TYR B  35 
 ARG   0.003   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03365 (  343)
  hydrogen bonds       : angle       3.90757 (  978)
  covalent geometry    : bond        0.00339 ( 4610)
  covalent geometry    : angle       0.55860 ( 6330)
  Misc. bond           : bond        0.09074 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 43
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LYS cc_start: 0.8105 (tptp) cc_final: 0.7611 (ttmm)
REVERT: A   61 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7595 (mtpt)
REVERT: A   76 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6651 (mmt)
REVERT: A   92 ARG cc_start: 0.8703 (mtt-85) cc_final: 0.7827 (mtm-85)
REVERT: B   14 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7864 (tp)
REVERT: B   26 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7469 (mm-30)
REVERT: B   66 LYS cc_start: 0.8391 (mmmm) cc_final: 0.7838 (mtpt)
REVERT: B  120 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7376 (tttt)
REVERT: C   76 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6807 (mtt)
REVERT: D  120 LYS cc_start: 0.7545 (mmtp) cc_final: 0.7211 (mmmt)
  outliers start: 17
  outliers final: 10
  residues processed: 50
  average time/residue: 0.2264
  time to fit residues: 13.8169
Evaluate side-chains
  56 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   90 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    0.0570
   chunk 7 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.7500

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

Flipped N/Q/H residues before XYZ refinement:
C  89 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.156808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.132020 restraints weight = 4191.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.21
r_work: 0.3216 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.142   4614  Z= 0.149
  Angle     :  0.579   6.541   6330  Z= 0.266
  Chirality :  0.039   0.125    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.752  82.922    620
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  :  8.59 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.93 (0.36), residues: 558
  helix:  2.39 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.34 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  14 
 HIS   0.006   0.001   HIS C  89 
 PHE   0.009   0.001   PHE D  85 
 TYR   0.005   0.001   TYR A  42 
 ARG   0.002   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03673 (  343)
  hydrogen bonds       : angle       4.00166 (  978)
  covalent geometry    : bond        0.00402 ( 4610)
  covalent geometry    : angle       0.57944 ( 6330)
  Misc. bond           : bond        0.10127 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 41
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.7978 (tptp) cc_final: 0.7348 (ttmm)
REVERT: A   61 LYS cc_start: 0.7855 (mtpp) cc_final: 0.7347 (mtpt)
REVERT: A   92 ARG cc_start: 0.8738 (mtt-85) cc_final: 0.7761 (mtm-85)
REVERT: B   26 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7308 (mm-30)
REVERT: B   66 LYS cc_start: 0.8196 (mmmm) cc_final: 0.7570 (mtpt)
REVERT: B  120 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7268 (tttt)
REVERT: C   60 LYS cc_start: 0.7879 (tptp) cc_final: 0.7098 (tppt)
REVERT: C   76 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6825 (mtt)
REVERT: D   43 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6354 (pm20)
REVERT: D  120 LYS cc_start: 0.7543 (mmtp) cc_final: 0.7156 (mmmt)
  outliers start: 16
  outliers final: 9
  residues processed: 49
  average time/residue: 0.2650
  time to fit residues: 15.7900
Evaluate side-chains
  53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   90 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0980
   chunk 28 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
C  89 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.158909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.136753 restraints weight = 4195.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 0.97
r_work: 0.3264 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.132   4614  Z= 0.117
  Angle     :  0.552   6.099   6330  Z= 0.250
  Chirality :  0.038   0.128    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.646  81.983    620
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  :  8.37 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.09 (0.36), residues: 558
  helix:  2.52 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.34 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  14 
 HIS   0.007   0.001   HIS C  89 
 PHE   0.006   0.001   PHE C  43 
 TYR   0.005   0.001   TYR A  42 
 ARG   0.002   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03209 (  343)
  hydrogen bonds       : angle       3.89809 (  978)
  covalent geometry    : bond        0.00314 ( 4610)
  covalent geometry    : angle       0.55212 ( 6330)
  Misc. bond           : bond        0.08585 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 40
  time to evaluate  : 0.450 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8151 (tptp) cc_final: 0.7614 (ttmm)
REVERT: A   61 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7583 (mtpt)
REVERT: A   76 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.6599 (mmt)
REVERT: A   92 ARG cc_start: 0.8689 (mtt-85) cc_final: 0.7851 (mtm-85)
REVERT: B   26 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7453 (mm-30)
REVERT: B   66 LYS cc_start: 0.8366 (mmmm) cc_final: 0.7824 (mtpt)
REVERT: B  120 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7374 (tttt)
REVERT: C   60 LYS cc_start: 0.7992 (tptp) cc_final: 0.7306 (tppt)
REVERT: C   76 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6800 (mtt)
REVERT: D   43 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6639 (pm20)
REVERT: D  120 LYS cc_start: 0.7489 (mmtp) cc_final: 0.7163 (mmmt)
  outliers start: 17
  outliers final: 10
  residues processed: 48
  average time/residue: 0.2234
  time to fit residues: 13.1505
Evaluate side-chains
  54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 39
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   90 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 41 optimal weight:    0.0670
   chunk 37 optimal weight:    0.0870
   chunk 0 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 22 optimal weight:    0.0570
   chunk 27 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.3214

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

Flipped N/Q/H residues before XYZ refinement:
C  89 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.160564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.139352 restraints weight = 4130.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 0.93
r_work: 0.3280 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.123   4614  Z= 0.105
  Angle     :  0.537   5.765   6330  Z= 0.242
  Chirality :  0.037   0.119    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.584  81.842    620
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  :  9.03 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.24 (0.36), residues: 558
  helix:  2.64 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.33 (0.59), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  14 
 HIS   0.006   0.001   HIS C  89 
 PHE   0.005   0.001   PHE C 117 
 TYR   0.005   0.001   TYR B  35 
 ARG   0.003   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02939 (  343)
  hydrogen bonds       : angle       3.80873 (  978)
  covalent geometry    : bond        0.00277 ( 4610)
  covalent geometry    : angle       0.53679 ( 6330)
  Misc. bond           : bond        0.07693 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8119 (tptp) cc_final: 0.7629 (ttmm)
REVERT: A   61 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7624 (mtpt)
REVERT: A   76 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.6607 (mmt)
REVERT: A   92 ARG cc_start: 0.8672 (mtt-85) cc_final: 0.7849 (mtm-85)
REVERT: B    8 LYS cc_start: 0.7558 (tppt) cc_final: 0.7159 (mttm)
REVERT: B   26 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7348 (mm-30)
REVERT: B   66 LYS cc_start: 0.8369 (mmmm) cc_final: 0.7856 (mtpt)
REVERT: C   76 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6788 (mtt)
REVERT: D   43 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6583 (pm20)
REVERT: D  120 LYS cc_start: 0.7472 (mmtp) cc_final: 0.7144 (mmmt)
  outliers start: 15
  outliers final: 9
  residues processed: 49
  average time/residue: 0.2289
  time to fit residues: 13.9193
Evaluate side-chains
  53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   90 GLU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0570
   chunk 47 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 31 optimal weight:    0.2980
   chunk 19 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0970
   chunk 36 optimal weight:    7.9990
   overall best weight:    0.3496

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

Flipped N/Q/H residues before XYZ refinement:
B 102 ASN
C  89 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.160818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.139435 restraints weight = 4182.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 0.92
r_work: 0.3278 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.125   4614  Z= 0.107
  Angle     :  0.536   5.826   6330  Z= 0.242
  Chirality :  0.037   0.119    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.572  81.904    620
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  :  9.69 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.28 (0.36), residues: 558
  helix:  2.68 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.29 (0.59), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  14 
 HIS   0.006   0.001   HIS C  89 
 PHE   0.005   0.001   PHE C  43 
 TYR   0.005   0.001   TYR B  35 
 ARG   0.002   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02935 (  343)
  hydrogen bonds       : angle       3.78393 (  978)
  covalent geometry    : bond        0.00283 ( 4610)
  covalent geometry    : angle       0.53641 ( 6330)
  Misc. bond           : bond        0.07912 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.485 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8109 (tptp) cc_final: 0.7602 (ttmm)
REVERT: A   61 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7604 (mtpt)
REVERT: A   76 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6535 (mmt)
REVERT: A   92 ARG cc_start: 0.8676 (mtt-85) cc_final: 0.7838 (mtm-85)
REVERT: B    8 LYS cc_start: 0.7517 (tppt) cc_final: 0.7126 (mttm)
REVERT: B   26 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7330 (mm-30)
REVERT: B   66 LYS cc_start: 0.8349 (mmmm) cc_final: 0.7826 (mtpt)
REVERT: C   76 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6824 (mtt)
REVERT: D   43 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6683 (pm20)
REVERT: D  120 LYS cc_start: 0.7474 (mmtp) cc_final: 0.7142 (mmmt)
  outliers start: 14
  outliers final: 9
  residues processed: 49
  average time/residue: 0.2191
  time to fit residues: 13.2618
Evaluate side-chains
  55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   90 GLU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0030
   chunk 48 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.9996

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN
C  89 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.155343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.130544 restraints weight = 4224.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.21
r_work: 0.3194 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.155   4614  Z= 0.179
  Angle     :  0.607   7.081   6330  Z= 0.279
  Chirality :  0.041   0.132    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.830  85.133    620
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  :  9.91 %
    Favored  : 87.00 %
  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:  2.79 (0.36), residues: 558
  helix:  2.31 (0.24), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.20 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  14 
 HIS   0.007   0.001   HIS C  89 
 PHE   0.013   0.002   PHE D  85 
 TYR   0.008   0.001   TYR A  42 
 ARG   0.002   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04104 (  343)
  hydrogen bonds       : angle       4.08800 (  978)
  covalent geometry    : bond        0.00483 ( 4610)
  covalent geometry    : angle       0.60742 ( 6330)
  Misc. bond           : bond        0.11282 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.449 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8039 (tptp) cc_final: 0.7407 (ttmm)
REVERT: A   61 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7402 (mtpt)
REVERT: A   92 ARG cc_start: 0.8732 (mtt-85) cc_final: 0.7765 (mtm-85)
REVERT: B    8 LYS cc_start: 0.7362 (tppt) cc_final: 0.6976 (mttm)
REVERT: B   26 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7343 (mm-30)
REVERT: B   66 LYS cc_start: 0.8235 (mmmm) cc_final: 0.7606 (mtpt)
REVERT: B  120 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7289 (tttt)
REVERT: C   60 LYS cc_start: 0.7954 (tptp) cc_final: 0.7090 (ttmm)
REVERT: C   76 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6879 (mtt)
REVERT: D  120 LYS cc_start: 0.7530 (mmtp) cc_final: 0.7132 (mmmt)
  outliers start: 14
  outliers final: 10
  residues processed: 49
  average time/residue: 0.2288
  time to fit residues: 13.6667
Evaluate side-chains
  55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0070
   chunk 19 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
C  89 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.157657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.136213 restraints weight = 4209.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 0.92
r_work: 0.3246 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.137   4614  Z= 0.125
  Angle     :  0.557   6.388   6330  Z= 0.253
  Chirality :  0.038   0.118    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.662  83.468    620
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  :  9.91 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.98 (0.36), residues: 558
  helix:  2.46 (0.24), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.18 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  14 
 HIS   0.005   0.001   HIS C  89 
 PHE   0.006   0.001   PHE C  43 
 TYR   0.005   0.001   TYR B  35 
 ARG   0.002   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03342 (  343)
  hydrogen bonds       : angle       3.94287 (  978)
  covalent geometry    : bond        0.00335 ( 4610)
  covalent geometry    : angle       0.55693 ( 6330)
  Misc. bond           : bond        0.09156 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2708.15 seconds
wall clock time: 47 minutes 50.04 seconds (2870.04 seconds total)