Starting phenix.real_space_refine
on Fri Aug 22 15:22:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8poc_17788/08_2025/8poc_17788.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8poc_17788/08_2025/8poc_17788.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8poc_17788/08_2025/8poc_17788.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8poc_17788/08_2025/8poc_17788.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8poc_17788/08_2025/8poc_17788.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8poc_17788/08_2025/8poc_17788.map"
  }
  resolution = 4.0
  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=   0.027
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      28      5.16       5
     C    3108      2.51       5
     N     880      2.21       5
     O     908      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4924
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1231
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 6, 'TRANS': 147}
    Chain: "B"
      Number of atoms: 1231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1231
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 6, 'TRANS': 147}
    Chain: "C"
      Number of atoms: 1231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1231
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 6, 'TRANS': 147}
    Chain: "D"
      Number of atoms: 1231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1231
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 6, 'TRANS': 147}
  Time building chain proxies: 1.31, per 1000 atoms: 0.27
  Number of scatterers: 4924
  At special positions: 0
  Unit cell: (86.49, 76.26, 77.19, 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      28     16.00
     O     908      8.00
     N     880      7.00
     C    3108      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.30
  Conformation dependent library (CDL) restraints added in 168.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1136

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 4 sheets defined
      60.1% alpha, 11.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 15
    Processing helix  chain 'A' and resid 20 through 37
    Processing helix  chain 'A' and resid 38 through 56
      removed outlier: 3.539A  pdb=" N   ARG A  55 " --> pdb=" O   GLN A  51 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   TYR A  56 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 4.100A  pdb=" N   LEU A  77 " --> pdb=" O   ARG A  73 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   PHE A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 131
      removed outlier: 3.896A  pdb=" N   GLY A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 15
    Processing helix  chain 'B' and resid 20 through 37
    Processing helix  chain 'B' and resid 38 through 56
      removed outlier: 3.574A  pdb=" N   ARG B  55 " --> pdb=" O   GLN B  51 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   TYR B  56 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 79
      removed outlier: 4.039A  pdb=" N   LEU B  77 " --> pdb=" O   ARG B  73 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   PHE B  78 " --> pdb=" O   VAL B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 130
    Processing helix  chain 'C' and resid 2 through 15
    Processing helix  chain 'C' and resid 20 through 37
    Processing helix  chain 'C' and resid 38 through 56
      removed outlier: 3.596A  pdb=" N   ARG C  55 " --> pdb=" O   GLN C  51 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   TYR C  56 " --> pdb=" O   LEU C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 79
      removed outlier: 4.027A  pdb=" N   LEU C  77 " --> pdb=" O   ARG C  73 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   PHE C  78 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 130
    Processing helix  chain 'D' and resid 2 through 15
    Processing helix  chain 'D' and resid 20 through 37
    Processing helix  chain 'D' and resid 38 through 56
      removed outlier: 3.548A  pdb=" N   ARG D  55 " --> pdb=" O   GLN D  51 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   TYR D  56 " --> pdb=" O   LEU D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 63 through 79
      removed outlier: 4.039A  pdb=" N   LEU D  77 " --> pdb=" O   ARG D  73 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   PHE D  78 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 107 through 131
      removed outlier: 3.905A  pdb=" N   GLY D 131 " --> pdb=" O   LEU D 127 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 87
    Processing sheet with id=AA2, first strand: chain 'B' and resid 82 through 87
    Processing sheet with id=AA3, first strand: chain 'C' and resid 82 through 87
    Processing sheet with id=AA4, first strand: chain 'D' and resid 82 through 87

    336 hydrogen bonds defined for protein.
    966 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: 0.72

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1680
        1.34 -     1.46: 1134
        1.46 -     1.58: 2174
        1.58 -     1.70: 0
        1.70 -     1.81: 48
  Bond restraints: 5036
  Sorted by residual:
  bond pdb=" CG1 ILE A  94 "
       pdb=" CD1 ILE A  94 "
    ideal  model  delta    sigma   weight residual
    1.513  1.470  0.043 3.90e-02 6.57e+02 1.20e+00
  bond pdb=" CB  GLN B  14 "
       pdb=" CG  GLN B  14 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.15e+00
  bond pdb=" CG1 ILE D  94 "
       pdb=" CD1 ILE D  94 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.13e+00
  bond pdb=" CB  GLN C  14 "
       pdb=" CG  GLN C  14 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.11e+00
  bond pdb=" CG  LEU A  85 "
       pdb=" CD2 LEU A  85 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.51e-01
  ... (remaining 5031 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 6663
        1.71 -     3.41: 129
        3.41 -     5.12: 27
        5.12 -     6.83: 10
        6.83 -     8.53: 3
  Bond angle restraints: 6832
  Sorted by residual:
  angle pdb=" C   GLN D  16 "
        pdb=" N   LEU D  17 "
        pdb=" CA  LEU D  17 "
      ideal   model   delta    sigma   weight residual
     122.31  113.78    8.53 2.34e+00 1.83e-01 1.33e+01
  angle pdb=" C   GLN C  16 "
        pdb=" N   LEU C  17 "
        pdb=" CA  LEU C  17 "
      ideal   model   delta    sigma   weight residual
     122.31  114.00    8.31 2.34e+00 1.83e-01 1.26e+01
  angle pdb=" C   GLN B  16 "
        pdb=" N   LEU B  17 "
        pdb=" CA  LEU B  17 "
      ideal   model   delta    sigma   weight residual
     122.31  114.55    7.76 2.34e+00 1.83e-01 1.10e+01
  angle pdb=" CA  GLN C  14 "
        pdb=" CB  GLN C  14 "
        pdb=" CG  GLN C  14 "
      ideal   model   delta    sigma   weight residual
     114.10  119.51   -5.41 2.00e+00 2.50e-01 7.32e+00
  angle pdb=" CA  GLN B  14 "
        pdb=" CB  GLN B  14 "
        pdb=" CG  GLN B  14 "
      ideal   model   delta    sigma   weight residual
     114.10  119.51   -5.41 2.00e+00 2.50e-01 7.30e+00
  ... (remaining 6827 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 2649
       17.13 -    34.26: 276
       34.26 -    51.39: 35
       51.39 -    68.52: 6
       68.52 -    85.65: 18
  Dihedral angle restraints: 2984
    sinusoidal: 1208
      harmonic: 1776
  Sorted by residual:
  dihedral pdb=" CA  ASN B  35 "
           pdb=" C   ASN B  35 "
           pdb=" N   ALA B  36 "
           pdb=" CA  ALA B  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.77  -15.23     0      5.00e+00 4.00e-02 9.27e+00
  dihedral pdb=" CA  ARG A  13 "
           pdb=" CB  ARG A  13 "
           pdb=" CG  ARG A  13 "
           pdb=" CD  ARG A  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.88   53.88     3      1.50e+01 4.44e-03 9.24e+00
  dihedral pdb=" CA  ARG B  13 "
           pdb=" CB  ARG B  13 "
           pdb=" CG  ARG B  13 "
           pdb=" CD  ARG B  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.61   53.61     3      1.50e+01 4.44e-03 9.22e+00
  ... (remaining 2981 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 569
       0.038 -    0.075: 151
       0.075 -    0.113: 4
       0.113 -    0.150: 0
       0.150 -    0.188: 4
  Chirality restraints: 728
  Sorted by residual:
  chirality pdb=" CA  ILE A  94 "
            pdb=" N   ILE A  94 "
            pdb=" C   ILE A  94 "
            pdb=" CB  ILE A  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.82e-01
  chirality pdb=" CA  ILE D  94 "
            pdb=" N   ILE D  94 "
            pdb=" C   ILE D  94 "
            pdb=" CB  ILE D  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.40e-01
  chirality pdb=" CA  ILE C  94 "
            pdb=" N   ILE C  94 "
            pdb=" C   ILE C  94 "
            pdb=" CB  ILE C  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.65e-01
  ... (remaining 725 not shown)

  Planarity restraints: 896
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C  99 "   -0.024 5.00e-02 4.00e+02   3.64e-02 2.12e+00
        pdb=" N   PRO C 100 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO C 100 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 100 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  11 "    0.008 2.00e-02 2.50e+03   1.03e-02 2.11e+00
        pdb=" CG  TYR B  11 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  11 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  11 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  11 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  11 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  11 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  11 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  99 "    0.024 5.00e-02 4.00e+02   3.62e-02 2.09e+00
        pdb=" N   PRO B 100 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 100 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 100 "    0.020 5.00e-02 4.00e+02
  ... (remaining 893 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1472
        2.84 -     3.35: 4800
        3.35 -     3.87: 7565
        3.87 -     4.38: 7525
        4.38 -     4.90: 14384
  Nonbonded interactions: 35746
  Sorted by model distance:
  nonbonded pdb=" O   GLU D  68 "
            pdb=" ND2 ASN D  72 "
     model   vdw
     2.324 3.120
  nonbonded pdb=" N   GLU A  89 "
            pdb=" OE1 GLU A  89 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" N   GLU C  89 "
            pdb=" OE1 GLU C  89 "
     model   vdw
     2.343 3.120
  nonbonded pdb=" O   GLU B  68 "
            pdb=" ND2 ASN B  72 "
     model   vdw
     2.346 3.120
  nonbonded pdb=" NH2 ARG C 112 "
            pdb=" OE1 GLU C 142 "
     model   vdw
     2.382 3.120
  ... (remaining 35741 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 'B'
  selection = chain 'C'
  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 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:             1.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.760
  Find NCS groups from input model:        0.080
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
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      :  0.003   0.043   5036  Z= 0.147
  Angle     :  0.667   8.532   6832  Z= 0.349
  Chirality :  0.034   0.188    728
  Planarity :  0.004   0.037    896
  Dihedral  : 14.858  85.653   1848
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.33), residues: 608
  helix:  2.97 (0.27), residues: 344
  sheet:  0.47 (0.44), residues: 96
  loop : -1.49 (0.42), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  39 
 TYR   0.025   0.001   TYR B  11 
 PHE   0.007   0.001   PHE D  44 
 TRP   0.023   0.001   TRP C 126 
 HIS   0.006   0.002   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 5036)
  covalent geometry    : angle       0.66717 ( 6832)
  hydrogen bonds       : bond        0.10976 (  336)
  hydrogen bonds       : angle       5.16406 (  966)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.117 
Fit side-chains
REVERT: C   93 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8032 (mt-10)
REVERT: D    1 MET cc_start: 0.7142 (mpp) cc_final: 0.6575 (mpp)
REVERT: D   89 GLU cc_start: 0.8233 (pm20) cc_final: 0.7988 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0664
  time to fit residues: 11.5421
Evaluate side-chains
  108 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    0.3980
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0370
   chunk 25 optimal weight:    0.4980
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
A  79 HIS
B   7 HIS
B  79 HIS
C   7 HIS
C  79 HIS
D   7 HIS
D  96 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.162859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.118894 restraints weight = 6706.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.121216 restraints weight = 5670.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.122898 restraints weight = 5057.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.123421 restraints weight = 4685.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.123943 restraints weight = 4516.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5036  Z= 0.121
  Angle     :  0.560   5.390   6832  Z= 0.280
  Chirality :  0.035   0.188    728
  Planarity :  0.004   0.035    896
  Dihedral  :  3.348  14.762    692
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 11.92 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.34), residues: 608
  helix:  2.97 (0.27), residues: 356
  sheet:  0.70 (0.46), residues: 96
  loop : -1.51 (0.45), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 125 
 TYR   0.006   0.001   TYR A 153 
 PHE   0.005   0.001   PHE D  25 
 TRP   0.006   0.001   TRP C 126 
 HIS   0.004   0.001   HIS D   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 5036)
  covalent geometry    : angle       0.56011 ( 6832)
  hydrogen bonds       : bond        0.03606 (  336)
  hydrogen bonds       : angle       4.19833 (  966)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   93 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8083 (mt-10)
REVERT: B   93 GLU cc_start: 0.8431 (tt0) cc_final: 0.8156 (mt-10)
REVERT: C   93 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8058 (mt-10)
REVERT: D    1 MET cc_start: 0.7717 (mpp) cc_final: 0.7238 (mpp)
REVERT: D   93 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8091 (mt-10)
  outliers start: 13
  outliers final: 8
  residues processed: 130
  average time/residue: 0.0801
  time to fit residues: 13.1815
Evaluate side-chains
  128 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   68 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 104 ASN
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 104 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.150807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.106363 restraints weight = 6945.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.108409 restraints weight = 5874.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.109860 restraints weight = 5274.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.110445 restraints weight = 4917.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.111242 restraints weight = 4729.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   5036  Z= 0.280
  Angle     :  0.678   5.245   6832  Z= 0.349
  Chirality :  0.038   0.171    728
  Planarity :  0.005   0.038    896
  Dihedral  :  3.756  16.304    692
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 15.77 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.34), residues: 608
  helix:  2.58 (0.27), residues: 356
  sheet:  0.81 (0.47), residues: 96
  loop : -1.43 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 112 
 TYR   0.010   0.002   TYR B  95 
 PHE   0.013   0.003   PHE D  25 
 TRP   0.014   0.002   TRP C 126 
 HIS   0.006   0.002   HIS D  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00672 ( 5036)
  covalent geometry    : angle       0.67766 ( 6832)
  hydrogen bonds       : bond        0.05927 (  336)
  hydrogen bonds       : angle       4.77424 (  966)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.195 
Fit side-chains
REVERT: B   93 GLU cc_start: 0.8593 (tt0) cc_final: 0.8041 (mt-10)
REVERT: C   93 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8201 (mt-10)
REVERT: D    1 MET cc_start: 0.7863 (mpp) cc_final: 0.7555 (mpp)
REVERT: D   89 GLU cc_start: 0.8411 (pm20) cc_final: 0.8136 (pm20)
REVERT: D   93 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8079 (mt-10)
  outliers start: 23
  outliers final: 13
  residues processed: 139
  average time/residue: 0.0733
  time to fit residues: 13.1367
Evaluate side-chains
  134 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 ASP
Chi-restraints excluded: chain A residue   38 GLU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain B residue    3 ASP
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 HIS
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.158433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.115330 restraints weight = 6580.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.116785 restraints weight = 5788.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.118047 restraints weight = 5311.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.118418 restraints weight = 5025.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.118427 restraints weight = 4883.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5036  Z= 0.137
  Angle     :  0.556   4.981   6832  Z= 0.279
  Chirality :  0.035   0.177    728
  Planarity :  0.004   0.034    896
  Dihedral  :  3.447  15.162    692
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 17.12 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.46 (0.34), residues: 608
  helix:  2.99 (0.27), residues: 356
  sheet:  0.81 (0.46), residues: 96
  loop : -1.23 (0.48), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 152 
 TYR   0.005   0.001   TYR B  95 
 PHE   0.005   0.001   PHE B  78 
 TRP   0.004   0.001   TRP C 111 
 HIS   0.003   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 5036)
  covalent geometry    : angle       0.55551 ( 6832)
  hydrogen bonds       : bond        0.03859 (  336)
  hydrogen bonds       : angle       4.27945 (  966)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A   17 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8522 (pp)
REVERT: B   93 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8018 (mt-10)
REVERT: D   17 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8529 (pp)
REVERT: D   93 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8170 (mt-10)
  outliers start: 27
  outliers final: 12
  residues processed: 131
  average time/residue: 0.0744
  time to fit residues: 12.6347
Evaluate side-chains
  132 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.154176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.109958 restraints weight = 6833.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.112367 restraints weight = 5598.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.113679 restraints weight = 4916.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.115189 restraints weight = 4528.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.115992 restraints weight = 4256.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5036  Z= 0.141
  Angle     :  0.544   5.956   6832  Z= 0.270
  Chirality :  0.034   0.177    728
  Planarity :  0.004   0.035    896
  Dihedral  :  3.322  14.809    692
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 17.31 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.56 (0.34), residues: 608
  helix:  3.05 (0.26), residues: 356
  sheet:  0.83 (0.46), residues: 96
  loop : -1.10 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 152 
 TYR   0.004   0.001   TYR A  11 
 PHE   0.006   0.001   PHE B  25 
 TRP   0.004   0.001   TRP C  21 
 HIS   0.003   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 5036)
  covalent geometry    : angle       0.54419 ( 6832)
  hydrogen bonds       : bond        0.03840 (  336)
  hydrogen bonds       : angle       4.17187 (  966)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 111
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   17 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8491 (pp)
REVERT: B   17 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8517 (pp)
REVERT: B   93 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8108 (mt-10)
REVERT: C   17 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8484 (pp)
REVERT: D   17 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8472 (pp)
REVERT: D   89 GLU cc_start: 0.8354 (pm20) cc_final: 0.8009 (pm20)
REVERT: D   93 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8188 (mt-10)
  outliers start: 29
  outliers final: 15
  residues processed: 129
  average time/residue: 0.0758
  time to fit residues: 12.6634
Evaluate side-chains
  130 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain C residue    3 ASP
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.156432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.112231 restraints weight = 6896.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.114792 restraints weight = 5609.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.116600 restraints weight = 4897.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.117963 restraints weight = 4471.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.118386 restraints weight = 4188.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5036  Z= 0.131
  Angle     :  0.551   6.645   6832  Z= 0.271
  Chirality :  0.035   0.176    728
  Planarity :  0.004   0.035    896
  Dihedral  :  3.269  14.641    692
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 16.92 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.64 (0.34), residues: 608
  helix:  3.12 (0.26), residues: 356
  sheet:  0.76 (0.45), residues: 96
  loop : -1.01 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 152 
 TYR   0.003   0.001   TYR A 153 
 PHE   0.005   0.001   PHE D  25 
 TRP   0.003   0.001   TRP C  21 
 HIS   0.003   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 5036)
  covalent geometry    : angle       0.55135 ( 6832)
  hydrogen bonds       : bond        0.03584 (  336)
  hydrogen bonds       : angle       4.11295 (  966)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A   17 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8482 (pp)
REVERT: B   15 GLN cc_start: 0.8679 (tp40) cc_final: 0.8355 (mt0)
REVERT: B   17 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8541 (pp)
REVERT: B   93 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8186 (mt-10)
REVERT: C   17 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8504 (pp)
REVERT: C  152 ARG cc_start: 0.8744 (tpp80) cc_final: 0.8130 (mtt90)
REVERT: D   17 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8431 (pp)
REVERT: D   93 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8219 (mt-10)
  outliers start: 31
  outliers final: 17
  residues processed: 131
  average time/residue: 0.0687
  time to fit residues: 11.8264
Evaluate side-chains
  129 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain C residue    3 ASP
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue    3 ASP
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  30 ASN
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.154587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.110312 restraints weight = 6819.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.112564 restraints weight = 5642.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.114353 restraints weight = 4987.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.115259 restraints weight = 4579.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.115662 restraints weight = 4338.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5036  Z= 0.143
  Angle     :  0.559   7.175   6832  Z= 0.273
  Chirality :  0.034   0.176    728
  Planarity :  0.004   0.035    896
  Dihedral  :  3.264  14.540    692
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 17.31 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.70 (0.33), residues: 608
  helix:  3.13 (0.27), residues: 356
  sheet:  0.78 (0.43), residues: 96
  loop : -0.90 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 152 
 TYR   0.004   0.001   TYR A  95 
 PHE   0.013   0.002   PHE D  78 
 TRP   0.007   0.001   TRP D  80 
 HIS   0.003   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 5036)
  covalent geometry    : angle       0.55918 ( 6832)
  hydrogen bonds       : bond        0.03764 (  336)
  hydrogen bonds       : angle       4.12952 (  966)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A   17 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8470 (pp)
REVERT: B   15 GLN cc_start: 0.8635 (tp40) cc_final: 0.8348 (mt0)
REVERT: B   17 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8561 (pp)
REVERT: B   93 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8112 (mt-10)
REVERT: C   17 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8478 (pp)
REVERT: C   93 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8100 (mt-10)
REVERT: D   17 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8425 (pp)
REVERT: D   93 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8220 (mt-10)
  outliers start: 32
  outliers final: 17
  residues processed: 136
  average time/residue: 0.0705
  time to fit residues: 12.5611
Evaluate side-chains
  136 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain C residue    3 ASP
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue    3 ASP
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 17 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 6 optimal weight:    6.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 HIS
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.156578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.113005 restraints weight = 6756.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.115152 restraints weight = 5544.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.117279 restraints weight = 4873.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.118272 restraints weight = 4439.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.119300 restraints weight = 4178.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5036  Z= 0.133
  Angle     :  0.573   7.979   6832  Z= 0.278
  Chirality :  0.034   0.174    728
  Planarity :  0.004   0.036    896
  Dihedral  :  3.256  14.471    692
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 17.50 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.73 (0.33), residues: 608
  helix:  3.17 (0.27), residues: 356
  sheet:  0.78 (0.43), residues: 96
  loop : -0.91 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 152 
 TYR   0.004   0.001   TYR A  95 
 PHE   0.010   0.001   PHE D  78 
 TRP   0.005   0.001   TRP D  80 
 HIS   0.003   0.001   HIS D  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 5036)
  covalent geometry    : angle       0.57253 ( 6832)
  hydrogen bonds       : bond        0.03582 (  336)
  hydrogen bonds       : angle       4.09607 (  966)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A   17 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8480 (pp)
REVERT: B   15 GLN cc_start: 0.8600 (tp40) cc_final: 0.8316 (mt0)
REVERT: B   17 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8515 (pp)
REVERT: B   93 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8110 (mt-10)
REVERT: C   17 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8490 (pp)
REVERT: C   93 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8110 (mt-10)
REVERT: C  152 ARG cc_start: 0.8721 (tpp80) cc_final: 0.8202 (mtt90)
REVERT: D   17 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8424 (pp)
  outliers start: 30
  outliers final: 16
  residues processed: 135
  average time/residue: 0.0706
  time to fit residues: 12.5180
Evaluate side-chains
  133 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain C residue    3 ASP
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0980
   chunk 59 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0010
   chunk 0 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0010
   chunk 6 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 41 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.3392

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

Flipped N/Q/H residues before XYZ refinement:
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.159267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.115913 restraints weight = 6703.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.118336 restraints weight = 5477.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.120166 restraints weight = 4790.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 16)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.120990 restraints weight = 4375.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.122302 restraints weight = 4143.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5036  Z= 0.115
  Angle     :  0.587   7.943   6832  Z= 0.287
  Chirality :  0.034   0.174    728
  Planarity :  0.004   0.036    896
  Dihedral  :  3.234  13.755    692
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 18.08 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.82 (0.34), residues: 608
  helix:  3.22 (0.27), residues: 356
  sheet:  0.80 (0.43), residues: 96
  loop : -0.79 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 152 
 TYR   0.006   0.001   TYR D  56 
 PHE   0.011   0.001   PHE D  78 
 TRP   0.012   0.001   TRP D  80 
 HIS   0.004   0.001   HIS D  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 5036)
  covalent geometry    : angle       0.58682 ( 6832)
  hydrogen bonds       : bond        0.03037 (  336)
  hydrogen bonds       : angle       3.91990 (  966)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A   17 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8433 (pp)
REVERT: B   15 GLN cc_start: 0.8549 (tp40) cc_final: 0.8334 (mt0)
REVERT: B   17 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8442 (pp)
REVERT: B   93 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8111 (mt-10)
REVERT: C   17 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8455 (pp)
REVERT: C   93 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8115 (mt-10)
REVERT: D   17 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8364 (pp)
REVERT: D   93 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8198 (mt-10)
  outliers start: 26
  outliers final: 15
  residues processed: 129
  average time/residue: 0.0685
  time to fit residues: 11.6928
Evaluate side-chains
  135 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 58 optimal weight:    7.9990
   chunk 21 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0570
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 HIS
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.156660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.113037 restraints weight = 6901.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.115420 restraints weight = 5675.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.117260 restraints weight = 4986.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.117845 restraints weight = 4565.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.119101 restraints weight = 4370.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.3143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5036  Z= 0.133
  Angle     :  0.599   8.609   6832  Z= 0.291
  Chirality :  0.034   0.172    728
  Planarity :  0.004   0.036    896
  Dihedral  :  3.198  13.973    692
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 18.85 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.81 (0.33), residues: 608
  helix:  3.22 (0.27), residues: 356
  sheet:  0.82 (0.42), residues: 96
  loop : -0.84 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 152 
 TYR   0.009   0.001   TYR B 123 
 PHE   0.005   0.001   PHE C  78 
 TRP   0.003   0.001   TRP D 111 
 HIS   0.003   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 5036)
  covalent geometry    : angle       0.59938 ( 6832)
  hydrogen bonds       : bond        0.03478 (  336)
  hydrogen bonds       : angle       3.96509 (  966)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A   17 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8464 (pp)
REVERT: B   15 GLN cc_start: 0.8684 (tp40) cc_final: 0.8314 (mt0)
REVERT: B   17 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8486 (pp)
REVERT: B   93 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8071 (mt-10)
REVERT: C   17 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8496 (pp)
REVERT: C   89 GLU cc_start: 0.8084 (pm20) cc_final: 0.7837 (pm20)
REVERT: C   93 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8104 (mt-10)
REVERT: C  146 GLU cc_start: 0.7407 (mp0) cc_final: 0.7194 (mp0)
REVERT: D   17 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8393 (pp)
  outliers start: 23
  outliers final: 13
  residues processed: 130
  average time/residue: 0.0706
  time to fit residues: 11.9707
Evaluate side-chains
  131 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 13 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 25 optimal weight:    0.2980
   chunk 49 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.155642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.112211 restraints weight = 6906.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.114512 restraints weight = 5689.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.116255 restraints weight = 5017.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.116794 restraints weight = 4596.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.117672 restraints weight = 4412.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5036  Z= 0.153
  Angle     :  0.617   8.452   6832  Z= 0.302
  Chirality :  0.035   0.170    728
  Planarity :  0.004   0.036    896
  Dihedral  :  3.238  14.202    692
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 18.65 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.78 (0.34), residues: 608
  helix:  3.20 (0.27), residues: 356
  sheet:  0.84 (0.42), residues: 96
  loop : -0.90 (0.45), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 152 
 TYR   0.020   0.001   TYR B 123 
 PHE   0.006   0.001   PHE D  25 
 TRP   0.010   0.001   TRP D  80 
 HIS   0.006   0.001   HIS D  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 5036)
  covalent geometry    : angle       0.61727 ( 6832)
  hydrogen bonds       : bond        0.03775 (  336)
  hydrogen bonds       : angle       4.04267 (  966)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 919.42 seconds
wall clock time: 16 minutes 34.96 seconds (994.96 seconds total)