Starting phenix.real_space_refine
on Fri May  9 19:55:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5u_37304/05_2025/8w5u_37304.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5u_37304/05_2025/8w5u_37304.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w5u_37304/05_2025/8w5u_37304.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5u_37304/05_2025/8w5u_37304.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5u_37304/05_2025/8w5u_37304.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5u_37304/05_2025/8w5u_37304.cif"
  }
  resolution = 3.9
  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=   0.010 sd=   0.087
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      11      5.16       5
     C    2261      2.51       5
     N     604      2.21       5
     O     712      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3588
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "L"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 818
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 873
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 3, 'TRANS': 109}
    Chain: "C"
      Number of atoms: 938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 938
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 8, 'TRANS': 117}
          Chain breaks: 1
    Chain: "c"
      Number of atoms: 959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 959
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 8, 'TRANS': 119}
          Chain breaks: 1
  Time building chain proxies: 2.94, per 1000 atoms: 0.82
  Number of scatterers: 3588
  At special positions: 0
  Unit cell: (96.36, 66, 79.2, 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      11     16.00
     O     712      8.00
     N     604      7.00
     C    2261      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 462.1 milliseconds
  

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  876

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 5 sheets defined
      11.6% alpha, 31.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'C' and resid 101 through 116
      removed outlier: 3.613A  pdb=" N   ARG C 105 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 127
    Processing helix  chain 'c' and resid 41 through 45
      removed outlier: 4.066A  pdb=" N   GLU c  45 " --> pdb=" O   PRO c  42 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 102 through 116
    Processing helix  chain 'c' and resid 118 through 126
      removed outlier: 4.099A  pdb=" N   ASP c 123 " --> pdb=" O   PRO c 119 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 7 through 9
    Processing sheet with id=AA2, first strand: chain 'L' and resid 62 through 63
      removed outlier: 6.407A  pdb=" N   TRP L  44 " --> pdb=" O   LEU L  56 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   TYR L  58 " --> pdb=" O   LEU L  42 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   LEU L  42 " --> pdb=" O   TYR L  58 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 9
      removed outlier: 3.724A  pdb=" N   GLN H   6 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER H  28 " --> pdb=" O   GLN H   6 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   THR H  81 " --> pdb=" O   ASP H  76 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASP H  76 " --> pdb=" O   THR H  81 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TYR H  83 " --> pdb=" O   THR H  74 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   THR H  74 " --> pdb=" O   TYR H  83 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR H  72 " --> pdb=" O   ASP H  85 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 62 through 63
      removed outlier: 4.025A  pdb=" N   ILE H  62 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR H  53 " --> pdb=" O   ILE H  62 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU H  37 " --> pdb=" O   PHE H  54 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   SER H 110 " --> pdb=" O   THR H 101 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 11
      removed outlier: 4.137A  pdb=" N   PHE C  10 " --> pdb=" O   GLN C  17 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   GLN C  17 " --> pdb=" O   PHE C  10 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   SER C  34 " --> pdb=" O   ARG C  24 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   VAL C  26 " --> pdb=" O   VAL C  32 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   VAL C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   ARG C  86 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   CYS C  74 " --> pdb=" O   VAL C  84 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   VAL C  84 " --> pdb=" O   CYS C  74 " (cutoff:3.500A)
      removed outlier: 5.561A  pdb=" N   VAL c  84 " --> pdb=" O   CYS c  74 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   CYS c  74 " --> pdb=" O   VAL c  84 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   ARG c  86 " --> pdb=" O   THR c  72 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   VAL c  32 " --> pdb=" O   VAL c  26 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   VAL c  26 " --> pdb=" O   VAL c  32 " (cutoff:3.500A)
      removed outlier: 5.625A  pdb=" N   SER c  34 " --> pdb=" O   ARG c  24 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   GLN c  17 " --> pdb=" O   PHE c  10 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   PHE c  10 " --> pdb=" O   GLN c  17 " (cutoff:3.500A)

    125 hydrogen bonds defined for protein.
    336 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: 0.88

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1164
        1.34 -     1.46: 812
        1.46 -     1.57: 1670
        1.57 -     1.69: 0
        1.69 -     1.81: 14
  Bond restraints: 3660
  Sorted by residual:
  bond pdb=" CA  PHE H  54 "
       pdb=" CB  PHE H  54 "
    ideal  model  delta    sigma   weight residual
    1.526  1.507  0.019 1.70e-02 3.46e+03 1.21e+00
  bond pdb=" C   SER L  10 "
       pdb=" N   PRO L  11 "
    ideal  model  delta    sigma   weight residual
    1.332  1.345 -0.013 1.33e-02 5.65e+03 9.98e-01
  bond pdb=" CG  LEU L  42 "
       pdb=" CD1 LEU L  42 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.25e-01
  bond pdb=" CG  LEU C 116 "
       pdb=" CD2 LEU C 116 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.39e-01
  bond pdb=" CB  VAL C  52 "
       pdb=" CG2 VAL C  52 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 7.99e-01
  ... (remaining 3655 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 4770
        1.58 -     3.15: 180
        3.15 -     4.73: 24
        4.73 -     6.30: 4
        6.30 -     7.88: 1
  Bond angle restraints: 4979
  Sorted by residual:
  angle pdb=" CA  VAL C  41 "
        pdb=" C   VAL C  41 "
        pdb=" N   PRO C  42 "
      ideal   model   delta    sigma   weight residual
     116.57  119.75   -3.18 9.80e-01 1.04e+00 1.05e+01
  angle pdb=" C   VAL C  41 "
        pdb=" CA  VAL C  41 "
        pdb=" CB  VAL C  41 "
      ideal   model   delta    sigma   weight residual
     109.33  112.23   -2.90 9.80e-01 1.04e+00 8.73e+00
  angle pdb=" C   TRP L  59 "
        pdb=" N   ALA L  60 "
        pdb=" CA  ALA L  60 "
      ideal   model   delta    sigma   weight residual
     121.54  126.30   -4.76 1.91e+00 2.74e-01 6.22e+00
  angle pdb=" CA  LEU H  48 "
        pdb=" CB  LEU H  48 "
        pdb=" CG  LEU H  48 "
      ideal   model   delta    sigma   weight residual
     116.30  124.18   -7.88 3.50e+00 8.16e-02 5.07e+00
  angle pdb=" C   THR c  18 "
        pdb=" N   LEU c  19 "
        pdb=" CA  LEU c  19 "
      ideal   model   delta    sigma   weight residual
     122.73  119.32    3.41 1.62e+00 3.81e-01 4.42e+00
  ... (remaining 4974 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.29: 1937
       16.29 -    32.57: 200
       32.57 -    48.85: 35
       48.85 -    65.14: 7
       65.14 -    81.42: 5
  Dihedral angle restraints: 2184
    sinusoidal: 821
      harmonic: 1363
  Sorted by residual:
  dihedral pdb=" CA  SER H  10 "
           pdb=" C   SER H  10 "
           pdb=" N   GLY H  11 "
           pdb=" CA  GLY H  11 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.90   23.10     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  GLN L  98 "
           pdb=" C   GLN L  98 "
           pdb=" N   GLN L  99 "
           pdb=" CA  GLN L  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.54   21.46     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  PRO L  11 "
           pdb=" C   PRO L  11 "
           pdb=" N   SER L  12 "
           pdb=" CA  SER L  12 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.20  -19.80     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 2181 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 338
       0.031 -    0.061: 137
       0.061 -    0.092: 60
       0.092 -    0.122: 34
       0.122 -    0.153: 5
  Chirality restraints: 574
  Sorted by residual:
  chirality pdb=" CB  THR H  90 "
            pdb=" CA  THR H  90 "
            pdb=" OG1 THR H  90 "
            pdb=" CG2 THR H  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.85e-01
  chirality pdb=" CA  ILE L  57 "
            pdb=" N   ILE L  57 "
            pdb=" C   ILE L  57 "
            pdb=" CB  ILE L  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.31e-01
  chirality pdb=" CA  VAL c  48 "
            pdb=" N   VAL c  48 "
            pdb=" C   VAL c  48 "
            pdb=" CB  VAL c  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.20e-01
  ... (remaining 571 not shown)

  Planarity restraints: 641
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  39 "   -0.010 2.00e-02 2.50e+03   9.51e-03 2.26e+00
        pdb=" CG  TRP H  39 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  39 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  39 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  39 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  39 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  39 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  39 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  39 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  39 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 129 "    0.023 5.00e-02 4.00e+02   3.43e-02 1.88e+00
        pdb=" N   PRO C 130 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO C 130 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C 130 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  86 "   -0.105 9.50e-02 1.11e+02   4.74e-02 1.64e+00
        pdb=" NE  ARG C  86 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  86 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  86 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  86 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 638 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 145
        2.70 -     3.25: 3625
        3.25 -     3.80: 5487
        3.80 -     4.35: 6422
        4.35 -     4.90: 11057
  Nonbonded interactions: 26736
  Sorted by model distance:
  nonbonded pdb=" O   LEU c   8 "
            pdb=" OG1 THR c  18 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" OG  SER L  76 "
            pdb=" O   ASP L  79 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OG  SER c  79 "
            pdb=" OD1 ASP c  81 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   SER L  85 "
            pdb=" NZ  LYS L  88 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" ND2 ASN c  27 "
            pdb=" OD1 ASN c  30 "
     model   vdw
     2.242 3.120
  ... (remaining 26731 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = (chain 'c' and (resid 1 through 55 or resid 61 through 131))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.230
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.700
  Find NCS groups from input model:        0.090
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
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      :  0.005   0.034   3661  Z= 0.235
  Angle     :  0.696   7.879   4981  Z= 0.370
  Chirality :  0.045   0.153    574
  Planarity :  0.004   0.047    641
  Dihedral  : 13.917  81.424   1305
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  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: -2.34 (0.38), residues: 461
  helix: -0.25 (0.74), residues: 45
  sheet: -0.80 (0.39), residues: 179
  loop : -2.47 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP H  39 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.007   0.001   PHE c  94 
 TYR   0.017   0.001   TYR L 100 
 ARG   0.009   0.001   ARG C  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18328 (  125)
  hydrogen bonds       : angle       7.38679 (  336)
  SS BOND              : bond        0.00285 (    1)
  SS BOND              : angle       0.16395 (    2)
  covalent geometry    : bond        0.00525 ( 3660)
  covalent geometry    : angle       0.69592 ( 4979)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
REVERT: L  100 TYR cc_start: 0.9278 (p90) cc_final: 0.8494 (p90)
REVERT: H    7 LEU cc_start: 0.9149 (pt) cc_final: 0.8446 (pt)
REVERT: H   54 PHE cc_start: 0.8914 (t80) cc_final: 0.8655 (t80)
REVERT: H   76 ASP cc_start: 0.8764 (p0) cc_final: 0.8430 (p0)
REVERT: H  113 GLN cc_start: 0.8262 (pm20) cc_final: 0.7923 (pm20)
REVERT: C   13 LYS cc_start: 0.8324 (mttt) cc_final: 0.8045 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1866
  time to fit residues: 26.8063
Evaluate side-chains
  108 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
L  98 GLN
H   6 GLN
C  69 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.101113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.076919 restraints weight = 6952.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.078984 restraints weight = 4279.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.080453 restraints weight = 3129.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3661  Z= 0.146
  Angle     :  0.652   8.019   4981  Z= 0.332
  Chirality :  0.045   0.158    574
  Planarity :  0.004   0.036    641
  Dihedral  :  4.844  20.147    501
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.61 %
    Favored  : 83.88 %
  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: -2.12 (0.38), residues: 461
  helix:  0.32 (0.77), residues: 45
  sheet: -0.63 (0.40), residues: 187
  loop : -2.51 (0.36), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  39 
 HIS   0.002   0.001   HIS H  44 
 PHE   0.010   0.001   PHE L  80 
 TYR   0.017   0.001   TYR H  30 
 ARG   0.004   0.000   ARG C  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03920 (  125)
  hydrogen bonds       : angle       5.61365 (  336)
  SS BOND              : bond        0.00453 (    1)
  SS BOND              : angle       0.45823 (    2)
  covalent geometry    : bond        0.00333 ( 3660)
  covalent geometry    : angle       0.65207 ( 4979)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 123
  time to evaluate  : 0.433 
Fit side-chains
REVERT: L   30 GLN cc_start: 0.8569 (tm-30) cc_final: 0.7990 (tm-30)
REVERT: L  100 TYR cc_start: 0.9291 (p90) cc_final: 0.8259 (p90)
REVERT: H   84 MET cc_start: 0.8520 (ptt) cc_final: 0.8062 (ptt)
REVERT: H  113 GLN cc_start: 0.8270 (pm20) cc_final: 0.8011 (pm20)
REVERT: C   14 ASP cc_start: 0.8431 (p0) cc_final: 0.8086 (p0)
REVERT: C   46 LYS cc_start: 0.9201 (mppt) cc_final: 0.9000 (mptt)
REVERT: C  123 ASP cc_start: 0.8244 (t0) cc_final: 0.8002 (t70)
REVERT: c   46 LYS cc_start: 0.9101 (mttm) cc_final: 0.8876 (mtpp)
REVERT: c  103 GLU cc_start: 0.8347 (pp20) cc_final: 0.8137 (pp20)
  outliers start: 6
  outliers final: 5
  residues processed: 124
  average time/residue: 0.1854
  time to fit residues: 27.1212
Evaluate side-chains
  114 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   25 THR
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain C residue   74 CYS
Chi-restraints excluded: chain c residue  118 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 21 optimal weight:    0.2980
   chunk 36 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 3 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
L  98 GLN
C  69 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.103207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.079086 restraints weight = 6840.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.081216 restraints weight = 4178.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.082654 restraints weight = 3013.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3661  Z= 0.122
  Angle     :  0.629   7.770   4981  Z= 0.321
  Chirality :  0.043   0.152    574
  Planarity :  0.004   0.029    641
  Dihedral  :  4.761  20.774    501
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.12 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.38), residues: 461
  helix:  0.28 (0.77), residues: 47
  sheet: -0.25 (0.40), residues: 182
  loop : -2.61 (0.35), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  39 
 HIS   0.001   0.000   HIS H  44 
 PHE   0.008   0.001   PHE L 106 
 TYR   0.021   0.001   TYR H  53 
 ARG   0.002   0.000   ARG C  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03432 (  125)
  hydrogen bonds       : angle       5.25340 (  336)
  SS BOND              : bond        0.00499 (    1)
  SS BOND              : angle       1.15757 (    2)
  covalent geometry    : bond        0.00280 ( 3660)
  covalent geometry    : angle       0.62886 ( 4979)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 124
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: L   30 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8021 (tm-30)
REVERT: L  100 TYR cc_start: 0.9241 (p90) cc_final: 0.8167 (p90)
REVERT: H   30 TYR cc_start: 0.7518 (p90) cc_final: 0.7237 (p90)
REVERT: H   84 MET cc_start: 0.8355 (ptt) cc_final: 0.8010 (ptt)
REVERT: H   89 LEU cc_start: 0.8640 (mt) cc_final: 0.8007 (pp)
REVERT: H  104 ASP cc_start: 0.7988 (m-30) cc_final: 0.7602 (m-30)
REVERT: H  113 GLN cc_start: 0.8410 (pm20) cc_final: 0.8193 (pm20)
REVERT: C   14 ASP cc_start: 0.8515 (p0) cc_final: 0.8135 (p0)
REVERT: C   46 LYS cc_start: 0.9205 (mppt) cc_final: 0.8989 (mptt)
REVERT: C   69 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7845 (mm110)
REVERT: C  123 ASP cc_start: 0.8124 (t0) cc_final: 0.7873 (t70)
REVERT: c  103 GLU cc_start: 0.8257 (pp20) cc_final: 0.8044 (pp20)
  outliers start: 7
  outliers final: 5
  residues processed: 127
  average time/residue: 0.1873
  time to fit residues: 28.1331
Evaluate side-chains
  119 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain H residue   83 TYR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain C residue   74 CYS
Chi-restraints excluded: chain c residue  118 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0870
   chunk 9 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 40 optimal weight:   20.0000
   chunk 20 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 39 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9990
   overall best weight:    1.4764

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

Flipped N/Q/H residues before XYZ refinement:
L   9 GLN
L  48 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.103717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.079845 restraints weight = 6921.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.081889 restraints weight = 4308.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.083322 restraints weight = 3142.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3661  Z= 0.116
  Angle     :  0.635   7.357   4981  Z= 0.322
  Chirality :  0.043   0.140    574
  Planarity :  0.003   0.028    641
  Dihedral  :  4.634  20.339    501
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.39 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.38), residues: 461
  helix:  0.36 (0.77), residues: 48
  sheet: -0.19 (0.41), residues: 183
  loop : -2.49 (0.36), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  39 
 HIS   0.001   0.000   HIS H  44 
 PHE   0.008   0.001   PHE L 106 
 TYR   0.020   0.001   TYR H  53 
 ARG   0.003   0.000   ARG C  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03210 (  125)
  hydrogen bonds       : angle       5.10696 (  336)
  SS BOND              : bond        0.00067 (    1)
  SS BOND              : angle       0.77927 (    2)
  covalent geometry    : bond        0.00269 ( 3660)
  covalent geometry    : angle       0.63472 ( 4979)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.384 
Fit side-chains
REVERT: L   30 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8021 (tm-30)
REVERT: H   39 TRP cc_start: 0.9179 (m100) cc_final: 0.8973 (m100)
REVERT: H   89 LEU cc_start: 0.8579 (mt) cc_final: 0.8101 (pp)
REVERT: H  104 ASP cc_start: 0.7912 (m-30) cc_final: 0.7530 (m-30)
REVERT: C   14 ASP cc_start: 0.8548 (p0) cc_final: 0.8180 (p0)
REVERT: C   46 LYS cc_start: 0.9183 (mppt) cc_final: 0.8977 (mptt)
REVERT: C   95 SER cc_start: 0.8661 (t) cc_final: 0.8426 (t)
  outliers start: 11
  outliers final: 7
  residues processed: 129
  average time/residue: 0.1721
  time to fit residues: 26.3719
Evaluate side-chains
  121 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   25 THR
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue   97 CYS
Chi-restraints excluded: chain H residue   83 TYR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain C residue   74 CYS
Chi-restraints excluded: chain c residue  118 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 43 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0060
   chunk 36 optimal weight:    4.9990
   overall best weight:    2.8002

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

Flipped N/Q/H residues before XYZ refinement:
C  69 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.102641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.078692 restraints weight = 6987.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.080788 restraints weight = 4250.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.082246 restraints weight = 3058.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3661  Z= 0.161
  Angle     :  0.655   6.648   4981  Z= 0.336
  Chirality :  0.043   0.149    574
  Planarity :  0.004   0.029    641
  Dihedral  :  4.781  20.462    501
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.90 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.38), residues: 461
  helix:  0.55 (0.74), residues: 49
  sheet: -0.27 (0.40), residues: 182
  loop : -2.41 (0.37), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP L  44 
 HIS   0.002   0.001   HIS H  44 
 PHE   0.007   0.001   PHE L  80 
 TYR   0.021   0.001   TYR H  53 
 ARG   0.004   0.001   ARG C  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03305 (  125)
  hydrogen bonds       : angle       5.11163 (  336)
  SS BOND              : bond        0.00378 (    1)
  SS BOND              : angle       0.65795 (    2)
  covalent geometry    : bond        0.00375 ( 3660)
  covalent geometry    : angle       0.65526 ( 4979)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.444 
Fit side-chains
REVERT: L    7 MET cc_start: 0.8891 (mmm) cc_final: 0.8530 (mmm)
REVERT: L   30 GLN cc_start: 0.8517 (tm-30) cc_final: 0.7982 (tm-30)
REVERT: L  100 TYR cc_start: 0.9177 (p90) cc_final: 0.8799 (p90)
REVERT: H   39 TRP cc_start: 0.9215 (m100) cc_final: 0.8668 (m100)
REVERT: H   73 LEU cc_start: 0.8875 (mm) cc_final: 0.8553 (mm)
REVERT: H   84 MET cc_start: 0.8551 (ptt) cc_final: 0.7955 (ptp)
REVERT: H   89 LEU cc_start: 0.8621 (mt) cc_final: 0.8095 (pp)
REVERT: H  104 ASP cc_start: 0.7970 (m-30) cc_final: 0.7618 (m-30)
REVERT: C   14 ASP cc_start: 0.8588 (p0) cc_final: 0.8254 (p0)
REVERT: C   46 LYS cc_start: 0.9224 (mppt) cc_final: 0.8999 (mptt)
REVERT: C   69 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7854 (mm110)
REVERT: C   95 SER cc_start: 0.8682 (t) cc_final: 0.8450 (t)
REVERT: C  123 ASP cc_start: 0.8109 (t0) cc_final: 0.7898 (t70)
  outliers start: 14
  outliers final: 10
  residues processed: 133
  average time/residue: 0.1799
  time to fit residues: 28.3602
Evaluate side-chains
  131 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   25 THR
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue   97 CYS
Chi-restraints excluded: chain H residue   23 LEU
Chi-restraints excluded: chain H residue   83 TYR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   74 CYS
Chi-restraints excluded: chain c residue  118 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 1 optimal weight:    0.0070
   chunk 25 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   chunk 22 optimal weight:    0.2980
   chunk 9 optimal weight:    5.9990
   overall best weight:    2.4602

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.103404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.078825 restraints weight = 6992.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.080864 restraints weight = 4295.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.082328 restraints weight = 3135.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3661  Z= 0.150
  Angle     :  0.647   6.466   4981  Z= 0.332
  Chirality :  0.043   0.146    574
  Planarity :  0.004   0.028    641
  Dihedral  :  4.745  20.601    501
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 19.14 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.38), residues: 461
  helix:  0.50 (0.74), residues: 47
  sheet: -0.28 (0.40), residues: 183
  loop : -2.29 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP L  44 
 HIS   0.001   0.000   HIS H  44 
 PHE   0.008   0.001   PHE L 106 
 TYR   0.014   0.001   TYR H  53 
 ARG   0.005   0.001   ARG C  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03207 (  125)
  hydrogen bonds       : angle       4.98602 (  336)
  SS BOND              : bond        0.00597 (    1)
  SS BOND              : angle       1.06000 (    2)
  covalent geometry    : bond        0.00350 ( 3660)
  covalent geometry    : angle       0.64631 ( 4979)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.399 
Fit side-chains
REVERT: L    7 MET cc_start: 0.8931 (mmm) cc_final: 0.8663 (mmm)
REVERT: L   30 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8004 (tm-30)
REVERT: L   56 LEU cc_start: 0.9355 (mm) cc_final: 0.9132 (mp)
REVERT: L  100 TYR cc_start: 0.9199 (p90) cc_final: 0.8798 (p90)
REVERT: H   39 TRP cc_start: 0.9247 (m100) cc_final: 0.8802 (m100)
REVERT: H   73 LEU cc_start: 0.8866 (mm) cc_final: 0.8577 (mm)
REVERT: H   84 MET cc_start: 0.8545 (ptt) cc_final: 0.8278 (pmm)
REVERT: H   89 LEU cc_start: 0.8626 (mt) cc_final: 0.8040 (pp)
REVERT: H  104 ASP cc_start: 0.8069 (m-30) cc_final: 0.7723 (m-30)
REVERT: C   14 ASP cc_start: 0.8597 (p0) cc_final: 0.8241 (p0)
REVERT: C   46 LYS cc_start: 0.9251 (mppt) cc_final: 0.8982 (mptt)
REVERT: C   69 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7883 (mm110)
REVERT: C   95 SER cc_start: 0.8684 (t) cc_final: 0.8445 (t)
REVERT: C  123 ASP cc_start: 0.8168 (t0) cc_final: 0.7920 (t70)
  outliers start: 17
  outliers final: 12
  residues processed: 132
  average time/residue: 0.1674
  time to fit residues: 26.2388
Evaluate side-chains
  130 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   25 THR
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue   97 CYS
Chi-restraints excluded: chain H residue   23 LEU
Chi-restraints excluded: chain H residue   83 TYR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   74 CYS
Chi-restraints excluded: chain c residue   46 LYS
Chi-restraints excluded: chain c residue  118 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0870
   chunk 40 optimal weight:   20.0000
   chunk 13 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    1.5564

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.104157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.080054 restraints weight = 6960.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.082075 restraints weight = 4222.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.083542 restraints weight = 3064.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3661  Z= 0.125
  Angle     :  0.651   6.391   4981  Z= 0.334
  Chirality :  0.043   0.144    574
  Planarity :  0.004   0.030    641
  Dihedral  :  4.641  19.841    501
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 20.91 %
    Favored  : 76.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.38), residues: 461
  helix:  0.65 (0.73), residues: 49
  sheet: -0.20 (0.40), residues: 183
  loop : -2.27 (0.37), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP L  44 
 HIS   0.001   0.000   HIS H  44 
 PHE   0.007   0.001   PHE L 106 
 TYR   0.022   0.001   TYR H  53 
 ARG   0.004   0.001   ARG C  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03018 (  125)
  hydrogen bonds       : angle       4.95480 (  336)
  SS BOND              : bond        0.00405 (    1)
  SS BOND              : angle       1.03062 (    2)
  covalent geometry    : bond        0.00296 ( 3660)
  covalent geometry    : angle       0.65069 ( 4979)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 0.431 
Fit side-chains
REVERT: L    7 MET cc_start: 0.8939 (mmm) cc_final: 0.8732 (mmm)
REVERT: L   30 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8082 (tm-30)
REVERT: L  100 TYR cc_start: 0.9142 (p90) cc_final: 0.8756 (p90)
REVERT: H   39 TRP cc_start: 0.9186 (m100) cc_final: 0.8785 (m100)
REVERT: H   73 LEU cc_start: 0.8814 (mm) cc_final: 0.8532 (mm)
REVERT: H   88 ASN cc_start: 0.8488 (t0) cc_final: 0.8277 (t0)
REVERT: H   89 LEU cc_start: 0.8633 (mt) cc_final: 0.8221 (pp)
REVERT: H  104 ASP cc_start: 0.7973 (m-30) cc_final: 0.7626 (m-30)
REVERT: C   14 ASP cc_start: 0.8523 (p0) cc_final: 0.8162 (p0)
REVERT: C   46 LYS cc_start: 0.9218 (mppt) cc_final: 0.8987 (mptt)
REVERT: C   95 SER cc_start: 0.8659 (t) cc_final: 0.8425 (t)
  outliers start: 12
  outliers final: 9
  residues processed: 132
  average time/residue: 0.1785
  time to fit residues: 27.9026
Evaluate side-chains
  130 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue   97 CYS
Chi-restraints excluded: chain H residue   83 TYR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   74 CYS
Chi-restraints excluded: chain c residue   46 LYS
Chi-restraints excluded: chain c residue  118 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 26 optimal weight:    0.0870
   chunk 23 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 4 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 19 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:    2.4164

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

Flipped N/Q/H residues before XYZ refinement:
C  69 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.103812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.079462 restraints weight = 6953.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.081590 restraints weight = 4185.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.082973 restraints weight = 2994.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3661  Z= 0.156
  Angle     :  0.693   7.052   4981  Z= 0.358
  Chirality :  0.043   0.156    574
  Planarity :  0.004   0.034    641
  Dihedral  :  4.783  20.970    501
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 21.91 %
    Favored  : 74.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.39), residues: 461
  helix:  0.81 (0.73), residues: 49
  sheet: -0.16 (0.40), residues: 183
  loop : -2.22 (0.37), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  39 
 HIS   0.001   0.000   HIS H  44 
 PHE   0.007   0.001   PHE L 106 
 TYR   0.021   0.001   TYR H  53 
 ARG   0.006   0.001   ARG C  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03261 (  125)
  hydrogen bonds       : angle       5.01407 (  336)
  SS BOND              : bond        0.00614 (    1)
  SS BOND              : angle       0.87270 (    2)
  covalent geometry    : bond        0.00367 ( 3660)
  covalent geometry    : angle       0.69339 ( 4979)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
REVERT: L  100 TYR cc_start: 0.9172 (p90) cc_final: 0.8790 (p90)
REVERT: H    9 GLN cc_start: 0.8482 (tp40) cc_final: 0.7705 (tt0)
REVERT: H   84 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7962 (pmm)
REVERT: H   89 LEU cc_start: 0.8603 (mt) cc_final: 0.8130 (pp)
REVERT: H  104 ASP cc_start: 0.7990 (m-30) cc_final: 0.7635 (m-30)
REVERT: C   14 ASP cc_start: 0.8524 (p0) cc_final: 0.8163 (p0)
REVERT: C   46 LYS cc_start: 0.9210 (mppt) cc_final: 0.8960 (mptt)
REVERT: C   69 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7894 (mm110)
REVERT: C   95 SER cc_start: 0.8676 (t) cc_final: 0.8436 (t)
REVERT: C  123 ASP cc_start: 0.8173 (t0) cc_final: 0.7964 (t70)
  outliers start: 14
  outliers final: 11
  residues processed: 135
  average time/residue: 0.1784
  time to fit residues: 28.5977
Evaluate side-chains
  132 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   25 THR
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue   97 CYS
Chi-restraints excluded: chain H residue   83 TYR
Chi-restraints excluded: chain H residue   84 MET
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   74 CYS
Chi-restraints excluded: chain c residue   46 LYS
Chi-restraints excluded: chain c residue  118 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 2 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 13 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.102973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.079217 restraints weight = 6968.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.081198 restraints weight = 4259.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.082644 restraints weight = 3105.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3661  Z= 0.163
  Angle     :  0.741  11.391   4981  Z= 0.375
  Chirality :  0.044   0.158    574
  Planarity :  0.004   0.034    641
  Dihedral  :  4.871  21.325    501
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 23.17 %
    Favored  : 73.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.39), residues: 461
  helix:  0.66 (0.72), residues: 49
  sheet: -0.06 (0.41), residues: 178
  loop : -2.27 (0.37), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP H  39 
 HIS   0.001   0.001   HIS H  44 
 PHE   0.007   0.001   PHE L 106 
 TYR   0.022   0.001   TYR H  53 
 ARG   0.007   0.001   ARG C  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03306 (  125)
  hydrogen bonds       : angle       5.07348 (  336)
  SS BOND              : bond        0.00896 (    1)
  SS BOND              : angle       1.68477 (    2)
  covalent geometry    : bond        0.00384 ( 3660)
  covalent geometry    : angle       0.74000 ( 4979)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
REVERT: L  100 TYR cc_start: 0.9126 (p90) cc_final: 0.8803 (p90)
REVERT: H   84 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8320 (pmm)
REVERT: H   88 ASN cc_start: 0.8462 (t0) cc_final: 0.7667 (m-40)
REVERT: H   89 LEU cc_start: 0.8630 (mt) cc_final: 0.7652 (pp)
REVERT: H  104 ASP cc_start: 0.7957 (m-30) cc_final: 0.7615 (m-30)
REVERT: C   14 ASP cc_start: 0.8479 (p0) cc_final: 0.8132 (p0)
REVERT: C   89 TYR cc_start: 0.8932 (m-80) cc_final: 0.8669 (m-10)
REVERT: C   95 SER cc_start: 0.8674 (t) cc_final: 0.8434 (t)
REVERT: C  123 ASP cc_start: 0.8145 (t0) cc_final: 0.7924 (t70)
  outliers start: 14
  outliers final: 9
  residues processed: 126
  average time/residue: 0.1708
  time to fit residues: 25.7250
Evaluate side-chains
  130 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue   97 CYS
Chi-restraints excluded: chain H residue   83 TYR
Chi-restraints excluded: chain H residue   84 MET
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   74 CYS
Chi-restraints excluded: chain c residue   46 LYS
Chi-restraints excluded: chain c residue  118 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    2.7386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.102467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.078453 restraints weight = 7027.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.080472 restraints weight = 4292.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.081906 restraints weight = 3106.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3661  Z= 0.173
  Angle     :  0.760  10.938   4981  Z= 0.386
  Chirality :  0.044   0.156    574
  Planarity :  0.004   0.044    641
  Dihedral  :  4.955  20.484    501
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 25.19 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.39), residues: 461
  helix:  0.80 (0.72), residues: 49
  sheet: -0.06 (0.41), residues: 178
  loop : -2.28 (0.37), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP H  39 
 HIS   0.002   0.000   HIS H  44 
 PHE   0.007   0.001   PHE L  80 
 TYR   0.022   0.001   TYR H  53 
 ARG   0.009   0.001   ARG c  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03387 (  125)
  hydrogen bonds       : angle       5.04532 (  336)
  SS BOND              : bond        0.00872 (    1)
  SS BOND              : angle       2.03111 (    2)
  covalent geometry    : bond        0.00406 ( 3660)
  covalent geometry    : angle       0.75904 ( 4979)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: L    7 MET cc_start: 0.8855 (mmm) cc_final: 0.8650 (mmm)
REVERT: L  100 TYR cc_start: 0.9156 (p90) cc_final: 0.8827 (p90)
REVERT: H    9 GLN cc_start: 0.8641 (tp40) cc_final: 0.7968 (tt0)
REVERT: H   89 LEU cc_start: 0.8691 (mt) cc_final: 0.8120 (pp)
REVERT: H  104 ASP cc_start: 0.7954 (m-30) cc_final: 0.7628 (m-30)
REVERT: C   14 ASP cc_start: 0.8483 (p0) cc_final: 0.8134 (p0)
REVERT: C   69 GLN cc_start: 0.8253 (tp40) cc_final: 0.7755 (mm110)
REVERT: C   95 SER cc_start: 0.8689 (t) cc_final: 0.8447 (t)
REVERT: C  123 ASP cc_start: 0.8159 (t0) cc_final: 0.7940 (t70)
  outliers start: 9
  outliers final: 8
  residues processed: 126
  average time/residue: 0.1729
  time to fit residues: 26.2632
Evaluate side-chains
  127 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue   97 CYS
Chi-restraints excluded: chain H residue   83 TYR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   74 CYS
Chi-restraints excluded: chain c residue   46 LYS
Chi-restraints excluded: chain c residue  118 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 40 optimal weight:   20.0000
   chunk 1 optimal weight:    0.0170
   chunk 9 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    2.2022

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

Flipped N/Q/H residues before XYZ refinement:
L   9 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.103197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.079259 restraints weight = 6953.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.081344 restraints weight = 4244.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.082787 restraints weight = 3068.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3661  Z= 0.156
  Angle     :  0.766  10.350   4981  Z= 0.389
  Chirality :  0.044   0.153    574
  Planarity :  0.004   0.049    641
  Dihedral  :  4.935  20.279    501
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.38 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 24.94 %
    Favored  : 72.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.39), residues: 461
  helix:  0.65 (0.72), residues: 48
  sheet: -0.07 (0.41), residues: 178
  loop : -2.30 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP H  39 
 HIS   0.001   0.000   HIS H  44 
 PHE   0.008   0.001   PHE L 106 
 TYR   0.022   0.001   TYR H  53 
 ARG   0.008   0.001   ARG C  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03304 (  125)
  hydrogen bonds       : angle       4.98409 (  336)
  SS BOND              : bond        0.00800 (    1)
  SS BOND              : angle       1.92899 (    2)
  covalent geometry    : bond        0.00371 ( 3660)
  covalent geometry    : angle       0.76555 ( 4979)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1493.21 seconds
wall clock time: 26 minutes 49.30 seconds (1609.30 seconds total)