Starting phenix.real_space_refine
on Thu Jul  2 03:04:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9e0h_47356/07_2026/9e0h_47356.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9e0h_47356/07_2026/9e0h_47356.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9e0h_47356/07_2026/9e0h_47356.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9e0h_47356/07_2026/9e0h_47356.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9e0h_47356/07_2026/9e0h_47356.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9e0h_47356/07_2026/9e0h_47356.cif"
  }
  resolution = 4.62
  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=  -0.001 sd=   0.028
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      14      5.16       5
     C    3724      2.51       5
     N    1204      2.21       5
     O    1127      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6069
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 867
          Classifications: {'peptide': 151}
          Incomplete info: {'truncation_to_alanine': 79}
          Link IDs: {'PTRANS': 4, 'TRANS': 146}
          Unresolved non-hydrogen bonds: 303
          Unresolved non-hydrogen angles: 398
          Unresolved non-hydrogen dihedrals: 241
          Unresolved non-hydrogen chiralities: 49
          Planarities with less than four sites: {'GLU:plan': 13, 'PHE:plan': 5, 'TYR:plan': 3, 'ARG:plan': 4, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 141
  Restraints were copied for chains:
    B, C, D, E, F, G
  Time building chain proxies: 0.88, per 1000 atoms: 0.14
  Number of scatterers: 6069
  At special positions: 0
  Unit cell: (87.36, 85.68, 82.32, 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      14     16.00
     O    1127      8.00
     N    1204      7.00
     C    3724      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: 0.38
  Conformation dependent library (CDL) restraints added in 327.3 milliseconds
  

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2002

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      97.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 31
      removed outlier: 4.300A  pdb=" N   LEU A  31 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 67
      removed outlier: 3.625A  pdb=" N   GLY A  67 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 102
    Processing helix  chain 'A' and resid 103 through 151
      removed outlier: 3.764A  pdb=" N   GLU A 108 " --> pdb=" O   PRO A 104 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   ALA A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU A 139 " --> pdb=" O   ALA A 135 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLU A 141 " --> pdb=" O   GLU A 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 31
      removed outlier: 4.300A  pdb=" N   LEU B  31 " --> pdb=" O   VAL B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 67
      removed outlier: 3.626A  pdb=" N   GLY B  67 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 102
    Processing helix  chain 'B' and resid 103 through 151
      removed outlier: 3.763A  pdb=" N   GLU B 108 " --> pdb=" O   PRO B 104 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   ALA B 109 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU B 139 " --> pdb=" O   ALA B 135 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU B 141 " --> pdb=" O   GLU B 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 31
      removed outlier: 4.300A  pdb=" N   LEU C  31 " --> pdb=" O   VAL C  27 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 67
      removed outlier: 3.625A  pdb=" N   GLY C  67 " --> pdb=" O   ALA C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 102
    Processing helix  chain 'C' and resid 103 through 151
      removed outlier: 3.765A  pdb=" N   GLU C 108 " --> pdb=" O   PRO C 104 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   ALA C 109 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU C 139 " --> pdb=" O   ALA C 135 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU C 141 " --> pdb=" O   GLU C 137 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 31
      removed outlier: 4.300A  pdb=" N   LEU D  31 " --> pdb=" O   VAL D  27 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 67
      removed outlier: 3.626A  pdb=" N   GLY D  67 " --> pdb=" O   ALA D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 102
    Processing helix  chain 'D' and resid 103 through 151
      removed outlier: 3.764A  pdb=" N   GLU D 108 " --> pdb=" O   PRO D 104 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   ALA D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU D 139 " --> pdb=" O   ALA D 135 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU D 141 " --> pdb=" O   GLU D 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 31
      removed outlier: 4.300A  pdb=" N   LEU E  31 " --> pdb=" O   VAL E  27 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 34 through 67
      removed outlier: 3.626A  pdb=" N   GLY E  67 " --> pdb=" O   ALA E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 69 through 102
    Processing helix  chain 'E' and resid 103 through 151
      removed outlier: 3.764A  pdb=" N   GLU E 108 " --> pdb=" O   PRO E 104 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   ALA E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU E 139 " --> pdb=" O   ALA E 135 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLU E 141 " --> pdb=" O   GLU E 137 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 31
      removed outlier: 4.300A  pdb=" N   LEU F  31 " --> pdb=" O   VAL F  27 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 34 through 67
      removed outlier: 3.626A  pdb=" N   GLY F  67 " --> pdb=" O   ALA F  63 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 69 through 102
    Processing helix  chain 'F' and resid 103 through 151
      removed outlier: 3.764A  pdb=" N   GLU F 108 " --> pdb=" O   PRO F 104 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   ALA F 109 " --> pdb=" O   GLU F 105 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU F 139 " --> pdb=" O   ALA F 135 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLU F 141 " --> pdb=" O   GLU F 137 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 31
      removed outlier: 4.300A  pdb=" N   LEU G  31 " --> pdb=" O   VAL G  27 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 34 through 67
      removed outlier: 3.625A  pdb=" N   GLY G  67 " --> pdb=" O   ALA G  63 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 69 through 102
    Processing helix  chain 'G' and resid 103 through 151
      removed outlier: 3.764A  pdb=" N   GLU G 108 " --> pdb=" O   PRO G 104 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   ALA G 109 " --> pdb=" O   GLU G 105 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU G 139 " --> pdb=" O   ALA G 135 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU G 141 " --> pdb=" O   GLU G 137 " (cutoff:3.500A)

    875 hydrogen bonds defined for protein.
    2625 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: 0.90

  Time building geometry restraints manager: 0.52 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: 2289
        1.34 -     1.46: 736
        1.46 -     1.57: 3065
        1.57 -     1.69: 0
        1.69 -     1.80: 28
  Bond restraints: 6118
  Sorted by residual:
  bond pdb=" C   PRO D 103 "
       pdb=" N   PRO D 104 "
    ideal  model  delta    sigma   weight residual
    1.335  1.341 -0.006 1.28e-02 6.10e+03 2.38e-01
  bond pdb=" N   PRO A 103 "
       pdb=" CA  PRO A 103 "
    ideal  model  delta    sigma   weight residual
    1.459  1.466 -0.007 1.40e-02 5.10e+03 2.35e-01
  bond pdb=" N   PRO F 103 "
       pdb=" CA  PRO F 103 "
    ideal  model  delta    sigma   weight residual
    1.459  1.466 -0.007 1.40e-02 5.10e+03 2.28e-01
  bond pdb=" C   PRO A 103 "
       pdb=" N   PRO A 104 "
    ideal  model  delta    sigma   weight residual
    1.335  1.341 -0.006 1.28e-02 6.10e+03 2.17e-01
  bond pdb=" C   PRO G 103 "
       pdb=" N   PRO G 104 "
    ideal  model  delta    sigma   weight residual
    1.335  1.340 -0.006 1.28e-02 6.10e+03 2.09e-01
  ... (remaining 6113 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.75: 8126
        0.75 -     1.50: 210
        1.50 -     2.26: 38
        2.26 -     3.01: 40
        3.01 -     3.76: 28
  Bond angle restraints: 8442
  Sorted by residual:
  angle pdb=" C   LEU D   3 "
        pdb=" CA  LEU D   3 "
        pdb=" CB  LEU D   3 "
      ideal   model   delta    sigma   weight residual
     110.88  108.66    2.22 1.57e+00 4.06e-01 2.00e+00
  angle pdb=" C   LEU E   3 "
        pdb=" CA  LEU E   3 "
        pdb=" CB  LEU E   3 "
      ideal   model   delta    sigma   weight residual
     110.88  108.66    2.22 1.57e+00 4.06e-01 1.99e+00
  angle pdb=" C   LEU G   3 "
        pdb=" CA  LEU G   3 "
        pdb=" CB  LEU G   3 "
      ideal   model   delta    sigma   weight residual
     110.88  108.66    2.22 1.57e+00 4.06e-01 1.99e+00
  angle pdb=" C   LEU A   3 "
        pdb=" CA  LEU A   3 "
        pdb=" CB  LEU A   3 "
      ideal   model   delta    sigma   weight residual
     110.88  108.66    2.22 1.57e+00 4.06e-01 1.99e+00
  angle pdb=" C   LEU C   3 "
        pdb=" CA  LEU C   3 "
        pdb=" CB  LEU C   3 "
      ideal   model   delta    sigma   weight residual
     110.88  108.67    2.21 1.57e+00 4.06e-01 1.97e+00
  ... (remaining 8437 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.55: 3353
        8.55 -    17.10: 154
       17.10 -    25.64: 84
       25.64 -    34.19: 49
       34.19 -    42.74: 28
  Dihedral angle restraints: 3668
    sinusoidal: 609
      harmonic: 3059
  Sorted by residual:
  dihedral pdb=" CA  LEU A   8 "
           pdb=" CB  LEU A   8 "
           pdb=" CG  LEU A   8 "
           pdb=" CD1 LEU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.26   42.74     3      1.50e+01 4.44e-03 7.67e+00
  dihedral pdb=" CA  LEU B   8 "
           pdb=" CB  LEU B   8 "
           pdb=" CG  LEU B   8 "
           pdb=" CD1 LEU B   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.29   42.71     3      1.50e+01 4.44e-03 7.67e+00
  dihedral pdb=" CA  LEU E   8 "
           pdb=" CB  LEU E   8 "
           pdb=" CG  LEU E   8 "
           pdb=" CD1 LEU E   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.30   42.70     3      1.50e+01 4.44e-03 7.67e+00
  ... (remaining 3665 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.017: 678
       0.017 -    0.034: 187
       0.034 -    0.051: 93
       0.051 -    0.068: 108
       0.068 -    0.085: 26
  Chirality restraints: 1092
  Sorted by residual:
  chirality pdb=" CA  PRO B  35 "
            pdb=" N   PRO B  35 "
            pdb=" C   PRO B  35 "
            pdb=" CB  PRO B  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.63    0.09 2.00e-01 2.50e+01 1.81e-01
  chirality pdb=" CA  PRO E  35 "
            pdb=" N   PRO E  35 "
            pdb=" C   PRO E  35 "
            pdb=" CB  PRO E  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.64    0.08 2.00e-01 2.50e+01 1.70e-01
  chirality pdb=" CA  PRO D  35 "
            pdb=" N   PRO D  35 "
            pdb=" C   PRO D  35 "
            pdb=" CB  PRO D  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.64    0.08 2.00e-01 2.50e+01 1.67e-01
  ... (remaining 1089 not shown)

  Planarity restraints: 1162
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  69 "    0.009 5.00e-02 4.00e+02   1.37e-02 2.99e-01
        pdb=" N   PRO B  70 "   -0.024 5.00e-02 4.00e+02
        pdb=" CA  PRO B  70 "    0.007 5.00e-02 4.00e+02
        pdb=" CD  PRO B  70 "    0.008 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E  69 "   -0.009 5.00e-02 4.00e+02   1.35e-02 2.93e-01
        pdb=" N   PRO E  70 "    0.023 5.00e-02 4.00e+02
        pdb=" CA  PRO E  70 "   -0.007 5.00e-02 4.00e+02
        pdb=" CD  PRO E  70 "   -0.008 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER F  69 "    0.009 5.00e-02 4.00e+02   1.35e-02 2.91e-01
        pdb=" N   PRO F  70 "   -0.023 5.00e-02 4.00e+02
        pdb=" CA  PRO F  70 "    0.007 5.00e-02 4.00e+02
        pdb=" CD  PRO F  70 "    0.008 5.00e-02 4.00e+02
  ... (remaining 1159 not shown)

  Histogram of nonbonded interaction distances:
        2.64 -     3.09: 4511
        3.09 -     3.55: 8141
        3.55 -     4.00: 7850
        4.00 -     4.45: 11126
        4.45 -     4.90: 13800
  Nonbonded interactions: 45428
  Sorted by model distance:
  nonbonded pdb=" O   GLU A  32 "
            pdb=" NE  ARG A  38 "
     model   vdw
     2.642 3.120
  nonbonded pdb=" O   GLU E  32 "
            pdb=" NE  ARG E  38 "
     model   vdw
     2.642 3.120
  nonbonded pdb=" O   GLU G  32 "
            pdb=" NE  ARG G  38 "
     model   vdw
     2.642 3.120
  nonbonded pdb=" O   GLU B  32 "
            pdb=" NE  ARG B  38 "
     model   vdw
     2.642 3.120
  nonbonded pdb=" O   GLU F  32 "
            pdb=" NE  ARG F  38 "
     model   vdw
     2.643 3.120
  ... (remaining 45423 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}
Set refine NCS operators
  NCS operators will be refined.
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:             2.790
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.170
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.010
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
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      :  0.001   0.020   6118  Z= 0.074
  Angle     :  0.397   3.762   8442  Z= 0.216
  Chirality :  0.028   0.085   1092
  Planarity :  0.002   0.014   1162
  Dihedral  :  9.578  42.741   1666
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 0.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.77 (0.22), residues: 1043
  helix:  3.22 (0.13), residues: 980
  sheet:  None (None), residues: 0
  loop :  1.21 (0.88), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B   4 
 TYR   0.001   0.000   TYR E  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.003   0.001   TRP F  13 
 HIS   0.001   0.000   HIS D  97 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00138 /  0.07 ( 6118)
  covalent geometry    : angle       0.39682 /  0.22 ( 8442)
  hydrogen bonds       : bond        0.16230 / 11.80 (  875)
  hydrogen bonds       : angle       4.70655 /  3.69 ( 2625)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.035 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.1318
  time to fit residues: 2.2151
Evaluate side-chains
  16 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.7380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.115973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.091391 restraints weight = 2261.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.092998 restraints weight = 1957.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.094349 restraints weight = 1730.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.095456 restraints weight = 1556.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.096499 restraints weight = 1428.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   6118  Z= 0.123
  Angle     :  0.509   8.011   8442  Z= 0.252
  Chirality :  0.031   0.113   1092
  Planarity :  0.003   0.023   1162
  Dihedral  :  3.087  10.229   1099
  Min Nonbonded Distance : 2.695

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  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 are not related in a simple way.
  whole:  5.80 (0.22), residues: 1043
  helix:  3.91 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  0.85 (0.75), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C   4 
 TYR   0.002   0.001   TYR C  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.009   0.002   TRP E  13 
 HIS   0.001   0.001   HIS F  97 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00211 /  0.12 ( 6118)
  covalent geometry    : angle       0.50912 /  0.25 ( 8442)
  hydrogen bonds       : bond        0.03354 /  2.46 (  875)
  hydrogen bonds       : angle       3.08982 /  2.40 ( 2625)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.035 
Fit side-chains
REVERT: B  110 MET cc_start: 0.7519 (mmt) cc_final: 0.7268 (mmt)
REVERT: B  146 ARG cc_start: 0.8596 (tpt90) cc_final: 0.8288 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0868
  time to fit residues: 1.1623
Evaluate side-chains
  12 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 96 optimal weight:    0.1980
   chunk 60 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 97 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.7582
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.114691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.091532 restraints weight = 2298.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.093184 restraints weight = 1983.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.094536 restraints weight = 1747.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.095406 restraints weight = 1568.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.096457 restraints weight = 1443.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   6118  Z= 0.117
  Angle     :  0.449   4.602   8442  Z= 0.231
  Chirality :  0.030   0.105   1092
  Planarity :  0.003   0.023   1162
  Dihedral  :  3.030  11.278   1099
  Min Nonbonded Distance : 2.705

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  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 are not related in a simple way.
  whole:  6.21 (0.22), residues: 1043
  helix:  4.17 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  1.14 (0.76), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B   4 
 TYR   0.005   0.001   TYR F  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.006   0.001   TRP C  13 
 HIS   0.000   0.000   HIS E  97 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00193 /  0.12 ( 6118)
  covalent geometry    : angle       0.44865 /  0.23 ( 8442)
  hydrogen bonds       : bond        0.02978 /  2.21 (  875)
  hydrogen bonds       : angle       2.98974 /  2.33 ( 2625)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.029 
Fit side-chains
REVERT: B  110 MET cc_start: 0.7549 (mmt) cc_final: 0.7244 (mmm)
REVERT: B  146 ARG cc_start: 0.8588 (tpt90) cc_final: 0.8164 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0811
  time to fit residues: 1.0713
Evaluate side-chains
  12 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 93 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0870
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.9160
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.111868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.089897 restraints weight = 2344.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.091437 restraints weight = 2017.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.092714 restraints weight = 1769.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.093755 restraints weight = 1579.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.094331 restraints weight = 1434.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   6118  Z= 0.129
  Angle     :  0.476   5.405   8442  Z= 0.241
  Chirality :  0.030   0.105   1092
  Planarity :  0.003   0.027   1162
  Dihedral  :  3.040  10.582   1099
  Min Nonbonded Distance : 2.701

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  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 are not related in a simple way.
  whole:  6.30 (0.22), residues: 1043
  helix:  4.19 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  1.80 (0.84), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B   4 
 TYR   0.006   0.001   TYR B  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.003   0.001   TRP C  13 
 HIS   0.000   0.000   HIS E  97 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00203 /  0.13 ( 6118)
  covalent geometry    : angle       0.47572 /  0.24 ( 8442)
  hydrogen bonds       : bond        0.02890 /  2.15 (  875)
  hydrogen bonds       : angle       2.92742 /  2.28 ( 2625)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.030 
Fit side-chains
REVERT: B  110 MET cc_start: 0.7608 (mmt) cc_final: 0.7282 (mmm)
REVERT: B  146 ARG cc_start: 0.8610 (tpt90) cc_final: 0.8120 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0795
  time to fit residues: 1.0381
Evaluate side-chains
  12 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 70 optimal weight:    0.2980
   chunk 1 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 104 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 42 optimal weight:    0.4980
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.4980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.112624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.088599 restraints weight = 2510.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.090296 restraints weight = 2173.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.091719 restraints weight = 1912.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.092688 restraints weight = 1710.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.093914 restraints weight = 1566.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   6118  Z= 0.090
  Angle     :  0.442   4.822   8442  Z= 0.218
  Chirality :  0.031   0.105   1092
  Planarity :  0.003   0.030   1162
  Dihedral  :  3.024  11.115   1099
  Min Nonbonded Distance : 2.710

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  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 are not related in a simple way.
  whole:  6.41 (0.22), residues: 1043
  helix:  4.25 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  1.98 (0.84), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C   4 
 TYR   0.005   0.001   TYR A  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.004   0.001   TRP B  13 
 HIS   0.000   0.000   HIS F  97 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00160 /  0.09 ( 6118)
  covalent geometry    : angle       0.44215 /  0.22 ( 8442)
  hydrogen bonds       : bond        0.02507 /  1.86 (  875)
  hydrogen bonds       : angle       2.73097 /  2.12 ( 2625)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.019 
Fit side-chains
REVERT: G  146 ARG cc_start: 0.8167 (tpt90) cc_final: 0.7417 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0736
  time to fit residues: 1.0383
Evaluate side-chains
  13 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 97 optimal weight:    0.6980
   chunk 101 optimal weight:    0.6980
   chunk 22 optimal weight:    0.4980
   chunk 94 optimal weight:    0.8980
   chunk 8 optimal weight:    0.1980
   chunk 33 optimal weight:    0.0170
   chunk 56 optimal weight:    0.8980
   chunk 41 optimal weight:    0.3980
   chunk 48 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.3618
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.112325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.089258 restraints weight = 2455.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.090803 restraints weight = 2135.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.092151 restraints weight = 1897.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.092832 restraints weight = 1704.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.093996 restraints weight = 1588.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6118  Z= 0.100
  Angle     :  0.464   4.993   8442  Z= 0.221
  Chirality :  0.031   0.105   1092
  Planarity :  0.006   0.070   1162
  Dihedral  :  3.117  10.310   1099
  Min Nonbonded Distance : 2.712

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  6.29 (0.23), residues: 1043
  helix:  4.17 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  2.07 (0.84), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E   4 
 TYR   0.004   0.001   TYR B  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.003   0.001   TRP D  13 
 HIS   0.000   0.000   HIS F  97 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00203 /  0.10 ( 6118)
  covalent geometry    : angle       0.46389 /  0.22 ( 8442)
  hydrogen bonds       : bond        0.02403 /  1.79 (  875)
  hydrogen bonds       : angle       2.71480 /  2.11 ( 2625)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.019 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0693
  time to fit residues: 0.9809
Evaluate side-chains
  13 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 98 optimal weight:    0.0980
   chunk 101 optimal weight:    0.0870
   chunk 2 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.4958
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.110292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.084316 restraints weight = 2486.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.085270 restraints weight = 2223.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.086868 restraints weight = 2046.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.088089 restraints weight = 1866.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.088762 restraints weight = 1717.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   6118  Z= 0.087
  Angle     :  0.462   5.262   8442  Z= 0.221
  Chirality :  0.031   0.121   1092
  Planarity :  0.003   0.028   1162
  Dihedral  :  2.962  10.119   1099
  Min Nonbonded Distance : 2.711

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  6.62 (0.22), residues: 1043
  helix:  4.40 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  1.89 (0.81), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B   4 
 TYR   0.005   0.001   TYR A  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.003   0.001   TRP D  13 
 HIS   0.000   0.000   HIS F  97 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00153 /  0.09 ( 6118)
  covalent geometry    : angle       0.46217 /  0.22 ( 8442)
  hydrogen bonds       : bond        0.02359 /  1.76 (  875)
  hydrogen bonds       : angle       2.64467 /  2.06 ( 2625)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.028 
Fit side-chains
REVERT: A   12 ARG cc_start: 0.8203 (ttt90) cc_final: 0.7974 (ttt90)
REVERT: A  146 ARG cc_start: 0.8214 (tpt90) cc_final: 0.7683 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0943
  time to fit residues: 1.3447
Evaluate side-chains
  13 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 3 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 101 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.7580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.108281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.082685 restraints weight = 2554.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.084180 restraints weight = 2275.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.085042 restraints weight = 2052.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.086361 restraints weight = 1899.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.087450 restraints weight = 1749.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.010   6118  Z= 0.112
  Angle     :  0.470   5.519   8442  Z= 0.231
  Chirality :  0.032   0.135   1092
  Planarity :  0.003   0.029   1162
  Dihedral  :  3.000  10.812   1099
  Min Nonbonded Distance : 2.709

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  6.69 (0.22), residues: 1043
  helix:  4.46 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  1.63 (0.77), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G   4 
 TYR   0.007   0.001   TYR C  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.001   0.000   TRP A  13 
 HIS   0.000   0.000   HIS B  97 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00184 /  0.11 ( 6118)
  covalent geometry    : angle       0.46986 /  0.23 ( 8442)
  hydrogen bonds       : bond        0.02581 /  1.93 (  875)
  hydrogen bonds       : angle       2.78190 /  2.17 ( 2625)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.032 
Fit side-chains
REVERT: A   12 ARG cc_start: 0.8195 (ttt90) cc_final: 0.7983 (ttt90)
REVERT: A  146 ARG cc_start: 0.8209 (tpt90) cc_final: 0.7711 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0726
  time to fit residues: 0.9615
Evaluate side-chains
  12 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 81 optimal weight:    0.0470
   chunk 45 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 43 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.9482
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.106357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.082739 restraints weight = 2575.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.084176 restraints weight = 2281.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.085228 restraints weight = 2051.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.086353 restraints weight = 1881.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.087155 restraints weight = 1732.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.3103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   6118  Z= 0.133
  Angle     :  0.500   6.904   8442  Z= 0.246
  Chirality :  0.033   0.173   1092
  Planarity :  0.003   0.029   1162
  Dihedral  :  3.007  10.564   1099
  Min Nonbonded Distance : 2.693

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  6.59 (0.22), residues: 1043
  helix:  4.38 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  1.90 (0.82), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B   4 
 TYR   0.008   0.002   TYR C  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.002   0.001   TRP E  13 
 HIS   0.000   0.000   HIS C  97 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00209 /  0.13 ( 6118)
  covalent geometry    : angle       0.49990 /  0.25 ( 8442)
  hydrogen bonds       : bond        0.02740 /  2.05 (  875)
  hydrogen bonds       : angle       2.88857 /  2.25 ( 2625)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.019 
Fit side-chains
REVERT: G    4 ARG cc_start: 0.6911 (mtp-110) cc_final: 0.6034 (ttt180)
REVERT: G  146 ARG cc_start: 0.8212 (tpt90) cc_final: 0.7443 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0799
  time to fit residues: 1.0410
Evaluate side-chains
  12 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 84 optimal weight:    0.0770
   chunk 9 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0060
   chunk 11 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.3754
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.108299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.084657 restraints weight = 2473.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.085949 restraints weight = 2208.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.086904 restraints weight = 2001.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.087974 restraints weight = 1842.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.088572 restraints weight = 1707.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.012   6118  Z= 0.080
  Angle     :  0.465   5.500   8442  Z= 0.218
  Chirality :  0.032   0.158   1092
  Planarity :  0.003   0.031   1162
  Dihedral  :  2.964  10.517   1099
  Min Nonbonded Distance : 2.695

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  6.75 (0.22), residues: 1043
  helix:  4.44 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  2.72 (0.91), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G   4 
 TYR   0.004   0.001   TYR F  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.001   0.000   TRP D  13 
 HIS   0.001   0.000   HIS F  97 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00147 /  0.08 ( 6118)
  covalent geometry    : angle       0.46494 /  0.22 ( 8442)
  hydrogen bonds       : bond        0.02312 /  1.73 (  875)
  hydrogen bonds       : angle       2.58295 /  2.01 ( 2625)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.051 
Fit side-chains
REVERT: G    4 ARG cc_start: 0.6830 (mtp-110) cc_final: 0.6017 (ttt180)
REVERT: G  146 ARG cc_start: 0.8151 (tpt90) cc_final: 0.7382 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0811
  time to fit residues: 1.0792
Evaluate side-chains
  12 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 16 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 69 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.9582
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.106165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.083404 restraints weight = 2597.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.084725 restraints weight = 2311.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.085700 restraints weight = 2089.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.086739 restraints weight = 1924.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.087408 restraints weight = 1778.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.3276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   6118  Z= 0.129
  Angle     :  0.488   6.302   8442  Z= 0.240
  Chirality :  0.033   0.170   1092
  Planarity :  0.003   0.030   1162
  Dihedral  :  2.970  10.139   1099
  Min Nonbonded Distance : 2.681

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  6.79 (0.22), residues: 1043
  helix:  4.49 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  2.22 (0.82), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B   4 
 TYR   0.009   0.002   TYR A  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.001   0.000   TRP E  13 
 HIS   0.000   0.000   HIS D  97 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00204 /  0.13 ( 6118)
  covalent geometry    : angle       0.48767 /  0.24 ( 8442)
  hydrogen bonds       : bond        0.02680 /  2.01 (  875)
  hydrogen bonds       : angle       2.77141 /  2.16 ( 2625)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 692.88 seconds
wall clock time: 12 minutes 41.50 seconds (761.50 seconds total)