Starting phenix.real_space_refine
on Tue Feb  3 18:26:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9e0h_47356/02_2026/9e0h_47356.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9e0h_47356/02_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_47356/02_2026/9e0h_47356.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9e0h_47356/02_2026/9e0h_47356.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9e0h_47356/02_2026/9e0h_47356.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9e0h_47356/02_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-2.0-5952/lib/python3.9/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: 0.83, 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: 0.59
  Conformation dependent library (CDL) restraints added in 410.1 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: 0.11
  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: 0.77

  Time building geometry restraints manager: 0.79 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:             4.180
  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:             0.020
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.670
  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:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
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
  covalent geometry    : bond        0.00138 ( 6118)
  covalent geometry    : angle       0.39682 ( 8442)
  hydrogen bonds       : bond        0.16230 (  875)
  hydrogen bonds       : angle       4.70655 ( 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: 0.1472
  time to fit residues: 2.4474
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  : 0.018 
-------------------------------------------------------------------------------
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...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
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: 0.7105
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
  covalent geometry    : bond        0.00211 ( 6118)
  covalent geometry    : angle       0.50912 ( 8442)
  hydrogen bonds       : bond        0.03354 (  875)
  hydrogen bonds       : angle       3.08982 ( 2625)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 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: 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: 0.0735
  time to fit residues: 0.9526
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:    0.4980
   chunk 69 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.6982
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.115384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.092056 restraints weight = 2289.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.093628 restraints weight = 1982.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.094929 restraints weight = 1755.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 16)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.095745 restraints weight = 1580.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.096868 restraints weight = 1458.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.1766

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= 0.108
  Angle     :  0.441   4.612   8442  Z= 0.226
  Chirality :  0.031   0.105   1092
  Planarity :  0.003   0.024   1162
  Dihedral  :  3.039  11.404   1099
  Min Nonbonded Distance : 2.707

Molprobity Statistics.
  All-atom Clashscore : 2.26
  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:  6.06 (0.23), residues: 1043
  helix:  4.07 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  1.13 (0.76), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B   4 
 TYR   0.005   0.002   TYR C  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.005   0.001   TRP F  13 
 HIS   0.000   0.000   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00180 ( 6118)
  covalent geometry    : angle       0.44145 ( 8442)
  hydrogen bonds       : bond        0.02902 (  875)
  hydrogen bonds       : angle       2.96011 ( 2625)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 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  : 0.037 
Fit side-chains
REVERT: B  110 MET cc_start: 0.7541 (mmt) cc_final: 0.7245 (mmm)
REVERT: B  146 ARG cc_start: 0.8556 (tpt90) cc_final: 0.8128 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0723
  time to fit residues: 0.9518
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  : 0.028 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    1.0982
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.110964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.088682 restraints weight = 2354.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.089818 restraints weight = 2036.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.091193 restraints weight = 1825.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.092311 restraints weight = 1646.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.092881 restraints weight = 1497.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.2249

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= 0.154
  Angle     :  0.494   5.915   8442  Z= 0.257
  Chirality :  0.030   0.106   1092
  Planarity :  0.003   0.027   1162
  Dihedral  :  3.151  10.724   1099
  Min Nonbonded Distance : 2.691

Molprobity Statistics.
  All-atom Clashscore : 2.64
  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:  5.88 (0.23), residues: 1043
  helix:  3.93 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  1.50 (0.81), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B   4 
 TYR   0.007   0.001   TYR F  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.004   0.001   TRP A  13 
 HIS   0.000   0.000   HIS D  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6118)
  covalent geometry    : angle       0.49433 ( 8442)
  hydrogen bonds       : bond        0.03145 (  875)
  hydrogen bonds       : angle       3.12826 ( 2625)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 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: B  110 MET cc_start: 0.7622 (mmt) cc_final: 0.7280 (mmm)
REVERT: B  146 ARG cc_start: 0.8635 (tpt90) cc_final: 0.8155 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0665
  time to fit residues: 0.8769
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 63 optimal weight:    4.9990
   chunk 104 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.7980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.110764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.088423 restraints weight = 2529.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.089958 restraints weight = 2195.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.091339 restraints weight = 1941.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.092442 restraints weight = 1735.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.093244 restraints weight = 1575.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.2370

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= 0.116
  Angle     :  0.455   4.808   8442  Z= 0.230
  Chirality :  0.031   0.105   1092
  Planarity :  0.003   0.031   1162
  Dihedral  :  3.107  10.578   1099
  Min Nonbonded Distance : 2.708

Molprobity Statistics.
  All-atom Clashscore : 6.59
  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:  5.93 (0.23), residues: 1043
  helix:  3.96 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  1.66 (0.79), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F   4 
 TYR   0.006   0.001   TYR D  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.005   0.001   TRP D  13 
 HIS   0.000   0.000   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 6118)
  covalent geometry    : angle       0.45517 ( 8442)
  hydrogen bonds       : bond        0.02765 (  875)
  hydrogen bonds       : angle       2.95375 ( 2625)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 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  : 0.029 
Fit side-chains
REVERT: G  146 ARG cc_start: 0.8173 (tpt90) cc_final: 0.7433 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0799
  time to fit residues: 1.1346
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  : 0.033 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 97 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 94 optimal weight:    0.6980
   chunk 8 optimal weight:    0.2980
   chunk 33 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0040
   chunk 65 optimal weight:    0.1980
   overall best weight:    0.3992
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.110839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.086052 restraints weight = 2494.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.087730 restraints weight = 2179.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.089151 restraints weight = 1936.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.090291 restraints weight = 1739.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.091285 restraints weight = 1585.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.014   6118  Z= 0.083
  Angle     :  0.475   7.049   8442  Z= 0.221
  Chirality :  0.030   0.103   1092
  Planarity :  0.003   0.029   1162
  Dihedral  :  3.090  10.574   1099
  Min Nonbonded Distance : 2.712

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:  5.87 (0.23), residues: 1043
  helix:  3.90 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  2.03 (0.82), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D   4 
 TYR   0.004   0.001   TYR B  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.003   0.000   TRP D  13 
 HIS   0.001   0.000   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00150 ( 6118)
  covalent geometry    : angle       0.47486 ( 8442)
  hydrogen bonds       : bond        0.02418 (  875)
  hydrogen bonds       : angle       2.76735 ( 2625)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 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  : 0.031 
Fit side-chains
REVERT: G  146 ARG cc_start: 0.8174 (tpt90) cc_final: 0.7424 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0790
  time to fit residues: 1.1215
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  : 0.035 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 98 optimal weight:    0.7980
   chunk 101 optimal weight:    0.0970
   chunk 2 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0770
   chunk 23 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.5536
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.110292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.086037 restraints weight = 2453.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.087570 restraints weight = 2155.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.088987 restraints weight = 1922.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.090137 restraints weight = 1734.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.090938 restraints weight = 1578.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.2651

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= 0.092
  Angle     :  0.476   6.653   8442  Z= 0.226
  Chirality :  0.031   0.134   1092
  Planarity :  0.003   0.029   1162
  Dihedral  :  3.043  11.091   1099
  Min Nonbonded Distance : 2.711

Molprobity Statistics.
  All-atom Clashscore : 4.71
  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:  6.09 (0.23), residues: 1043
  helix:  4.02 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  2.44 (0.85), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A   4 
 TYR   0.006   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 F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00157 ( 6118)
  covalent geometry    : angle       0.47561 ( 8442)
  hydrogen bonds       : bond        0.02419 (  875)
  hydrogen bonds       : angle       2.71436 ( 2625)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.029 
Fit side-chains
REVERT: G  146 ARG cc_start: 0.8193 (tpt90) cc_final: 0.7474 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0922
  time to fit residues: 1.3725
Evaluate side-chains
  14 residues out of total 113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.026 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 3 optimal weight:    0.0970
   chunk 40 optimal weight:    0.0470
   chunk 14 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0670
   chunk 67 optimal weight:    0.7980
   chunk 101 optimal weight:    0.0670
   chunk 23 optimal weight:    0.4980
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.1552
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.112760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.088990 restraints weight = 2470.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.090664 restraints weight = 2135.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.092208 restraints weight = 1884.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.093407 restraints weight = 1682.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.094454 restraints weight = 1523.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6118  Z= 0.099
  Angle     :  0.480   5.356   8442  Z= 0.221
  Chirality :  0.032   0.122   1092
  Planarity :  0.006   0.063   1162
  Dihedral  :  3.180  10.056   1099
  Min Nonbonded Distance : 2.712

Molprobity Statistics.
  All-atom Clashscore : 5.56
  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:  5.66 (0.23), residues: 1043
  helix:  3.73 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  2.57 (0.94), residues: 63

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 6118)
  covalent geometry    : angle       0.48044 ( 8442)
  hydrogen bonds       : bond        0.02236 (  875)
  hydrogen bonds       : angle       2.64242 ( 2625)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 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  : 0.030 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0619
  time to fit residues: 0.8905
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  : 0.018 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 45 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   overall best weight:    0.7580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.108565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.083719 restraints weight = 2510.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.085379 restraints weight = 2192.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.086405 restraints weight = 1946.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.087864 restraints weight = 1775.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.088682 restraints weight = 1614.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.2874

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= 0.113
  Angle     :  0.494   5.824   8442  Z= 0.241
  Chirality :  0.032   0.144   1092
  Planarity :  0.003   0.030   1162
  Dihedral  :  2.939   9.782   1099
  Min Nonbonded Distance : 2.704

Molprobity Statistics.
  All-atom Clashscore : 5.93
  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:  6.14 (0.23), residues: 1043
  helix:  4.06 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  2.37 (0.87), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B   4 
 TYR   0.007   0.001   TYR B  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.001   0.000   TRP D  13 
 HIS   0.000   0.000   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00187 ( 6118)
  covalent geometry    : angle       0.49403 ( 8442)
  hydrogen bonds       : bond        0.02442 (  875)
  hydrogen bonds       : angle       2.68354 ( 2625)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 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: G    4 ARG cc_start: 0.6741 (mtp-110) cc_final: 0.5995 (ttt180)
REVERT: G  146 ARG cc_start: 0.8212 (tpt90) cc_final: 0.7476 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0550
  time to fit residues: 0.7318
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  : 0.018 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 84 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   chunk 11 optimal weight:    0.1980
   chunk 36 optimal weight:    0.0770
   overall best weight:    0.4338
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.109473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.083251 restraints weight = 2399.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.084966 restraints weight = 2090.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.086427 restraints weight = 1852.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.087683 restraints weight = 1666.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.088395 restraints weight = 1518.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.015   6118  Z= 0.079
  Angle     :  0.470   5.253   8442  Z= 0.217
  Chirality :  0.031   0.140   1092
  Planarity :  0.004   0.029   1162
  Dihedral  :  2.923   9.739   1099
  Min Nonbonded Distance : 2.710

Molprobity Statistics.
  All-atom Clashscore : 5.93
  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:  6.17 (0.22), residues: 1043
  helix:  4.07 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  2.60 (0.92), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A   4 
 TYR   0.005   0.001   TYR F  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.000   0.000   TRP D  13 
 HIS   0.000   0.000   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00146 ( 6118)
  covalent geometry    : angle       0.47035 ( 8442)
  hydrogen bonds       : bond        0.02168 (  875)
  hydrogen bonds       : angle       2.57018 ( 2625)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 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: 0.6887 (mtp-110) cc_final: 0.5999 (ttt-90)
REVERT: G  146 ARG cc_start: 0.8188 (tpt90) cc_final: 0.7392 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0596
  time to fit residues: 0.7858
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 78 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 89 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0980
   overall best weight:    1.0984
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.106160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.081292 restraints weight = 2565.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.082632 restraints weight = 2225.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.084253 restraints weight = 1987.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.085505 restraints weight = 1787.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.086412 restraints weight = 1623.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.3159

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= 0.143
  Angle     :  0.513   6.834   8442  Z= 0.256
  Chirality :  0.033   0.171   1092
  Planarity :  0.004   0.030   1162
  Dihedral  :  3.077   9.828   1099
  Min Nonbonded Distance : 2.697

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  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:  6.20 (0.23), residues: 1043
  helix:  4.10 (0.14), residues: 980
  sheet:  None (None), residues: 0
  loop :  2.34 (0.85), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B   4 
 TYR   0.010   0.002   TYR D  60 
 PHE   0.000   0.000   PHE A  25 
 TRP   0.002   0.001   TRP D  13 
 HIS   0.000   0.000   HIS G  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 6118)
  covalent geometry    : angle       0.51306 ( 8442)
  hydrogen bonds       : bond        0.02780 (  875)
  hydrogen bonds       : angle       2.93824 ( 2625)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 618.68 seconds
wall clock time: 11 minutes 21.95 seconds (681.95 seconds total)