Starting phenix.real_space_refine
on Fri Aug 22 15:26:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pog_17791/08_2025/8pog_17791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pog_17791/08_2025/8pog_17791.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pog_17791/08_2025/8pog_17791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pog_17791/08_2025/8pog_17791.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pog_17791/08_2025/8pog_17791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pog_17791/08_2025/8pog_17791.map"
  }
  resolution = 4.15
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.024
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      24      5.16       5
     C    3132      2.51       5
     N     880      2.21       5
     O     928      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4964
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1241
          Classifications: {'peptide': 156}
          Link IDs: {'PTRANS': 6, 'TRANS': 149}
    Chain: "B"
      Number of atoms: 1241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1241
          Classifications: {'peptide': 156}
          Link IDs: {'PTRANS': 6, 'TRANS': 149}
    Chain: "C"
      Number of atoms: 1241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1241
          Classifications: {'peptide': 156}
          Link IDs: {'PTRANS': 6, 'TRANS': 149}
    Chain: "D"
      Number of atoms: 1241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1241
          Classifications: {'peptide': 156}
          Link IDs: {'PTRANS': 6, 'TRANS': 149}
  Time building chain proxies: 1.49, per 1000 atoms: 0.30
  Number of scatterers: 4964
  At special positions: 0
  Unit cell: (75.33, 87.42, 79.05, 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      24     16.00
     O     928      8.00
     N     880      7.00
     C    3132      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: 0.43
  Conformation dependent library (CDL) restraints added in 222.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1144

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 4 sheets defined
      59.0% alpha, 14.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 19
      removed outlier: 3.547A  pdb=" N   LEU A  11 " --> pdb=" O   ASN A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 39
    Processing helix  chain 'A' and resid 43 through 58
      removed outlier: 3.630A  pdb=" N   TYR A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 81
    Processing helix  chain 'A' and resid 106 through 130
      removed outlier: 3.503A  pdb=" N   GLN A 110 " --> pdb=" O   VAL A 106 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   SER A 111 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
      removed outlier: 5.377A  pdb=" N   ARG A 112 " --> pdb=" O   ASP A 108 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLY A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'B' and resid 7 through 19
      removed outlier: 3.705A  pdb=" N   LEU B  11 " --> pdb=" O   ASN B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 39
    Processing helix  chain 'B' and resid 43 through 58
      removed outlier: 3.528A  pdb=" N   GLN B  57 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   TYR B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 81
    Processing helix  chain 'B' and resid 106 through 130
      removed outlier: 4.524A  pdb=" N   SER B 111 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   ARG B 112 " --> pdb=" O   ASP B 108 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLY B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 133
      No H-bonds generated for 'chain 'B' and resid 131 through 133'
    Processing helix  chain 'C' and resid 7 through 19
      removed outlier: 3.682A  pdb=" N   LEU C  11 " --> pdb=" O   ASN C   7 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 39
    Processing helix  chain 'C' and resid 43 through 58
      removed outlier: 3.511A  pdb=" N   LEU C  47 " --> pdb=" O   SER C  43 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLN C  57 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   TYR C  58 " --> pdb=" O   LEU C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 81
    Processing helix  chain 'C' and resid 106 through 130
      removed outlier: 4.609A  pdb=" N   SER C 111 " --> pdb=" O   GLU C 107 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   ARG C 112 " --> pdb=" O   ASP C 108 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLY C 123 " --> pdb=" O   ALA C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 133
      No H-bonds generated for 'chain 'C' and resid 131 through 133'
    Processing helix  chain 'D' and resid 7 through 19
      removed outlier: 3.627A  pdb=" N   LEU D  11 " --> pdb=" O   ASN D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 39
    Processing helix  chain 'D' and resid 43 through 58
      removed outlier: 3.621A  pdb=" N   GLN D  57 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   TYR D  58 " --> pdb=" O   LEU D  54 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 65 through 81
    Processing helix  chain 'D' and resid 106 through 130
      removed outlier: 4.572A  pdb=" N   SER D 111 " --> pdb=" O   GLU D 107 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   ARG D 112 " --> pdb=" O   ASP D 108 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLY D 123 " --> pdb=" O   ALA D 119 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 131 through 133
      No H-bonds generated for 'chain 'D' and resid 131 through 133'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89
      removed outlier: 3.571A  pdb=" N   CYS A  84 " --> pdb=" O   GLN A  99 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   ASP A 150 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
      removed outlier: 5.879A  pdb=" N   LEU A 145 " --> pdb=" O   ASP A 150 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   GLN A 152 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   GLU A 143 " --> pdb=" O   GLN A 152 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   SER A 141 " --> pdb=" O   ARG A 154 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 84 through 89
      removed outlier: 3.525A  pdb=" N   CYS B  84 " --> pdb=" O   GLN B  99 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   ASP B 150 " --> pdb=" O   LEU B 145 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   LEU B 145 " --> pdb=" O   ASP B 150 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   GLN B 152 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   GLU B 143 " --> pdb=" O   GLN B 152 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER B 141 " --> pdb=" O   ARG B 154 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   HIS B 156 " --> pdb=" O   THR B 139 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   THR B 139 " --> pdb=" O   HIS B 156 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 89
      removed outlier: 3.556A  pdb=" N   CYS C  84 " --> pdb=" O   GLN C  99 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   ASP C 150 " --> pdb=" O   LEU C 145 " (cutoff:3.500A)
      removed outlier: 6.036A  pdb=" N   LEU C 145 " --> pdb=" O   ASP C 150 " (cutoff:3.500A)
      removed outlier: 8.432A  pdb=" N   GLN C 152 " --> pdb=" O   GLU C 143 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   GLU C 143 " --> pdb=" O   GLN C 152 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   HIS C 156 " --> pdb=" O   THR C 139 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   THR C 139 " --> pdb=" O   HIS C 156 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 84 through 89
      removed outlier: 3.518A  pdb=" N   CYS D  84 " --> pdb=" O   GLN D  99 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   ASP D 150 " --> pdb=" O   LEU D 145 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   LEU D 145 " --> pdb=" O   ASP D 150 " (cutoff:3.500A)
      removed outlier: 8.058A  pdb=" N   GLN D 152 " --> pdb=" O   GLU D 143 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   GLU D 143 " --> pdb=" O   GLN D 152 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG D 154 " --> pdb=" O   SER D 141 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER D 141 " --> pdb=" O   ARG D 154 " (cutoff:3.500A)

    299 hydrogen bonds defined for protein.
    885 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: 0.68

  Time building geometry restraints manager: 0.58 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: 1696
        1.34 -     1.46: 1031
        1.46 -     1.58: 2317
        1.58 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 5080
  Sorted by residual:
  bond pdb=" CB  GLN A 132 "
       pdb=" CG  GLN A 132 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.21e+00
  bond pdb=" C   VAL B  38 "
       pdb=" O   VAL B  38 "
    ideal  model  delta    sigma   weight residual
    1.231  1.241 -0.010 1.02e-02 9.61e+03 9.70e-01
  bond pdb=" CB  GLU C  40 "
       pdb=" CG  GLU C  40 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.84e-01
  bond pdb=" C   VAL D  38 "
       pdb=" O   VAL D  38 "
    ideal  model  delta    sigma   weight residual
    1.231  1.241 -0.010 1.07e-02 8.73e+03 8.43e-01
  bond pdb=" C   VAL A  38 "
       pdb=" O   VAL A  38 "
    ideal  model  delta    sigma   weight residual
    1.231  1.240 -0.009 1.07e-02 8.73e+03 7.60e-01
  ... (remaining 5075 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 6559
        1.17 -     2.34: 258
        2.34 -     3.50: 69
        3.50 -     4.67: 6
        4.67 -     5.84: 12
  Bond angle restraints: 6904
  Sorted by residual:
  angle pdb=" CA  GLU C  40 "
        pdb=" CB  GLU C  40 "
        pdb=" CG  GLU C  40 "
      ideal   model   delta    sigma   weight residual
     114.10  119.39   -5.29 2.00e+00 2.50e-01 7.01e+00
  angle pdb=" CB  GLN A 132 "
        pdb=" CG  GLN A 132 "
        pdb=" CD  GLN A 132 "
      ideal   model   delta    sigma   weight residual
     112.60  116.58   -3.98 1.70e+00 3.46e-01 5.48e+00
  angle pdb=" CA  GLN A 132 "
        pdb=" CB  GLN A 132 "
        pdb=" CG  GLN A 132 "
      ideal   model   delta    sigma   weight residual
     114.10  118.40   -4.30 2.00e+00 2.50e-01 4.61e+00
  angle pdb=" N   VAL B  38 "
        pdb=" CA  VAL B  38 "
        pdb=" C   VAL B  38 "
      ideal   model   delta    sigma   weight residual
     111.81  113.58   -1.77 8.60e-01 1.35e+00 4.24e+00
  angle pdb=" CA  GLU B  40 "
        pdb=" CB  GLU B  40 "
        pdb=" CG  GLU B  40 "
      ideal   model   delta    sigma   weight residual
     114.10  118.17   -4.07 2.00e+00 2.50e-01 4.14e+00
  ... (remaining 6899 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 2639
       17.95 -    35.89: 254
       35.89 -    53.84: 56
       53.84 -    71.79: 13
       71.79 -    89.73: 10
  Dihedral angle restraints: 2972
    sinusoidal: 1196
      harmonic: 1776
  Sorted by residual:
  dihedral pdb=" CB  GLU D  86 "
           pdb=" CG  GLU D  86 "
           pdb=" CD  GLU D  86 "
           pdb=" OE1 GLU D  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.73  -89.73     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU C  86 "
           pdb=" CG  GLU C  86 "
           pdb=" CD  GLU C  86 "
           pdb=" OE1 GLU C  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.73  -89.73     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU B  86 "
           pdb=" CG  GLU B  86 "
           pdb=" CD  GLU B  86 "
           pdb=" OE1 GLU B  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.63  -89.63     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 2969 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 476
       0.026 -    0.051: 173
       0.051 -    0.077: 47
       0.077 -    0.102: 39
       0.102 -    0.128: 13
  Chirality restraints: 748
  Sorted by residual:
  chirality pdb=" CA  VAL B 151 "
            pdb=" N   VAL B 151 "
            pdb=" C   VAL B 151 "
            pdb=" CB  VAL B 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CA  VAL B 140 "
            pdb=" N   VAL B 140 "
            pdb=" C   VAL B 140 "
            pdb=" CB  VAL B 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.45e-01
  chirality pdb=" CA  VAL D 151 "
            pdb=" N   VAL D 151 "
            pdb=" C   VAL D 151 "
            pdb=" CB  VAL D 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.37e-01
  ... (remaining 745 not shown)

  Planarity restraints: 908
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 124 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.59e+00
        pdb=" C   LEU B 124 "    0.033 2.00e-02 2.50e+03
        pdb=" O   LEU B 124 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   TYR B 125 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 124 "    0.009 2.00e-02 2.50e+03   1.84e-02 3.37e+00
        pdb=" C   LEU A 124 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   LEU A 124 "    0.012 2.00e-02 2.50e+03
        pdb=" N   TYR A 125 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 122 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.08e+00
        pdb=" C   GLU B 122 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   GLU B 122 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLY B 123 "    0.010 2.00e-02 2.50e+03
  ... (remaining 905 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 979
        2.77 -     3.31: 4882
        3.31 -     3.84: 7703
        3.84 -     4.37: 8138
        4.37 -     4.90: 14428
  Nonbonded interactions: 36130
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  90 "
            pdb=" OD1 ASP B  93 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OD1 ASP D  56 "
            pdb=" NH1 ARG D 127 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" OD2 ASP B  93 "
            pdb=" NH1 ARG B 154 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" N   GLU A  42 "
            pdb=" OE1 GLU A  42 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" OD1 ASP C  56 "
            pdb=" NH1 ARG C 127 "
     model   vdw
     2.307 3.120
  ... (remaining 36125 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.500
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5080  Z= 0.141
  Angle     :  0.588   5.841   6904  Z= 0.333
  Chirality :  0.037   0.128    748
  Planarity :  0.005   0.039    908
  Dihedral  : 15.834  89.734   1828
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.33), residues: 616
  helix:  0.73 (0.28), residues: 336
  sheet:  0.14 (0.55), residues: 84
  loop : -0.26 (0.43), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 142 
 TYR   0.014   0.001   TYR C  58 
 PHE   0.008   0.001   PHE C  46 
 TRP   0.006   0.001   TRP D  13 
 HIS   0.002   0.000   HIS B  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 5080)
  covalent geometry    : angle       0.58762 ( 6904)
  hydrogen bonds       : bond        0.20781 (  299)
  hydrogen bonds       : angle       7.53111 (  885)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: B   40 GLU cc_start: 0.5649 (pm20) cc_final: 0.5103 (tt0)
REVERT: B   64 GLU cc_start: 0.5687 (mm-30) cc_final: 0.5466 (mp0)
REVERT: B   72 ASN cc_start: 0.7195 (m110) cc_final: 0.6712 (m110)
REVERT: B  148 LEU cc_start: 0.8423 (mt) cc_final: 0.8162 (mt)
REVERT: C   72 ASN cc_start: 0.6919 (m110) cc_final: 0.6543 (m110)
REVERT: C  142 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.7977 (mtm110)
REVERT: C  148 LEU cc_start: 0.8582 (mt) cc_final: 0.8226 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0705
  time to fit residues: 11.2790
Evaluate side-chains
  108 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  44 GLN
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.174883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.136998 restraints weight = 7227.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.136999 restraints weight = 7234.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.136998 restraints weight = 7231.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.136998 restraints weight = 7231.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.136998 restraints weight = 7231.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   5080  Z= 0.217
  Angle     :  0.567   4.938   6904  Z= 0.308
  Chirality :  0.040   0.114    748
  Planarity :  0.004   0.034    908
  Dihedral  :  3.814  15.781    676
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.73 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.34), residues: 616
  helix:  2.15 (0.28), residues: 340
  sheet:  0.17 (0.56), residues: 84
  loop : -0.55 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 142 
 TYR   0.009   0.001   TYR B  58 
 PHE   0.016   0.003   PHE A  14 
 TRP   0.012   0.002   TRP B 113 
 HIS   0.007   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 5080)
  covalent geometry    : angle       0.56681 ( 6904)
  hydrogen bonds       : bond        0.06083 (  299)
  hydrogen bonds       : angle       4.92019 (  885)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7431 (tp30) cc_final: 0.6752 (tp30)
REVERT: A   72 ASN cc_start: 0.7172 (m110) cc_final: 0.6748 (m110)
REVERT: A  141 SER cc_start: 0.8123 (t) cc_final: 0.7918 (t)
REVERT: B  141 SER cc_start: 0.8522 (t) cc_final: 0.8299 (t)
REVERT: C   17 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8225 (tp40)
REVERT: D   50 MET cc_start: 0.7513 (mmt) cc_final: 0.7150 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0689
  time to fit residues: 11.0239
Evaluate side-chains
  100 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 54 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0870
   chunk 4 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0070
   overall best weight:    0.3976

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

Flipped N/Q/H residues before XYZ refinement:
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  17 GLN
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 152 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.183282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.146896 restraints weight = 6865.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.146896 restraints weight = 6751.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.146896 restraints weight = 6751.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.146896 restraints weight = 6751.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.146896 restraints weight = 6751.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5080  Z= 0.108
  Angle     :  0.480   5.012   6904  Z= 0.244
  Chirality :  0.037   0.118    748
  Planarity :  0.003   0.024    908
  Dihedral  :  3.507  12.353    676
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.35), residues: 616
  helix:  3.01 (0.28), residues: 340
  sheet:  0.23 (0.55), residues: 84
  loop : -0.40 (0.44), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 142 
 TYR   0.007   0.001   TYR D  58 
 PHE   0.010   0.001   PHE B 153 
 TRP   0.010   0.001   TRP A 128 
 HIS   0.003   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 5080)
  covalent geometry    : angle       0.47993 ( 6904)
  hydrogen bonds       : bond        0.04063 (  299)
  hydrogen bonds       : angle       4.02438 (  885)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 GLU cc_start: 0.7386 (tp30) cc_final: 0.6711 (tp30)
REVERT: A  122 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7255 (mm-30)
REVERT: B   69 LEU cc_start: 0.8483 (tp) cc_final: 0.8100 (tp)
REVERT: B   72 ASN cc_start: 0.7234 (m110) cc_final: 0.6981 (m110)
REVERT: B  141 SER cc_start: 0.8530 (t) cc_final: 0.8228 (t)
REVERT: B  153 PHE cc_start: 0.7788 (m-80) cc_final: 0.7500 (m-80)
REVERT: C   17 GLN cc_start: 0.8553 (tm130) cc_final: 0.8144 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0707
  time to fit residues: 11.1801
Evaluate side-chains
  95 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 28 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 30 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 39 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
B 110 GLN
B 115 HIS
** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 152 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.180732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.145655 restraints weight = 6966.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.145653 restraints weight = 7077.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.145653 restraints weight = 7078.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.145653 restraints weight = 7078.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.145653 restraints weight = 7078.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5080  Z= 0.133
  Angle     :  0.485   4.969   6904  Z= 0.251
  Chirality :  0.037   0.122    748
  Planarity :  0.003   0.024    908
  Dihedral  :  3.436  12.370    676
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.35), residues: 616
  helix:  2.80 (0.28), residues: 348
  sheet:  0.29 (0.54), residues: 84
  loop : -0.44 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 142 
 TYR   0.004   0.001   TYR B  58 
 PHE   0.012   0.002   PHE D 153 
 TRP   0.009   0.001   TRP C 113 
 HIS   0.004   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 5080)
  covalent geometry    : angle       0.48453 ( 6904)
  hydrogen bonds       : bond        0.04434 (  299)
  hydrogen bonds       : angle       4.10711 (  885)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 ASN cc_start: 0.7200 (m110) cc_final: 0.6994 (m110)
REVERT: C   17 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8143 (tp40)
REVERT: D  148 LEU cc_start: 0.8246 (mt) cc_final: 0.8031 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0827
  time to fit residues: 12.1184
Evaluate side-chains
  90 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0670
   overall best weight:    0.6920

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

Flipped N/Q/H residues before XYZ refinement:
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 152 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.180971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.144717 restraints weight = 6920.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.144717 restraints weight = 6856.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.144717 restraints weight = 6856.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.144717 restraints weight = 6856.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.144717 restraints weight = 6856.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.3239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5080  Z= 0.126
  Angle     :  0.487   5.045   6904  Z= 0.250
  Chirality :  0.037   0.117    748
  Planarity :  0.003   0.024    908
  Dihedral  :  3.406  13.175    676
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.34 (0.34), residues: 616
  helix:  2.91 (0.27), residues: 344
  sheet:  0.30 (0.54), residues: 84
  loop : -0.47 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 142 
 TYR   0.011   0.001   TYR D  58 
 PHE   0.008   0.001   PHE D 117 
 TRP   0.009   0.001   TRP C 113 
 HIS   0.004   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 5080)
  covalent geometry    : angle       0.48654 ( 6904)
  hydrogen bonds       : bond        0.04210 (  299)
  hydrogen bonds       : angle       4.01738 (  885)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   17 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8116 (tp40)
REVERT: C  148 LEU cc_start: 0.8468 (mt) cc_final: 0.8252 (mt)
REVERT: D  148 LEU cc_start: 0.8278 (mt) cc_final: 0.8074 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0894
  time to fit residues: 12.8983
Evaluate side-chains
  92 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 28 optimal weight:    0.2980
   chunk 24 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 10 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 152 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.180751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.144737 restraints weight = 6963.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.144737 restraints weight = 6925.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.144736 restraints weight = 6925.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.144736 restraints weight = 6925.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.144736 restraints weight = 6925.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5080  Z= 0.128
  Angle     :  0.500   5.600   6904  Z= 0.255
  Chirality :  0.037   0.126    748
  Planarity :  0.003   0.025    908
  Dihedral  :  3.432  14.074    676
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.34), residues: 616
  helix:  2.91 (0.27), residues: 344
  sheet:  0.27 (0.54), residues: 84
  loop : -0.53 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 154 
 TYR   0.007   0.001   TYR D  58 
 PHE   0.010   0.001   PHE D 117 
 TRP   0.008   0.001   TRP C 113 
 HIS   0.003   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 5080)
  covalent geometry    : angle       0.50033 ( 6904)
  hydrogen bonds       : bond        0.04143 (  299)
  hydrogen bonds       : angle       4.06259 (  885)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: C   17 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8107 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0754
  time to fit residues: 11.1798
Evaluate side-chains
  97 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    0.1980
   chunk 37 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  17 GLN
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.180864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.144901 restraints weight = 6837.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.144901 restraints weight = 6931.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.144900 restraints weight = 6931.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.144900 restraints weight = 6931.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.144900 restraints weight = 6931.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5080  Z= 0.126
  Angle     :  0.516   6.176   6904  Z= 0.259
  Chirality :  0.038   0.116    748
  Planarity :  0.003   0.032    908
  Dihedral  :  3.419  13.758    676
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.34), residues: 616
  helix:  2.91 (0.27), residues: 344
  sheet:  0.08 (0.55), residues: 84
  loop : -0.56 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 142 
 TYR   0.011   0.001   TYR D  58 
 PHE   0.008   0.001   PHE B  24 
 TRP   0.008   0.001   TRP C 113 
 HIS   0.003   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 5080)
  covalent geometry    : angle       0.51618 ( 6904)
  hydrogen bonds       : bond        0.03999 (  299)
  hydrogen bonds       : angle       4.04527 (  885)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: C   17 GLN cc_start: 0.8464 (tm130) cc_final: 0.8132 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0698
  time to fit residues: 10.1511
Evaluate side-chains
  95 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0170
   chunk 7 optimal weight:    0.2980
   chunk 5 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.6420

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

Flipped N/Q/H residues before XYZ refinement:
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 115 HIS
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.181638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.147237 restraints weight = 6956.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.147237 restraints weight = 7112.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.147237 restraints weight = 7112.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.147237 restraints weight = 7112.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.147237 restraints weight = 7112.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.3680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5080  Z= 0.126
  Angle     :  0.529   6.865   6904  Z= 0.266
  Chirality :  0.038   0.114    748
  Planarity :  0.003   0.029    908
  Dihedral  :  3.391  13.094    676
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.23 (0.34), residues: 616
  helix:  2.91 (0.27), residues: 344
  sheet:  0.07 (0.55), residues: 84
  loop : -0.63 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 142 
 TYR   0.012   0.001   TYR C  58 
 PHE   0.010   0.001   PHE A  24 
 TRP   0.008   0.001   TRP B 113 
 HIS   0.004   0.001   HIS C 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5080)
  covalent geometry    : angle       0.52914 ( 6904)
  hydrogen bonds       : bond        0.03996 (  299)
  hydrogen bonds       : angle       4.09091 (  885)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 ASN cc_start: 0.6961 (m110) cc_final: 0.6760 (m110)
REVERT: C   17 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8036 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0647
  time to fit residues: 9.4779
Evaluate side-chains
  93 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 45 optimal weight:    0.2980
   chunk 36 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.180804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.145070 restraints weight = 6856.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.145070 restraints weight = 6937.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.145070 restraints weight = 6937.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.145070 restraints weight = 6937.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.145070 restraints weight = 6937.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.3817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5080  Z= 0.140
  Angle     :  0.538   7.198   6904  Z= 0.272
  Chirality :  0.038   0.119    748
  Planarity :  0.003   0.026    908
  Dihedral  :  3.365  13.279    676
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.34), residues: 616
  helix:  2.91 (0.27), residues: 344
  sheet: -0.00 (0.54), residues: 84
  loop : -0.68 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 142 
 TYR   0.010   0.001   TYR D  58 
 PHE   0.010   0.002   PHE D  24 
 TRP   0.008   0.001   TRP A 113 
 HIS   0.003   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 5080)
  covalent geometry    : angle       0.53775 ( 6904)
  hydrogen bonds       : bond        0.04193 (  299)
  hydrogen bonds       : angle       4.20361 (  885)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7507 (tp30) cc_final: 0.6934 (tp30)
REVERT: A   65 THR cc_start: 0.8729 (p) cc_final: 0.8161 (p)
REVERT: B   50 MET cc_start: 0.7419 (mmp) cc_final: 0.7163 (tpp)
REVERT: C   17 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8069 (tp40)
REVERT: C   72 ASN cc_start: 0.6992 (m110) cc_final: 0.6617 (m110)
REVERT: D   72 ASN cc_start: 0.6738 (m110) cc_final: 0.6423 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0587
  time to fit residues: 8.3065
Evaluate side-chains
  91 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 25 optimal weight:    0.2980
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    7.9990
   chunk 46 optimal weight:    0.4980
   chunk 21 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0030
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.4590

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

Flipped N/Q/H residues before XYZ refinement:
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.181292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.145692 restraints weight = 7012.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.145692 restraints weight = 6974.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.145692 restraints weight = 6974.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.145692 restraints weight = 6974.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.145692 restraints weight = 6974.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5080  Z= 0.116
  Angle     :  0.540   7.281   6904  Z= 0.271
  Chirality :  0.038   0.120    748
  Planarity :  0.003   0.026    908
  Dihedral  :  3.375  12.667    676
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.34), residues: 616
  helix:  2.88 (0.27), residues: 344
  sheet:  0.00 (0.55), residues: 84
  loop : -0.67 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 142 
 TYR   0.004   0.001   TYR D 155 
 PHE   0.007   0.001   PHE A  24 
 TRP   0.018   0.001   TRP D 128 
 HIS   0.003   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 5080)
  covalent geometry    : angle       0.54038 ( 6904)
  hydrogen bonds       : bond        0.03771 (  299)
  hydrogen bonds       : angle       4.11590 (  885)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7542 (tp30) cc_final: 0.6954 (tp30)
REVERT: A   72 ASN cc_start: 0.7110 (m110) cc_final: 0.6575 (m110)
REVERT: C   17 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7985 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0627
  time to fit residues: 8.6778
Evaluate side-chains
  86 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 17 optimal weight:    0.4980
   chunk 52 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0020
   chunk 1 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0570
   overall best weight:    0.3506

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

Flipped N/Q/H residues before XYZ refinement:
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.183997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.150048 restraints weight = 6987.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.148595 restraints weight = 8719.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.148739 restraints weight = 9302.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.149108 restraints weight = 8734.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.149002 restraints weight = 8540.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.3999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5080  Z= 0.109
  Angle     :  0.549   7.398   6904  Z= 0.275
  Chirality :  0.038   0.119    748
  Planarity :  0.003   0.026    908
  Dihedral  :  3.274  11.576    676
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.16 (0.34), residues: 616
  helix:  2.87 (0.27), residues: 344
  sheet: -0.01 (0.54), residues: 84
  loop : -0.68 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C  36 
 TYR   0.011   0.001   TYR B  58 
 PHE   0.006   0.001   PHE D  24 
 TRP   0.014   0.001   TRP D 128 
 HIS   0.002   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 5080)
  covalent geometry    : angle       0.54945 ( 6904)
  hydrogen bonds       : bond        0.03552 (  299)
  hydrogen bonds       : angle       4.03261 (  885)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 927.15 seconds
wall clock time: 16 minutes 42.26 seconds (1002.26 seconds total)