Starting phenix.real_space_refine
on Wed Mar  4 16:27:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pew_13359/03_2026/7pew_13359.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pew_13359/03_2026/7pew_13359.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pew_13359/03_2026/7pew_13359.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pew_13359/03_2026/7pew_13359.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pew_13359/03_2026/7pew_13359.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pew_13359/03_2026/7pew_13359.cif"
  }
  resolution = 4.6
  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=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P     352      5.49       5
     S      10      5.16       5
     C    7254      2.51       5
     N    2504      2.21       5
     O    3184      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13304
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "J"
      Number of atoms: 3636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 3636
          Classifications: {'DNA': 176}
          Link IDs: {'rna3p': 175}
    Chain: "I"
      Number of atoms: 3580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 3580
          Classifications: {'DNA': 176}
          Link IDs: {'rna3p': 175}
  Time building chain proxies: 2.95, per 1000 atoms: 0.22
  Number of scatterers: 13304
  At special positions: 0
  Unit cell: (131.25, 163.8, 117.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     352     15.00
     O    3184      8.00
     N    2504      7.00
     C    7254      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: 1.05
  Conformation dependent library (CDL) restraints added in 344.0 milliseconds
  

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 9 sheets defined
      71.9% alpha, 2.6% beta
      173 base pairs and 310 stacking pairs defined.
    Time for finding SS restraints: 2.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.690A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.623A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.583A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.119A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.291A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.500A  pdb=" N   VAL D  41 " --> pdb=" O   TYR D  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.664A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.254A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.216A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.641A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 124
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.733A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.602A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.917A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.228A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.026A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    407 hydrogen bonds defined for protein.
    1206 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      448 hydrogen bonds
      896 hydrogen bond angles
      0 basepair planarities
      173 basepair parallelities
      310 stacking parallelities
  Total time for adding SS restraints: 3.00

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2350
        1.33 -     1.46: 5344
        1.46 -     1.58: 5846
        1.58 -     1.70: 702
        1.70 -     1.83: 20
  Bond restraints: 14262
  Sorted by residual:
  bond pdb=" CG  GLU D 113 "
       pdb=" CD  GLU D 113 "
    ideal  model  delta    sigma   weight residual
    1.516  1.458  0.058 2.50e-02 1.60e+03 5.29e+00
  bond pdb=" C3'  DC I  12 "
       pdb=" O3'  DC I  12 "
    ideal  model  delta    sigma   weight residual
    1.422  1.486 -0.064 3.00e-02 1.11e+03 4.60e+00
  bond pdb=" C3'  DG I 140 "
       pdb=" O3'  DG I 140 "
    ideal  model  delta    sigma   weight residual
    1.422  1.482 -0.060 3.00e-02 1.11e+03 4.00e+00
  bond pdb=" C3'  DG I  28 "
       pdb=" O3'  DG I  28 "
    ideal  model  delta    sigma   weight residual
    1.422  1.477 -0.055 3.00e-02 1.11e+03 3.40e+00
  bond pdb=" CD  GLU D 113 "
       pdb=" OE1 GLU D 113 "
    ideal  model  delta    sigma   weight residual
    1.249  1.215  0.034 1.90e-02 2.77e+03 3.25e+00
  ... (remaining 14257 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 20094
        2.20 -     4.41: 583
        4.41 -     6.61: 69
        6.61 -     8.81: 22
        8.81 -    11.01: 6
  Bond angle restraints: 20774
  Sorted by residual:
  angle pdb=" N   GLU D 113 "
        pdb=" CA  GLU D 113 "
        pdb=" CB  GLU D 113 "
      ideal   model   delta    sigma   weight residual
     110.28  118.47   -8.19 1.55e+00 4.16e-01 2.79e+01
  angle pdb=" N   GLU A 105 "
        pdb=" CA  GLU A 105 "
        pdb=" CB  GLU A 105 "
      ideal   model   delta    sigma   weight residual
     110.28  118.46   -8.18 1.55e+00 4.16e-01 2.79e+01
  angle pdb=" N   GLU G  64 "
        pdb=" CA  GLU G  64 "
        pdb=" CB  GLU G  64 "
      ideal   model   delta    sigma   weight residual
     110.16  117.31   -7.15 1.48e+00 4.57e-01 2.33e+01
  angle pdb=" N   GLU E  50 "
        pdb=" CA  GLU E  50 "
        pdb=" CB  GLU E  50 "
      ideal   model   delta    sigma   weight residual
     110.28  117.42   -7.14 1.55e+00 4.16e-01 2.12e+01
  angle pdb=" N   GLN D  95 "
        pdb=" CA  GLN D  95 "
        pdb=" CB  GLN D  95 "
      ideal   model   delta    sigma   weight residual
     110.12  116.69   -6.57 1.47e+00 4.63e-01 2.00e+01
  ... (remaining 20769 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 5814
       35.97 -    71.94: 1791
       71.94 -   107.90: 26
      107.90 -   143.87: 2
      143.87 -   179.84: 3
  Dihedral angle restraints: 7636
    sinusoidal: 5414
      harmonic: 2222
  Sorted by residual:
  dihedral pdb=" CA  ARG B  23 "
           pdb=" C   ARG B  23 "
           pdb=" N   ASP B  24 "
           pdb=" CA  ASP B  24 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.56  -23.44     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  ARG H  33 "
           pdb=" C   ARG H  33 "
           pdb=" N   LYS H  34 "
           pdb=" CA  LYS H  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.97   22.03     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  GLU E  59 "
           pdb=" C   GLU E  59 "
           pdb=" N   LEU E  60 "
           pdb=" CA  LEU E  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.41  -21.59     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 7633 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1790
       0.050 -    0.100: 451
       0.100 -    0.150: 96
       0.150 -    0.200: 19
       0.200 -    0.251: 4
  Chirality restraints: 2360
  Sorted by residual:
  chirality pdb=" CB  THR B  54 "
            pdb=" CA  THR B  54 "
            pdb=" OG1 THR B  54 "
            pdb=" CG2 THR B  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.30    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  GLU A  94 "
            pdb=" N   GLU A  94 "
            pdb=" C   GLU A  94 "
            pdb=" CB  GLU A  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  PHE A 104 "
            pdb=" N   PHE A 104 "
            pdb=" C   PHE A 104 "
            pdb=" CB  PHE A 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 2357 not shown)

  Planarity restraints: 1408
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA G  60 "    0.012 2.00e-02 2.50e+03   2.33e-02 5.41e+00
        pdb=" C   ALA G  60 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ALA G  60 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLU G  61 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU D 113 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.16e+00
        pdb=" CD  GLU D 113 "    0.039 2.00e-02 2.50e+03
        pdb=" OE1 GLU D 113 "   -0.014 2.00e-02 2.50e+03
        pdb=" OE2 GLU D 113 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP E 106 "   -0.010 2.00e-02 2.50e+03   2.11e-02 4.45e+00
        pdb=" CG  ASP E 106 "    0.037 2.00e-02 2.50e+03
        pdb=" OD1 ASP E 106 "   -0.013 2.00e-02 2.50e+03
        pdb=" OD2 ASP E 106 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1405 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2643
        2.78 -     3.31: 12088
        3.31 -     3.84: 29169
        3.84 -     4.37: 32242
        4.37 -     4.90: 44010
  Nonbonded interactions: 120152
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH2 ARG E 131 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" O   LYS H 116 "
            pdb=" OG1 THR H 119 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   GLN A  93 "
            pdb=" OG  SER A  96 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" NE2 HIS A 113 "
            pdb=" OD1 ASP E 123 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" OD2 ASP D  68 "
            pdb=" OH  TYR F  98 "
     model   vdw
     2.291 3.040
  ... (remaining 120147 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

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:             2.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.000
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  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:   19.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
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      :  0.006   0.064  14262  Z= 0.271
  Angle     :  0.912  11.014  20774  Z= 0.518
  Chirality :  0.048   0.251   2360
  Planarity :  0.007   0.075   1408
  Dihedral  : 30.189 179.839   6204
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  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: -0.20 (0.27), residues: 752
  helix:  0.18 (0.21), residues: 520
  sheet:  None (None), residues: 0
  loop : -0.58 (0.35), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F  92 
 TYR   0.035   0.003   TYR D  37 
 PHE   0.024   0.003   PHE G  25 
 HIS   0.009   0.002   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00596 (14262)
  covalent geometry    : angle       0.91159 (20774)
  hydrogen bonds       : bond        0.11094 (  855)
  hydrogen bonds       : angle       4.80549 ( 2102)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9384 (mpp) cc_final: 0.8851 (mpp)
REVERT: A  104 PHE cc_start: 0.9170 (m-80) cc_final: 0.8786 (m-80)
REVERT: A  105 GLU cc_start: 0.9474 (pm20) cc_final: 0.9228 (pm20)
REVERT: A  106 ASP cc_start: 0.9444 (m-30) cc_final: 0.9074 (m-30)
REVERT: A  120 MET cc_start: 0.8366 (mtt) cc_final: 0.8082 (mpp)
REVERT: B   59 LYS cc_start: 0.9594 (tmtt) cc_final: 0.9373 (tptt)
REVERT: C   25 PHE cc_start: 0.8185 (m-10) cc_final: 0.7745 (m-10)
REVERT: D   34 LYS cc_start: 0.8279 (mmmm) cc_final: 0.7645 (tmmt)
REVERT: E   50 GLU cc_start: 0.9493 (mp0) cc_final: 0.8859 (pm20)
REVERT: E   51 ILE cc_start: 0.9570 (mt) cc_final: 0.9256 (mt)
REVERT: E   54 TYR cc_start: 0.9506 (m-80) cc_final: 0.9088 (m-80)
REVERT: E   59 GLU cc_start: 0.9093 (mp0) cc_final: 0.8764 (pm20)
REVERT: E   90 MET cc_start: 0.9429 (mmp) cc_final: 0.9145 (mmm)
REVERT: E   93 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8049 (tm-30)
REVERT: E   94 GLU cc_start: 0.9403 (tp30) cc_final: 0.9097 (tp30)
REVERT: E  104 PHE cc_start: 0.9622 (m-10) cc_final: 0.9332 (m-80)
REVERT: E  105 GLU cc_start: 0.9401 (pp20) cc_final: 0.9194 (pp20)
REVERT: E  120 MET cc_start: 0.8744 (mtm) cc_final: 0.8271 (mtt)
REVERT: E  123 ASP cc_start: 0.9563 (m-30) cc_final: 0.9310 (m-30)
REVERT: F   24 ASP cc_start: 0.9237 (t0) cc_final: 0.9013 (t0)
REVERT: F   59 LYS cc_start: 0.9663 (tttp) cc_final: 0.9225 (tppp)
REVERT: F   60 VAL cc_start: 0.9651 (t) cc_final: 0.9438 (p)
REVERT: F   62 LEU cc_start: 0.9793 (mt) cc_final: 0.9407 (pp)
REVERT: F   63 GLU cc_start: 0.9680 (mt-10) cc_final: 0.9299 (mt-10)
REVERT: F   85 ASP cc_start: 0.8345 (m-30) cc_final: 0.8126 (m-30)
REVERT: G  102 ILE cc_start: 0.8328 (mm) cc_final: 0.8101 (mm)
REVERT: H   47 GLN cc_start: 0.9202 (mp10) cc_final: 0.8942 (mp10)
REVERT: H  105 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8308 (tm-30)
REVERT: H  109 HIS cc_start: 0.9391 (m90) cc_final: 0.8442 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.1208
  time to fit residues: 29.5972
Evaluate side-chains
  120 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.3980
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    2.8788

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C 104 GLN
D 109 HIS
E  55 GLN
H  49 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.028501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2503 r_free = 0.2503 target = 0.020988 restraints weight = 174816.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2551 r_free = 0.2551 target = 0.021823 restraints weight = 83703.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.022389 restraints weight = 50022.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.022776 restraints weight = 34118.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2619 r_free = 0.2619 target = 0.023058 restraints weight = 25641.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.2577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  14262  Z= 0.225
  Angle     :  0.640   8.919  20774  Z= 0.380
  Chirality :  0.035   0.136   2360
  Planarity :  0.005   0.050   1408
  Dihedral  : 32.906 178.468   4680
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  5.35 %
    Favored  : 94.50 %
  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:  1.31 (0.29), residues: 752
  helix:  1.32 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.10 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  29 
 TYR   0.011   0.002   TYR G  39 
 PHE   0.019   0.002   PHE E  67 
 HIS   0.006   0.001   HIS D 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 (14262)
  covalent geometry    : angle       0.63960 (20774)
  hydrogen bonds       : bond        0.05375 (  855)
  hydrogen bonds       : angle       3.51083 ( 2102)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8838 (pm20) cc_final: 0.8635 (pm20)
REVERT: A   90 MET cc_start: 0.9370 (mpp) cc_final: 0.8892 (mpp)
REVERT: A  104 PHE cc_start: 0.9439 (m-80) cc_final: 0.9009 (m-80)
REVERT: A  106 ASP cc_start: 0.9386 (m-30) cc_final: 0.9147 (m-30)
REVERT: A  120 MET cc_start: 0.8342 (mtt) cc_final: 0.7097 (mpp)
REVERT: B   59 LYS cc_start: 0.9659 (tmtt) cc_final: 0.9427 (tptt)
REVERT: B   74 GLU cc_start: 0.9684 (tm-30) cc_final: 0.9428 (tm-30)
REVERT: C   50 TYR cc_start: 0.9074 (t80) cc_final: 0.8662 (t80)
REVERT: D   34 LYS cc_start: 0.8190 (mmmm) cc_final: 0.7625 (tmmt)
REVERT: D   68 ASP cc_start: 0.9259 (t0) cc_final: 0.9047 (t0)
REVERT: D  109 HIS cc_start: 0.9403 (m90) cc_final: 0.8940 (m170)
REVERT: E   59 GLU cc_start: 0.9165 (mp0) cc_final: 0.8752 (pm20)
REVERT: E   90 MET cc_start: 0.9464 (mmp) cc_final: 0.9211 (mmp)
REVERT: E   93 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8492 (tm-30)
REVERT: E  104 PHE cc_start: 0.9629 (m-10) cc_final: 0.9392 (m-10)
REVERT: E  105 GLU cc_start: 0.9193 (pp20) cc_final: 0.8979 (pp20)
REVERT: E  106 ASP cc_start: 0.8763 (m-30) cc_final: 0.8359 (m-30)
REVERT: E  120 MET cc_start: 0.8673 (mtm) cc_final: 0.7908 (mtt)
REVERT: E  123 ASP cc_start: 0.9413 (m-30) cc_final: 0.8675 (m-30)
REVERT: F   60 VAL cc_start: 0.9670 (t) cc_final: 0.9139 (t)
REVERT: F   62 LEU cc_start: 0.9798 (mt) cc_final: 0.9428 (pp)
REVERT: F   63 GLU cc_start: 0.9691 (mt-10) cc_final: 0.9322 (mt-10)
REVERT: F   74 GLU cc_start: 0.9239 (pp20) cc_final: 0.8956 (pp20)
REVERT: G   61 GLU cc_start: 0.9299 (pp20) cc_final: 0.9067 (pp20)
REVERT: G   64 GLU cc_start: 0.9137 (mp0) cc_final: 0.8889 (mp0)
REVERT: G   90 ASP cc_start: 0.8644 (t0) cc_final: 0.7925 (t0)
REVERT: G   92 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8225 (mt-10)
REVERT: G  102 ILE cc_start: 0.8457 (mm) cc_final: 0.8226 (mm)
REVERT: H   95 GLN cc_start: 0.9440 (pt0) cc_final: 0.9210 (pt0)
REVERT: H  105 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8595 (tm-30)
REVERT: H  108 LYS cc_start: 0.9343 (ptpp) cc_final: 0.9074 (ptpp)
REVERT: H  109 HIS cc_start: 0.9344 (m90) cc_final: 0.9070 (m-70)
  outliers start: 1
  outliers final: 1
  residues processed: 152
  average time/residue: 0.1230
  time to fit residues: 26.7005
Evaluate side-chains
  114 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 80 optimal weight:    8.9990
   chunk 86 optimal weight:    8.9990
   chunk 98 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 79 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 81 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  49 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.029434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2538 r_free = 0.2538 target = 0.021964 restraints weight = 172465.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.022761 restraints weight = 83488.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.023302 restraints weight = 50094.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.023677 restraints weight = 34448.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.023918 restraints weight = 25834.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14262  Z= 0.158
  Angle     :  0.585   6.604  20774  Z= 0.351
  Chirality :  0.034   0.144   2360
  Planarity :  0.004   0.048   1408
  Dihedral  : 32.390 178.519   4680
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  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:  1.68 (0.29), residues: 752
  helix:  1.64 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.09 (0.37), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  29 
 TYR   0.008   0.001   TYR E  99 
 PHE   0.015   0.002   PHE C  25 
 HIS   0.004   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (14262)
  covalent geometry    : angle       0.58476 (20774)
  hydrogen bonds       : bond        0.03630 (  855)
  hydrogen bonds       : angle       3.15538 ( 2102)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8801 (pm20) cc_final: 0.8588 (pm20)
REVERT: A   90 MET cc_start: 0.9418 (mpp) cc_final: 0.9009 (mmm)
REVERT: A  104 PHE cc_start: 0.9388 (m-80) cc_final: 0.8993 (m-80)
REVERT: A  106 ASP cc_start: 0.9390 (m-30) cc_final: 0.9168 (m-30)
REVERT: A  120 MET cc_start: 0.8227 (mtt) cc_final: 0.7944 (mtt)
REVERT: B   59 LYS cc_start: 0.9666 (tmtt) cc_final: 0.9414 (tptt)
REVERT: B   85 ASP cc_start: 0.8728 (m-30) cc_final: 0.8525 (m-30)
REVERT: C   50 TYR cc_start: 0.9104 (t80) cc_final: 0.8711 (t80)
REVERT: D   34 LYS cc_start: 0.8274 (mmmm) cc_final: 0.7635 (tmmt)
REVERT: D   68 ASP cc_start: 0.9242 (t0) cc_final: 0.9028 (t0)
REVERT: D  109 HIS cc_start: 0.9423 (m90) cc_final: 0.8919 (m90)
REVERT: E   59 GLU cc_start: 0.9052 (mp0) cc_final: 0.8659 (pm20)
REVERT: E   90 MET cc_start: 0.9468 (mmp) cc_final: 0.8782 (mmp)
REVERT: E  104 PHE cc_start: 0.9535 (m-10) cc_final: 0.9310 (m-80)
REVERT: E  120 MET cc_start: 0.8642 (mtm) cc_final: 0.7826 (mtt)
REVERT: E  123 ASP cc_start: 0.9168 (m-30) cc_final: 0.8513 (m-30)
REVERT: F   60 VAL cc_start: 0.9598 (t) cc_final: 0.9096 (t)
REVERT: F   63 GLU cc_start: 0.9658 (mt-10) cc_final: 0.9443 (mt-10)
REVERT: F   74 GLU cc_start: 0.9216 (pp20) cc_final: 0.8905 (pp20)
REVERT: F   79 LYS cc_start: 0.9484 (tptp) cc_final: 0.9198 (tttt)
REVERT: G   58 LEU cc_start: 0.9749 (mt) cc_final: 0.9460 (pp)
REVERT: G   64 GLU cc_start: 0.9163 (mp0) cc_final: 0.8923 (mp0)
REVERT: G   72 ASP cc_start: 0.9366 (m-30) cc_final: 0.9133 (m-30)
REVERT: H   82 HIS cc_start: 0.9510 (t70) cc_final: 0.9244 (t70)
REVERT: H   95 GLN cc_start: 0.9343 (pt0) cc_final: 0.9082 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1147
  time to fit residues: 27.9786
Evaluate side-chains
  111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 94 optimal weight:    7.9990
   chunk 83 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9980
   chunk 52 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 101 optimal weight:    5.9990
   chunk 85 optimal weight:    8.9990
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.027632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2467 r_free = 0.2467 target = 0.020388 restraints weight = 181095.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2514 r_free = 0.2514 target = 0.021176 restraints weight = 86853.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2544 r_free = 0.2544 target = 0.021707 restraints weight = 51922.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2565 r_free = 0.2565 target = 0.022072 restraints weight = 35347.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2579 r_free = 0.2579 target = 0.022318 restraints weight = 26471.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.2560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14262  Z= 0.237
  Angle     :  0.623   8.841  20774  Z= 0.373
  Chirality :  0.035   0.142   2360
  Planarity :  0.005   0.056   1408
  Dihedral  : 32.489 177.836   4680
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  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:  1.61 (0.29), residues: 752
  helix:  1.56 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.04 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  42 
 TYR   0.014   0.002   TYR D  40 
 PHE   0.012   0.002   PHE C  25 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 (14262)
  covalent geometry    : angle       0.62283 (20774)
  hydrogen bonds       : bond        0.05669 (  855)
  hydrogen bonds       : angle       3.50071 ( 2102)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9339 (mpp) cc_final: 0.9042 (mpp)
REVERT: A  104 PHE cc_start: 0.9450 (m-80) cc_final: 0.9100 (m-80)
REVERT: A  106 ASP cc_start: 0.9328 (m-30) cc_final: 0.9114 (m-30)
REVERT: A  120 MET cc_start: 0.8123 (mtt) cc_final: 0.7397 (mtt)
REVERT: B   59 LYS cc_start: 0.9659 (tmtt) cc_final: 0.9439 (tptt)
REVERT: B   74 GLU cc_start: 0.9695 (tm-30) cc_final: 0.9409 (tm-30)
REVERT: C   50 TYR cc_start: 0.9060 (t80) cc_final: 0.8576 (t80)
REVERT: D  108 LYS cc_start: 0.9665 (pttp) cc_final: 0.9441 (pttp)
REVERT: D  109 HIS cc_start: 0.9314 (m90) cc_final: 0.8815 (m90)
REVERT: E   50 GLU cc_start: 0.9489 (mp0) cc_final: 0.9253 (mp0)
REVERT: E   59 GLU cc_start: 0.9156 (mp0) cc_final: 0.8642 (pm20)
REVERT: E  104 PHE cc_start: 0.9607 (m-10) cc_final: 0.9294 (m-80)
REVERT: E  120 MET cc_start: 0.8450 (mtm) cc_final: 0.7729 (mtt)
REVERT: E  123 ASP cc_start: 0.9214 (m-30) cc_final: 0.8612 (m-30)
REVERT: F   60 VAL cc_start: 0.9641 (t) cc_final: 0.9121 (t)
REVERT: F   62 LEU cc_start: 0.9818 (mt) cc_final: 0.9481 (pp)
REVERT: F   63 GLU cc_start: 0.9693 (mt-10) cc_final: 0.9335 (mt-10)
REVERT: F   74 GLU cc_start: 0.9311 (pp20) cc_final: 0.9026 (pp20)
REVERT: F   79 LYS cc_start: 0.9599 (tptp) cc_final: 0.9325 (tttt)
REVERT: G   64 GLU cc_start: 0.9193 (mp0) cc_final: 0.8932 (mp0)
REVERT: G   90 ASP cc_start: 0.8601 (t0) cc_final: 0.7921 (t0)
REVERT: G   92 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8374 (mt-10)
REVERT: G  102 ILE cc_start: 0.8428 (mm) cc_final: 0.8217 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1235
  time to fit residues: 26.5264
Evaluate side-chains
  109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 87 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 102 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 105 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 103 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 27 optimal weight:    8.9990
   chunk 99 optimal weight:    7.9990
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.027654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2465 r_free = 0.2465 target = 0.020413 restraints weight = 179337.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2512 r_free = 0.2512 target = 0.021190 restraints weight = 85926.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2543 r_free = 0.2543 target = 0.021723 restraints weight = 51303.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.022072 restraints weight = 34987.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2578 r_free = 0.2578 target = 0.022320 restraints weight = 26272.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.2561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
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      :  0.005   0.037  14262  Z= 0.217
  Angle     :  0.611   8.192  20774  Z= 0.364
  Chirality :  0.034   0.134   2360
  Planarity :  0.004   0.059   1408
  Dihedral  : 32.503 179.340   4680
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.83 %
    Favored  : 96.86 %
  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 are not related in a simple way.
  whole:  1.68 (0.29), residues: 752
  helix:  1.61 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.06 (0.38), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  42 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.013   0.002   PHE H  65 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (14262)
  covalent geometry    : angle       0.61110 (20774)
  hydrogen bonds       : bond        0.04961 (  855)
  hydrogen bonds       : angle       3.39734 ( 2102)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 144
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8925 (pm20) cc_final: 0.8601 (pm20)
REVERT: A   90 MET cc_start: 0.9273 (mpp) cc_final: 0.9043 (mpp)
REVERT: A   94 GLU cc_start: 0.9356 (mp0) cc_final: 0.8883 (mp0)
REVERT: A  104 PHE cc_start: 0.9483 (m-80) cc_final: 0.9056 (m-80)
REVERT: A  120 MET cc_start: 0.8054 (mtt) cc_final: 0.7329 (mtt)
REVERT: B   59 LYS cc_start: 0.9677 (tmtt) cc_final: 0.9447 (tptt)
REVERT: B   74 GLU cc_start: 0.9703 (tm-30) cc_final: 0.9419 (tm-30)
REVERT: B   85 ASP cc_start: 0.8698 (m-30) cc_final: 0.8379 (m-30)
REVERT: B   91 LYS cc_start: 0.9458 (tmmt) cc_final: 0.9194 (tmmt)
REVERT: D  108 LYS cc_start: 0.9606 (pttp) cc_final: 0.9391 (pttp)
REVERT: E   50 GLU cc_start: 0.9497 (mp0) cc_final: 0.9279 (mp0)
REVERT: E   59 GLU cc_start: 0.9168 (mp0) cc_final: 0.8646 (pm20)
REVERT: E   90 MET cc_start: 0.9361 (mmp) cc_final: 0.9144 (mmm)
REVERT: E  104 PHE cc_start: 0.9633 (m-10) cc_final: 0.9341 (m-80)
REVERT: E  120 MET cc_start: 0.8456 (mtm) cc_final: 0.7743 (mtt)
REVERT: E  123 ASP cc_start: 0.9220 (m-30) cc_final: 0.8488 (m-30)
REVERT: F   60 VAL cc_start: 0.9640 (t) cc_final: 0.9164 (t)
REVERT: F   63 GLU cc_start: 0.9687 (mt-10) cc_final: 0.9472 (mt-10)
REVERT: F   74 GLU cc_start: 0.9330 (pp20) cc_final: 0.9079 (pp20)
REVERT: F   79 LYS cc_start: 0.9635 (tptp) cc_final: 0.9347 (tttt)
REVERT: G  102 ILE cc_start: 0.8454 (mm) cc_final: 0.8193 (mm)
REVERT: H   45 LEU cc_start: 0.9385 (tp) cc_final: 0.9177 (tp)
REVERT: H   95 GLN cc_start: 0.9380 (pt0) cc_final: 0.9125 (pt0)
REVERT: H  105 GLU cc_start: 0.8954 (pp20) cc_final: 0.8694 (pp20)
  outliers start: 2
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1153
  time to fit residues: 24.6408
Evaluate side-chains
  100 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 61 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 20 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 72 optimal weight:   20.0000
   chunk 45 optimal weight:   20.0000
   chunk 21 optimal weight:    0.9980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  89 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.028523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2509 r_free = 0.2509 target = 0.021310 restraints weight = 173558.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2556 r_free = 0.2556 target = 0.022115 restraints weight = 83663.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.022649 restraints weight = 49981.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2606 r_free = 0.2606 target = 0.023022 restraints weight = 34012.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.023277 restraints weight = 25187.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.3462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14262  Z= 0.166
  Angle     :  0.595   6.659  20774  Z= 0.354
  Chirality :  0.034   0.149   2360
  Planarity :  0.004   0.061   1408
  Dihedral  : 32.255 178.834   4680
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.52 %
    Favored  : 97.33 %
  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:  1.90 (0.30), residues: 752
  helix:  1.81 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.03 (0.38), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  33 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.014   0.002   PHE A  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (14262)
  covalent geometry    : angle       0.59472 (20774)
  hydrogen bonds       : bond        0.03954 (  855)
  hydrogen bonds       : angle       3.24821 ( 2102)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8878 (pm20) cc_final: 0.8665 (pm20)
REVERT: A   67 PHE cc_start: 0.9588 (t80) cc_final: 0.9370 (t80)
REVERT: A   97 GLU cc_start: 0.8997 (mp0) cc_final: 0.8771 (mp0)
REVERT: A  104 PHE cc_start: 0.9425 (m-80) cc_final: 0.9088 (m-80)
REVERT: A  120 MET cc_start: 0.8031 (mtt) cc_final: 0.7279 (mtt)
REVERT: B   59 LYS cc_start: 0.9663 (tmtt) cc_final: 0.9424 (tptt)
REVERT: B   74 GLU cc_start: 0.9704 (tm-30) cc_final: 0.9402 (tm-30)
REVERT: B   85 ASP cc_start: 0.8657 (m-30) cc_final: 0.8358 (m-30)
REVERT: B   91 LYS cc_start: 0.9330 (tmmt) cc_final: 0.8971 (pptt)
REVERT: C   50 TYR cc_start: 0.9166 (t80) cc_final: 0.8553 (t80)
REVERT: D   34 LYS cc_start: 0.8170 (mmmm) cc_final: 0.7381 (tmmt)
REVERT: D   68 ASP cc_start: 0.9282 (t0) cc_final: 0.8999 (t0)
REVERT: E   50 GLU cc_start: 0.9500 (mp0) cc_final: 0.9279 (pm20)
REVERT: E   59 GLU cc_start: 0.9093 (mp0) cc_final: 0.8602 (pm20)
REVERT: E  104 PHE cc_start: 0.9635 (m-10) cc_final: 0.9406 (m-80)
REVERT: E  120 MET cc_start: 0.8428 (mtm) cc_final: 0.7741 (mtt)
REVERT: E  123 ASP cc_start: 0.9202 (m-30) cc_final: 0.8475 (m-30)
REVERT: F   60 VAL cc_start: 0.9619 (t) cc_final: 0.9130 (t)
REVERT: F   74 GLU cc_start: 0.9283 (pp20) cc_final: 0.8995 (pp20)
REVERT: F   75 HIS cc_start: 0.9159 (t70) cc_final: 0.8723 (t70)
REVERT: F   79 LYS cc_start: 0.9582 (tptp) cc_final: 0.9359 (tttt)
REVERT: G   36 LYS cc_start: 0.9549 (mmmt) cc_final: 0.9253 (mmtm)
REVERT: G   64 GLU cc_start: 0.9215 (mp0) cc_final: 0.8899 (mp0)
REVERT: G   90 ASP cc_start: 0.8478 (t70) cc_final: 0.8184 (t0)
REVERT: G  102 ILE cc_start: 0.8348 (mm) cc_final: 0.8086 (mm)
REVERT: H   95 GLN cc_start: 0.9347 (pt0) cc_final: 0.9060 (pt0)
REVERT: H  120 LYS cc_start: 0.9616 (mppt) cc_final: 0.9266 (mttp)
  outliers start: 1
  outliers final: 1
  residues processed: 155
  average time/residue: 0.1196
  time to fit residues: 26.9106
Evaluate side-chains
  115 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 105 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 92 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 37 optimal weight:    8.9990
   chunk 31 optimal weight:    0.7980
   chunk 73 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.028273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2499 r_free = 0.2499 target = 0.021070 restraints weight = 178749.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2545 r_free = 0.2545 target = 0.021868 restraints weight = 87115.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.022397 restraints weight = 52460.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2596 r_free = 0.2596 target = 0.022771 restraints weight = 36136.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.023008 restraints weight = 27149.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.2592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.3610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14262  Z= 0.176
  Angle     :  0.597   7.090  20774  Z= 0.356
  Chirality :  0.034   0.136   2360
  Planarity :  0.004   0.059   1408
  Dihedral  : 32.210 178.434   4680
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  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:  1.87 (0.30), residues: 752
  helix:  1.80 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.09 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  79 
 TYR   0.010   0.001   TYR F  98 
 PHE   0.015   0.002   PHE A  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (14262)
  covalent geometry    : angle       0.59682 (20774)
  hydrogen bonds       : bond        0.04293 (  855)
  hydrogen bonds       : angle       3.26407 ( 2102)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8867 (pm20) cc_final: 0.8645 (pm20)
REVERT: A   90 MET cc_start: 0.9345 (mmp) cc_final: 0.8965 (mmm)
REVERT: A   93 GLN cc_start: 0.9005 (tp40) cc_final: 0.8455 (tp40)
REVERT: A  104 PHE cc_start: 0.9445 (m-80) cc_final: 0.9071 (m-80)
REVERT: A  120 MET cc_start: 0.7992 (mtt) cc_final: 0.7272 (mtt)
REVERT: B   59 LYS cc_start: 0.9668 (tmtt) cc_final: 0.9423 (tptt)
REVERT: B   74 GLU cc_start: 0.9692 (tm-30) cc_final: 0.9380 (tm-30)
REVERT: B   85 ASP cc_start: 0.8647 (m-30) cc_final: 0.8339 (m-30)
REVERT: B   91 LYS cc_start: 0.9357 (tmmt) cc_final: 0.8994 (pptt)
REVERT: C   50 TYR cc_start: 0.9215 (t80) cc_final: 0.8474 (t80)
REVERT: D  109 HIS cc_start: 0.9414 (m90) cc_final: 0.9211 (m170)
REVERT: E   50 GLU cc_start: 0.9499 (mp0) cc_final: 0.9262 (mp0)
REVERT: E   59 GLU cc_start: 0.9101 (mp0) cc_final: 0.8598 (pm20)
REVERT: E   82 LEU cc_start: 0.8120 (mm) cc_final: 0.7898 (mm)
REVERT: E   93 GLN cc_start: 0.9336 (pm20) cc_final: 0.9104 (pm20)
REVERT: E  104 PHE cc_start: 0.9655 (m-10) cc_final: 0.9416 (m-80)
REVERT: E  120 MET cc_start: 0.8448 (mtm) cc_final: 0.7760 (mtt)
REVERT: F   74 GLU cc_start: 0.9274 (pp20) cc_final: 0.8987 (pp20)
REVERT: F   75 HIS cc_start: 0.9056 (t70) cc_final: 0.8643 (t70)
REVERT: F   79 LYS cc_start: 0.9403 (tppt) cc_final: 0.9057 (tttt)
REVERT: G   36 LYS cc_start: 0.9555 (mmmt) cc_final: 0.9041 (mmtm)
REVERT: G   64 GLU cc_start: 0.9178 (mp0) cc_final: 0.8916 (mp0)
REVERT: G  102 ILE cc_start: 0.8390 (mm) cc_final: 0.8127 (mm)
REVERT: H   95 GLN cc_start: 0.9349 (pt0) cc_final: 0.9065 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1170
  time to fit residues: 25.4298
Evaluate side-chains
  109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 86 optimal weight:    8.9990
   chunk 72 optimal weight:   20.0000
   chunk 33 optimal weight:    0.7980
   chunk 77 optimal weight:    7.9990
   chunk 58 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0980
   chunk 66 optimal weight:    0.2980
   chunk 30 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 99 optimal weight:    7.9990
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
H 109 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.029422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2556 r_free = 0.2556 target = 0.022252 restraints weight = 170270.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.023085 restraints weight = 82707.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2632 r_free = 0.2632 target = 0.023644 restraints weight = 49625.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.024019 restraints weight = 33596.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.024285 restraints weight = 24965.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14262  Z= 0.151
  Angle     :  0.588   7.010  20774  Z= 0.351
  Chirality :  0.034   0.194   2360
  Planarity :  0.004   0.062   1408
  Dihedral  : 31.951 178.510   4680
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  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 are not related in a simple way.
  whole:  1.88 (0.30), residues: 752
  helix:  1.77 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop :  0.04 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  33 
 TYR   0.023   0.001   TYR G  50 
 PHE   0.018   0.002   PHE C  25 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (14262)
  covalent geometry    : angle       0.58822 (20774)
  hydrogen bonds       : bond        0.03639 (  855)
  hydrogen bonds       : angle       3.17921 ( 2102)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8819 (pm20) cc_final: 0.8608 (pm20)
REVERT: A   90 MET cc_start: 0.9198 (mmp) cc_final: 0.8818 (mmm)
REVERT: A   93 GLN cc_start: 0.9116 (tp40) cc_final: 0.8804 (tp40)
REVERT: A   94 GLU cc_start: 0.9252 (mp0) cc_final: 0.8978 (mp0)
REVERT: A  104 PHE cc_start: 0.9380 (m-80) cc_final: 0.9041 (m-80)
REVERT: A  120 MET cc_start: 0.7998 (mtt) cc_final: 0.7315 (mtt)
REVERT: B   59 LYS cc_start: 0.9662 (tmtt) cc_final: 0.9385 (tptt)
REVERT: B   85 ASP cc_start: 0.8625 (m-30) cc_final: 0.8315 (m-30)
REVERT: B   91 LYS cc_start: 0.9231 (tmmt) cc_final: 0.8906 (pptt)
REVERT: C   50 TYR cc_start: 0.9178 (t80) cc_final: 0.8620 (t80)
REVERT: C  102 ILE cc_start: 0.8002 (mm) cc_final: 0.7744 (mm)
REVERT: D  109 HIS cc_start: 0.9437 (m90) cc_final: 0.9175 (m170)
REVERT: E   59 GLU cc_start: 0.9049 (mp0) cc_final: 0.8624 (pm20)
REVERT: E   82 LEU cc_start: 0.8255 (mm) cc_final: 0.7971 (mm)
REVERT: E  120 MET cc_start: 0.8376 (mtm) cc_final: 0.7675 (mtt)
REVERT: F   60 VAL cc_start: 0.9606 (t) cc_final: 0.9129 (t)
REVERT: F   74 GLU cc_start: 0.9237 (pp20) cc_final: 0.8904 (pp20)
REVERT: F   79 LYS cc_start: 0.9373 (tppt) cc_final: 0.9041 (tttm)
REVERT: G   36 LYS cc_start: 0.9557 (mmmt) cc_final: 0.9045 (mmtm)
REVERT: G   64 GLU cc_start: 0.9188 (mp0) cc_final: 0.8923 (mp0)
REVERT: G  102 ILE cc_start: 0.8251 (mm) cc_final: 0.8016 (mm)
REVERT: H  120 LYS cc_start: 0.9615 (mppt) cc_final: 0.9364 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1225
  time to fit residues: 28.2162
Evaluate side-chains
  116 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 75 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 94 optimal weight:    7.9990
   chunk 70 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9990
   chunk 96 optimal weight:    7.9990
   chunk 63 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
C  84 GLN
** F  25 ASN ** 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 = 0.2912 r_free = 0.2912 target = 0.032275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.025690 restraints weight = 189361.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.026507 restraints weight = 87431.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.027086 restraints weight = 51620.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.027484 restraints weight = 34040.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.027751 restraints weight = 24524.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.3984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14262  Z= 0.161
  Angle     :  0.603   7.244  20774  Z= 0.359
  Chirality :  0.034   0.151   2360
  Planarity :  0.004   0.063   1408
  Dihedral  : 31.960 177.978   4680
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  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:  1.89 (0.30), residues: 752
  helix:  1.75 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop :  0.09 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  33 
 TYR   0.018   0.002   TYR G  50 
 PHE   0.030   0.002   PHE E 104 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (14262)
  covalent geometry    : angle       0.60348 (20774)
  hydrogen bonds       : bond        0.03905 (  855)
  hydrogen bonds       : angle       3.28632 ( 2102)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8851 (pm20) cc_final: 0.8633 (pm20)
REVERT: A   90 MET cc_start: 0.9228 (mmp) cc_final: 0.8842 (mmm)
REVERT: A   93 GLN cc_start: 0.9002 (tp40) cc_final: 0.8585 (tp40)
REVERT: A  104 PHE cc_start: 0.9387 (m-80) cc_final: 0.9067 (m-80)
REVERT: A  120 MET cc_start: 0.7961 (mtt) cc_final: 0.7269 (mtt)
REVERT: B   59 LYS cc_start: 0.9655 (tmtt) cc_final: 0.9377 (tptt)
REVERT: B   85 ASP cc_start: 0.8641 (m-30) cc_final: 0.8314 (m-30)
REVERT: B   91 LYS cc_start: 0.9271 (tmmt) cc_final: 0.9003 (pptt)
REVERT: C   50 TYR cc_start: 0.9191 (t80) cc_final: 0.8636 (t80)
REVERT: C   61 GLU cc_start: 0.9396 (tm-30) cc_final: 0.8940 (tm-30)
REVERT: E   50 GLU cc_start: 0.9486 (mp0) cc_final: 0.9284 (pm20)
REVERT: E   59 GLU cc_start: 0.9046 (mp0) cc_final: 0.8634 (pm20)
REVERT: E   82 LEU cc_start: 0.8205 (mm) cc_final: 0.7984 (mm)
REVERT: E  105 GLU cc_start: 0.9072 (pp20) cc_final: 0.8832 (pp20)
REVERT: E  106 ASP cc_start: 0.8579 (m-30) cc_final: 0.8118 (m-30)
REVERT: E  120 MET cc_start: 0.8404 (mtm) cc_final: 0.7781 (mtt)
REVERT: F   74 GLU cc_start: 0.9216 (pp20) cc_final: 0.8906 (pp20)
REVERT: F   75 HIS cc_start: 0.9123 (t70) cc_final: 0.8718 (t70)
REVERT: F   79 LYS cc_start: 0.9387 (tppt) cc_final: 0.9094 (tttt)
REVERT: G   36 LYS cc_start: 0.9560 (mmmt) cc_final: 0.9063 (mmtm)
REVERT: G   64 GLU cc_start: 0.9227 (mp0) cc_final: 0.8951 (mp0)
REVERT: G  102 ILE cc_start: 0.8282 (mm) cc_final: 0.8022 (mm)
REVERT: H   45 LEU cc_start: 0.9357 (tp) cc_final: 0.9149 (pp)
REVERT: H   46 LYS cc_start: 0.9552 (tppt) cc_final: 0.9289 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.1124
  time to fit residues: 24.7966
Evaluate side-chains
  114 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 101 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 24 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 84 optimal weight:    7.9990
   chunk 85 optimal weight:    8.9990
   chunk 50 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  25 ASN ** 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 = 0.2831 r_free = 0.2831 target = 0.027762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2480 r_free = 0.2480 target = 0.020659 restraints weight = 181161.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2527 r_free = 0.2527 target = 0.021457 restraints weight = 86946.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2558 r_free = 0.2558 target = 0.021992 restraints weight = 52124.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2578 r_free = 0.2578 target = 0.022348 restraints weight = 35421.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2592 r_free = 0.2592 target = 0.022596 restraints weight = 26514.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  14262  Z= 0.217
  Angle     :  0.637   8.646  20774  Z= 0.377
  Chirality :  0.035   0.189   2360
  Planarity :  0.005   0.067   1408
  Dihedral  : 32.264 177.619   4680
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.79 %
    Favored  : 99.06 %
  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:  1.78 (0.30), residues: 752
  helix:  1.67 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop :  0.06 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  42 
 TYR   0.017   0.002   TYR G  50 
 PHE   0.015   0.002   PHE C  25 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (14262)
  covalent geometry    : angle       0.63670 (20774)
  hydrogen bonds       : bond        0.05140 (  855)
  hydrogen bonds       : angle       3.55199 ( 2102)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8879 (pm20) cc_final: 0.8636 (pm20)
REVERT: A   90 MET cc_start: 0.9393 (mmp) cc_final: 0.9102 (mmp)
REVERT: A   93 GLN cc_start: 0.9300 (tp40) cc_final: 0.8845 (tp40)
REVERT: A  104 PHE cc_start: 0.9534 (m-80) cc_final: 0.9191 (m-80)
REVERT: A  120 MET cc_start: 0.7972 (mtt) cc_final: 0.7222 (mtt)
REVERT: B   59 LYS cc_start: 0.9669 (tmtt) cc_final: 0.9410 (tptt)
REVERT: B   74 GLU cc_start: 0.9695 (tm-30) cc_final: 0.9410 (tm-30)
REVERT: B   91 LYS cc_start: 0.9463 (tmmt) cc_final: 0.9143 (pptt)
REVERT: C   50 TYR cc_start: 0.9245 (t80) cc_final: 0.8541 (t80)
REVERT: C   61 GLU cc_start: 0.9303 (tm-30) cc_final: 0.8879 (tm-30)
REVERT: C   90 ASP cc_start: 0.7803 (t0) cc_final: 0.7540 (t0)
REVERT: D   34 LYS cc_start: 0.8269 (mmmm) cc_final: 0.7608 (ttpp)
REVERT: E   50 GLU cc_start: 0.9483 (mp0) cc_final: 0.9267 (pm20)
REVERT: E   59 GLU cc_start: 0.9084 (mp0) cc_final: 0.8713 (pm20)
REVERT: E   82 LEU cc_start: 0.8174 (mm) cc_final: 0.7883 (mm)
REVERT: E  105 GLU cc_start: 0.9122 (pp20) cc_final: 0.8858 (pp20)
REVERT: E  106 ASP cc_start: 0.8560 (m-30) cc_final: 0.8077 (m-30)
REVERT: E  120 MET cc_start: 0.8417 (mtm) cc_final: 0.7866 (mtt)
REVERT: F   62 LEU cc_start: 0.9819 (mt) cc_final: 0.9475 (pp)
REVERT: F   63 GLU cc_start: 0.9622 (mt-10) cc_final: 0.9314 (mt-10)
REVERT: F   74 GLU cc_start: 0.9302 (pp20) cc_final: 0.9020 (pp20)
REVERT: F   79 LYS cc_start: 0.9512 (tppt) cc_final: 0.9167 (tttt)
REVERT: G   64 GLU cc_start: 0.9242 (mp0) cc_final: 0.8985 (mp0)
REVERT: G   90 ASP cc_start: 0.8640 (t0) cc_final: 0.7939 (t70)
REVERT: G  102 ILE cc_start: 0.8434 (mm) cc_final: 0.8206 (mm)
REVERT: H   46 LYS cc_start: 0.9549 (tppt) cc_final: 0.9348 (mmmt)
REVERT: H  120 LYS cc_start: 0.9627 (mppt) cc_final: 0.9348 (mttp)
  outliers start: 1
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1176
  time to fit residues: 24.2469
Evaluate side-chains
  108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   chunk 34 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 94 optimal weight:    6.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
C  84 GLN
D  63 ASN
** F  25 ASN ** 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 = 0.2859 r_free = 0.2859 target = 0.028529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2514 r_free = 0.2514 target = 0.021426 restraints weight = 174989.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2561 r_free = 0.2561 target = 0.022238 restraints weight = 85153.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.022768 restraints weight = 51123.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.023136 restraints weight = 34902.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.023393 restraints weight = 26019.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14262  Z= 0.175
  Angle     :  0.629   7.259  20774  Z= 0.374
  Chirality :  0.034   0.174   2360
  Planarity :  0.004   0.061   1408
  Dihedral  : 32.125 178.038   4680
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.47 %
    Favored  : 99.37 %
  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:  1.71 (0.30), residues: 752
  helix:  1.64 (0.23), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.02 (0.38), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  79 
 TYR   0.022   0.002   TYR G  50 
 PHE   0.014   0.002   PHE C  25 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (14262)
  covalent geometry    : angle       0.62858 (20774)
  hydrogen bonds       : bond        0.04160 (  855)
  hydrogen bonds       : angle       3.48487 ( 2102)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1881.52 seconds
wall clock time: 33 minutes 21.66 seconds (2001.66 seconds total)